拟南芥核孔蛋白Nup96的鉴定及其在开花时间和生物钟调控中的功能分析
|
摘要
核孔复合物作为真核细胞中细胞质与细胞核之间物质交换的桥梁,在细胞生命活动中发挥着极其重要的作用。然而因研究手段和材料的限制,目前对于植物核孔复合物及其组分(即核孔蛋白)所参与的生物学过程及其分子机制的认识仍非常有限。
本实验室前期利用生物信息学分析手段在拟南芥基因组中筛选到一批可能编码核孔蛋白的候选基因,通过大量筛选相应的T-DNA插入突变体,最终获得多个发育表型较为明显的潜在核孔蛋白基因突变体,为研究核孔蛋白在植物生长发育过程中的功能创造了条件。本论文中的Nup96基因便是其中一个。拟南芥Nup96蛋白与脊椎动物Nup96和酵母Nup145C蛋白同源,是Nup107-160亚复合体的一个组分,可以与脊椎动物SEC13在拟南芥中的同源蛋白互作。Nup96蛋白N端存在一个保守的“自酶解结构域”,研究发现该结构域在原核和植物细胞中均有活性,且自酶解作用的失活并不影响Nup96蛋白在植物中功能,这种自酶解活性的生物学意义尚有待进一步研究。
Nup96基因突变会导致拟南芥提早开花,且其早花表型与光周期无关,对该基因参与开花调控机制的分子遗传学研究表明,该基因及蛋白在拟南芥体内呈组成型表达,在长日照条件下其早花表型可以被CONSTANS (CO)基因的突变所抑制,同时Nup96基因突变会导致植物的开花时间对环境低温不敏感；此外,Nup96突变还会影响开花抑制因子FLC染色质组蛋白H3Ac修饰水平,导致其表达量降低,促使拟南芥早花；在nup96突变体中miR156a,c的转录水平显著降低,推测Nup96可能通过影响miR156的转录影响miR156的累积,从而导致拟南芥早花。此外,Nup96的开花调控功能主要发生在维管组织和茎尖生长点。综上,拟南芥Nup96基因可以通过光周期、年龄、自主及环境温度等多条途径参与拟南芥开花调控。
Nup96基因突变还会影响拟南芥生物钟系统的功能。通过叶片运动节律、基因表达及生物钟启动子驱动荧光素酶报告基因实验分析发现,在连续光照和连续黑暗下,nup96突变体的生物钟周期约为28小时,比野生型植株延长3小时左右,表明该基因在拟南芥生物钟周期调控中发挥重要作用。相位响应曲线显示,nup96突变会增强生物钟对光信号的敏感性,影响生物钟对光信号的门控作用(Gating)。Nup96还参与生物钟的温度补偿,nup96突变体呈现温度补偿过度表型,且低温可以恢复突变体的长周期表型。此外,nup96突变会影响几乎所有已知生物钟关键基因的表达模式,使其表达节律的周期延长。以上结果证明,Nup96参与拟南芥生物钟周期长度的调控,是一个全新的生物钟调控因子。
Nuclear pore complex (NPC) embeds in the double membrane nuclear envelope (NE), the physical barrier separating the nucleus from cytosol, and serves as the sole channel for nucleocytoplasmic transport of macromolecules essential for cell survival (i.e. proteins and RNAs). Because of the limitations of research tools and materials, it was not until the last decade that the biological functions of these individual nucleoporins just began to be understood.
Previously in our lab, a set of candidate nucleoporin genes in Arabidopsis genome has been identified using bioinformatical approaches. After screening the Arabidopsis mutants for those candidate genes, a few lines with discernible developmental phenotypes have been isolated for further analysis and nup96in this thesis is one of them. Nup96is a single copy gene in Arabidopsis genome and encodes a protein whose sequence shows strong similarity with vertebrates Nup96and yeast Nup145C. Nup96is one of the stable constituents of Nup107-160subcomplex in NPC, which interacts with Arabidopsis SEC13protein both in vitro and in vivo. A conserved peptidase domain is included in the N terminus of Arabidopsis Nup96, which remains autoproteolytic activities both in prokaryotic and plant cells. Failure to complete autoproteolysis would not affect the functions of Nup96in Arabidopsis, therefore, the biological function of this proteolysis still needs to be elucidated.
Loss-of-function alleles of nup96exhibit a strong early-flowering phenotype regardless of photoperiod, which can be strongly suppressed by co mutation under long days. The flowering of nup96mutants is also non-responsive to different ambient temperatures. Moreover, our data shows that Nup96is required for FLC activation partially through a mechanism involving histone acetylation of FLC chromatin. Nup96mutations also reduce the expression level of miR156genes. In addition, expression of Nup96in both vascular tissue and shoot apical meristems could rescue the early-flowering phenotype of nup96mutants. Thus, we proposed that Nup96could negatively regulate flowering in Arabidopsis through multiple pathways.
Mutation of Nup96also has a broad affect on circadian clock function in Arabidopsis. Given by the leaf movement assay and bioluminescence of clock gene promoter activity, we found that nup96lengthens the circadian period both in continuous light and dark, suggesting that Nup96plays an important role in determining the circadian period of circadian clock. Phase response curve shows that nup96mutants are more sensitive to light pulses in the daytime than wild type, indicating that nup96could negatively regulate clock sensitivity for gating light signals, In addition, nup96mutation also results in a temperature overcompensation phenotype and low temperatures completely rescue the long period phenotype of nup96plants. Moreover, nup96mutation also lengthens the circadian period of clock gene expressions. Taken together, we demonstrate that Nup96is a novel regulator in clock period determination.
本实验室前期利用生物信息学分析手段在拟南芥基因组中筛选到一批可能编码核孔蛋白的候选基因,通过大量筛选相应的T-DNA插入突变体,最终获得多个发育表型较为明显的潜在核孔蛋白基因突变体,为研究核孔蛋白在植物生长发育过程中的功能创造了条件。本论文中的Nup96基因便是其中一个。拟南芥Nup96蛋白与脊椎动物Nup96和酵母Nup145C蛋白同源,是Nup107-160亚复合体的一个组分,可以与脊椎动物SEC13在拟南芥中的同源蛋白互作。Nup96蛋白N端存在一个保守的“自酶解结构域”,研究发现该结构域在原核和植物细胞中均有活性,且自酶解作用的失活并不影响Nup96蛋白在植物中功能,这种自酶解活性的生物学意义尚有待进一步研究。
Nup96基因突变会导致拟南芥提早开花,且其早花表型与光周期无关,对该基因参与开花调控机制的分子遗传学研究表明,该基因及蛋白在拟南芥体内呈组成型表达,在长日照条件下其早花表型可以被CONSTANS (CO)基因的突变所抑制,同时Nup96基因突变会导致植物的开花时间对环境低温不敏感；此外,Nup96突变还会影响开花抑制因子FLC染色质组蛋白H3Ac修饰水平,导致其表达量降低,促使拟南芥早花；在nup96突变体中miR156a,c的转录水平显著降低,推测Nup96可能通过影响miR156的转录影响miR156的累积,从而导致拟南芥早花。此外,Nup96的开花调控功能主要发生在维管组织和茎尖生长点。综上,拟南芥Nup96基因可以通过光周期、年龄、自主及环境温度等多条途径参与拟南芥开花调控。
Nup96基因突变还会影响拟南芥生物钟系统的功能。通过叶片运动节律、基因表达及生物钟启动子驱动荧光素酶报告基因实验分析发现,在连续光照和连续黑暗下,nup96突变体的生物钟周期约为28小时,比野生型植株延长3小时左右,表明该基因在拟南芥生物钟周期调控中发挥重要作用。相位响应曲线显示,nup96突变会增强生物钟对光信号的敏感性,影响生物钟对光信号的门控作用(Gating)。Nup96还参与生物钟的温度补偿,nup96突变体呈现温度补偿过度表型,且低温可以恢复突变体的长周期表型。此外,nup96突变会影响几乎所有已知生物钟关键基因的表达模式,使其表达节律的周期延长。以上结果证明,Nup96参与拟南芥生物钟周期长度的调控,是一个全新的生物钟调控因子。
Nuclear pore complex (NPC) embeds in the double membrane nuclear envelope (NE), the physical barrier separating the nucleus from cytosol, and serves as the sole channel for nucleocytoplasmic transport of macromolecules essential for cell survival (i.e. proteins and RNAs). Because of the limitations of research tools and materials, it was not until the last decade that the biological functions of these individual nucleoporins just began to be understood.
Previously in our lab, a set of candidate nucleoporin genes in Arabidopsis genome has been identified using bioinformatical approaches. After screening the Arabidopsis mutants for those candidate genes, a few lines with discernible developmental phenotypes have been isolated for further analysis and nup96in this thesis is one of them. Nup96is a single copy gene in Arabidopsis genome and encodes a protein whose sequence shows strong similarity with vertebrates Nup96and yeast Nup145C. Nup96is one of the stable constituents of Nup107-160subcomplex in NPC, which interacts with Arabidopsis SEC13protein both in vitro and in vivo. A conserved peptidase domain is included in the N terminus of Arabidopsis Nup96, which remains autoproteolytic activities both in prokaryotic and plant cells. Failure to complete autoproteolysis would not affect the functions of Nup96in Arabidopsis, therefore, the biological function of this proteolysis still needs to be elucidated.
Loss-of-function alleles of nup96exhibit a strong early-flowering phenotype regardless of photoperiod, which can be strongly suppressed by co mutation under long days. The flowering of nup96mutants is also non-responsive to different ambient temperatures. Moreover, our data shows that Nup96is required for FLC activation partially through a mechanism involving histone acetylation of FLC chromatin. Nup96mutations also reduce the expression level of miR156genes. In addition, expression of Nup96in both vascular tissue and shoot apical meristems could rescue the early-flowering phenotype of nup96mutants. Thus, we proposed that Nup96could negatively regulate flowering in Arabidopsis through multiple pathways.
Mutation of Nup96also has a broad affect on circadian clock function in Arabidopsis. Given by the leaf movement assay and bioluminescence of clock gene promoter activity, we found that nup96lengthens the circadian period both in continuous light and dark, suggesting that Nup96plays an important role in determining the circadian period of circadian clock. Phase response curve shows that nup96mutants are more sensitive to light pulses in the daytime than wild type, indicating that nup96could negatively regulate clock sensitivity for gating light signals, In addition, nup96mutation also results in a temperature overcompensation phenotype and low temperatures completely rescue the long period phenotype of nup96plants. Moreover, nup96mutation also lengthens the circadian period of clock gene expressions. Taken together, we demonstrate that Nup96is a novel regulator in clock period determination.
引文
[1]Achard, P., Baghour, M., Chapple, A., Hedden, P., Van Der Straeten, D., Genschik, P., Moritz, T., and Harberd, N.P. (2007). The plant stress hormone ethylene controls floral transition via DELLA-dependent regulation of floral meristem-identity genes. Proceedings of the National Academy of Sciences of the United States of America 104,6484-6489.
[2]Adrian, J., Farrona, S., Reimer, J.J., Albani, M.C., Coupland, G., and Turck, F. (2010). cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. The Plant Cell 22,1425-1440.
[3]Alabadi, D., Oyama, T., Yanovsky, M.J., Harmon, F.G., Mas, P., and Kay, S.A. (2001). Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293,880-883.
[4]Alber, F., Dokudovskaya, S., Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B.T., Sali, A., and Rout, M.P. (2007). The molecular architecture of the nuclear pore complex. Nature 450,695-701.
[5]Allen, J.L., and Douglas, M.G (1989). Organization of the nuclear pore complex in Saccharomyces cerevisiae. Journal of Ultrastructure and Molecular Structure Research 102, 95-108.
[6]An, H., Roussot, C., Suarez-Lopez, P., Corbesier, L., Vincent, C., Pineiro, M., Hepworth, S., Mouradov, A., Justin, S., Turnbull, C., and Coupland, G. (2004). CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development 131,3615-3626.
[7]Andres, F., and Coupland, G. (2012). The genetic basis of flowering responses to seasonal cues. Nature reviews. Genetics 13,627-639.
[8]Anwer, M.U., and Davis, S.J. (2013). An overview of natural variation studies in the Arabidopsis thaliana circadian clock. Seminars in Cell & Developmental Biology 24, 422-429.
[9]Askjaer, P., Galy, V., Hannak, E., and Mattaj, I.W. (2002). Ran GTPase cycle and importins alpha and beta are essential for spindle formation and nuclear envelope assembly in living Caenorhabditis elegans embryos. Molecular Biology of the Cell 13,4355-4370.
[10]Ausin, I., Alonso-Blanco, C., Jarillo, J.A., Ruiz-Garcia, L., and Martinez-Zapater, J.M. (2004). Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nature Genetics 36,162-166.
[11]Balasubramanian, S., Sureshkumar, S., Lempe, J., and Weigel, D. (2006). Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genetics 2, e106.
[12]Baudry, A., Ito, S., Song, Y.H., Strait, A.A., Kiba, T., Lu, S., Henriques, R., Pruneda-Paz, J.L., Chua, N.H., Tobin, E.M., Kay, S.A., and Imaizumi, T. (2010). F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. The Plant Cell 22,606-622.
[13]Baurle, I., and Dean, C. (2008). Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets. PloS One 3, e2733.
[14]Bell-Pedersen, D., Cassone, V.M., Earnest, D.J., Golden, S.S., Hardin, P.E., Thomas, T.L., and Zoran, M.J. (2005). Circadian rhythms from multiple oscillators:lessons from diverse organisms. Nature Reviews, Genetics 6,544-556.
[15]Bilokapic, S., and Schwartz, T.U. (2012). Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex. Proceedings of the National Academy of Sciences of the United States of America 109,15241-15246.
[16]Blazquez, M.A., Ahn, J.H., and Weigel, D. (2003). A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nature Genetics 33,168-171.
[17]Blazquez, M.A., Green, R., Nilsson, O., Sussman, M.R., and Weigel, D. (1998). Gibberellins promote flowering of arabidopsis by activating the LEAFY promoter. The Plant Cell 10,791-800.
[18]Bodoor, K., Shaikh, S., Salina, D., Raharjo, W.H., Bastos, R., Lohka, M., and Burke, B. (1999). Sequential recruitment of NPC proteins to the nuclear periphery at the end of mitosis. Journal of Cell Science 112,2253-2264.
[19]Boikoglou, E., Ma, Z., von Korff, M., Davis, A.M., Nagy, F., and Davis, S.J. (2011). Environmental memory from a circadian oscillator:the Arabidopsis thaliana clock differentially integrates perception of photic vs. thermal entrainment. Genetics 189,655-664.
[20]Boruc, J., Zhou, X., and Meier, I. (2012). Dynamics of the plant nuclear envelope and nuclear pore. Plant Physiology 158,78-86.
[21]Braud, C., Zheng, W., and Xiao, W. (2012). LONO1 encoding a nucleoporin is required for embryogenesis and seed viability in Arabidopsis. Plant Physiology 160,823-836.
[22]Bustamante, J.O., Michelette, E.R., Geibel, J.P., Dean, D.A., Hanover, J.A., and McDonnell, T.J. (2000). Calcium, ATP and nuclear pore channel gating. Pflugers Archiv 439, 433-444.
[23]Cardon, G., Hohmann, S., Klein, J., Nettesheim, K., Saedler, H., and Huijser, P. (1999). Molecular characterisation of the Arabidopsis SBP-box genes. Gene 237,91-104.
[24]Castillejo, C., and Pelaz, S. (2008). The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering. Current Biology 18,1338-1343.
[25]Cavalier-Smith, T. (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematic and Evolutionary Microbiology 52,297-354.
[26]Cheng, Y.T., Germain, H., Wiermer, M., Bi, D., Xu, F., Garcia, A.V., Wirthmueller, L., Despres, C., Parker, J.E., Zhang, Y., and Li, X. (2009). Nuclear pore complex component MOS7/Nup88 is required for innate immunity and nuclear accumulation of defense regulators in Arabidopsis. The Plant Cell 21,2503-2516.
[27]Cho, H.J., Kim, J.J., Lee, J.H., Kim, W., Jung, J.H., Park, C.M., and Ahn, J.H. (2012). SHORT VEGETATIVE PHASE (SVP) protein negatively regulates miR172 transcription via direct binding to the pri-miR172a promoter in Arabidopsis. FEBS Letters 586,2332-2337.
[28]Chow, B.Y., Heifer, A., Nusinow, D.A., and Kay, S.A. (2012). ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock. Plant Signaling & Behavior 7,170-173.
[29]Clarke, P.R., and Zhang, C. (2004). Spatial and temporal control of nuclear envelope assembly by Ran GTPase. Symposia of the Society for Experimental Biology,193-204.
[30]Colot, H.V., Loros, J.J., and Dunlap, J.C. (2005). Temperature-modulated alternative splicing and promoter use in the Circadian clock gene frequency. Molecular Biology of the Cell 16,5563-5571.
[31]Corbesier, L., Lejeune, P., and Bernier, G (1998). The role of carbohydrates in the induction of flowering in Arabidopsis thaliana:comparison between the wild type and a starchless mutant. Planta 206,131-137.
[32]Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., Giakountis, A., Farrona, S., Gissot, L., Turnbull, C., and Coupland, G. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316, 1030-1033.
[33]Cronshaw, J.M., Krutchinsky, A.N., Zhang, W., Chait, B.T., and Matunis, M.J. (2002). Proteomic analysis of the mammalian nuclear pore complex. The Journal of Cell Biology 158, 915-927.
[34]D'Angelo, M.A., and Hetzer, M.W. (2008). Structure, dynamics and function of nuclear pore complexes. Trends Cell Biol 18,456-466.
[35]Dai, S., Wei, X., Pei, L., Thompson, R.L., Liu, Y., Heard, J.E., Ruff, T.G, and Beachy, R.N. (2011). BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock. The Plant Cell 23,961-972.
[36]Daigle, N., Beaudouin, J., Hartnell, L., Imreh, G., Hallberg, E., Lippincott-Schwartz, J., and Ellenberg, J. (2001). Nuclear pore complexes form immobile networks and have a very low turnover in live mammalian cells. The Journal of Cell Biology 154,71-84.
[37]Daniel, X., Sugano, S., and Tobin, E.M. (2004). CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 101,3292-3297.
[38]Danker, T., and Oberleithner, H. (2000). Nuclear pore function viewed with atomic force microscopy. Pflugers Archiv 439,671-681.
[39]Darrah, C., Taylor, B.L., Edwards, K.D., Brown, P.E., Hall, A., and McWatters, H.G (2006). Analysis of phase of LUCIFERASE expression reveals novel circadian quantitative trait loci in Arabidopsis. Plant Physiology 140,1464-1474.
[40]David, K.M., Armbruster, U., Tama, N., and Putterill, J. (2006). Arabidopsis GIGANTEA protein is post-transcriptionally regulated by light and dark. FEBS Letters 580,1193-1197.
[41]Davis, S.J., and Millar, A.J. (2001). Watching the hands of the Arabidopsis biological clock. Genome Biology 2, Reviews 1008.1-Reviews1008.3.
[42]de Lucas, M., Daviere, J.M., Rodriguez-Falcon, M., Pontin, M., Iglesias-Pedraz, J.M., Lorrain, S., Fankhauser, C., Blazquez, M.A., Titarenko, E., and Prat, S. (2008). A molecular framework for light and gibberellin control of cell elongation. Nature 451,480-484.
[43]De Lucia, F., Crevillen, P., Jones, A.M., Greb, T., and Dean, C. (2008). A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proceedings of the National Academy of Sciences of the United States of America 105, 16831-16836.
[44]Deal, R.B., Kandasamy, M.K., McKinney, E.C., and Meagher, R.B. (2005). The nuclear actin-related protein ARP6 is a pleiotropic developmental regulator required for the maintenance of FLOWERING LOCUS C expression and repression of flowering in Arabidopsis. The Plant Cell 17,2633-2646.
[45]Deng, X., Gu, L., Liu, C., Lu, T., Lu, F., Lu, Z., Cui, P., Pei, Y., Wang, B., Hu, S., and Cao, X. (2010). Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America 107,19114-19119.
[46]Devlin, P.F., and Kay, S.A. (2000). Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. The Plant Cell 12,2499-2510.
[47]Diernfellner, A., Colot, H.V., Dintsis, O., Loros, J.J., Dunlap, J.C., and Brunner, M. (2007). Long and short isoforms of Neurospora clock protein FRQ support temperature-compensated circadian rhythms. FEBS Letters 581,5759-5764.
[48]Dill, A., Jung, H.S., and Sun, T.P. (2001). The DELLA motif is essential for gibberellin-induced degradation of RGA. Proceedings of the National Academy of Sciences of the United States of America 98,14162-14167.
[49]Ding, Z., Doyle, M.R., Amasino, R.M., and Davis, S.J. (2007). A complex genetic interaction between Arabidopsis thaliana TOC1 and CCA1/LHY in driving the circadian clock and in output regulation. Genetics 176,1501-1510.
[50]Dixon, L.E., Knox, K., Kozma-Bognar, L., Southern, M.M., Pokhilko, A., and Millar, A.J. (2011). Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis. Current Biology 21,120-125.
[51]Dong, C.H., Agarwal, M., Zhang, Y., Xie, Q., and Zhu, J.K. (2006a). The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proceedings of the National Academy of Sciences of the United States of America 103,8281-8286.
[52]Dong, C.H., Hu, X., Tang, W., Zheng, X., Kim, Y.S., Lee, B.H., and Zhu, J.K. (2006b). A putative Arabidopsis nucleoporin, AtNUP160, is critical for RNA export and required for plant tolerance to cold stress. Molecular and Cellular Biology 26,9533-9543.
[53]Doyle, M.R., Bizzell, CM., Keller, M.R., Michaels, S.D., Song, J., Noh, Y.S., and Amasino, R.M. (2005). HUA2 is required for the expression of floral repressors in Arabidopsis thaliana. The Plant Journal 41,376-385.
[54]Doyle, M.R., Davis, S.J., Bastow, R.M., McWatters, H.G., Kozma-Bognar, L., Nagy, F., Millar, A.J,, and Amasino, R.M. (2002). The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419,74-77.
[55]Enninga, J., Levay, A., and Fontoura, B.M. (2003). Sec13 shuttles between the nucleus and the cytoplasm and stably interacts with Nup96 at the nuclear pore complex. Molecular and Cellular Biology 23,7271-7284.
[56]Eriksson, S., Bohlenius, H., Moritz, T., and Nilsson, O. (2006). GA4 is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation. The Plant Cell 18,2172-2181.
[57]Fahrenkrog, B., and Aebi, U. (2003). The nuclear pore complex:nucleocytoplasmic transport and beyond. Nature reviews. Molecular Cell Biology 4,757-766.
[58]Fahrenkrog, B., Koser, J., and Aebi, U. (2004). The nuclear pore complex:a jack of all trades? Trends in Biochemical Sciences 29,175-182.
[59]Farinas, B., and Mas, P. (2011). Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. The Plant Journal 66,318-329.
[60]Farre, E.M., Harmer, S.L., Harmon, F.G., Yanovsky, M.J., and Kay, S.A. (2005). Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Current Biology 15,47-54.
[61]Ferrandez-Ayela, A., Alonso-Peral, M.M., Sanchez-Garcia, A.B., Micol-Ponce, R., Perez-Perez, J.M., Micol, J.L., and Ponce, M.R. (2013). Arabidopsis TRANSCURVATA1 encodes NUP58, a component of the nucleopore central channel. PloS One 8, e67661.
[62]Filichkin, S.A., Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E., Wong, W.K., and Mockler, T.C. (2010). Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Research 20,45-58.
[63]Fiserova, J., Kiseleva, E., and Goldberg, M.W. (2009). Nuclear envelope and nuclear pore complex structure and organization in tobacco BY-2 cells. The Plant Journal 59,243-255.
[64]Fontoura, B.M., Blobel, G, and Matunis, M.J. (1999). A conserved biogenesis pathway for nucleoporins:proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96. The Journal of Cell Biology 144,1097-1112.
[65]Fornara, F., de Montaigu, A., and Coupland, G (2010). SnapShot:Control of flowering in Arabidopsis. Cell 141,550,550.e1-550.e2.
[66]Fornara, F., Panigrahi, K.C., Gissot, L., Sauerbrunn, N., Ruhl, M., Jarillo, J.A., and Coupland, G (2009). Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Developmental Cell 17,75-86.
[67]Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A., and Paz-Ares, J. (2007). Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics 39,1033-1037.
[68]Fujiwara, S., Wang, L., Han, L., Suh, S.S., Salome, P.A., McClung, C.R., and Somers, D.E. (2008). Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins. The Journal of Biological Chemistry 283,23073-23083.
[69]Fukuda, H., Nakamichi, N., Hisatsune, M., Murase, H., and Mizuno, T. (2007). Synchronization of plant circadian oscillators with a phase delay effect of the vein network. Physical Review Letters 99,098102.
[70]Gendron, J.M., Pruneda-Paz, J.L., Doherty, C.J., Gross, A.M., Kang, S.E., and Kay, S.A. (2012). Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proceedings of the National Academy of Sciences of the United States of America 109, 3167-3172.
[71]Giebultowicz, J. (2004). Chronobiology:biological timekeeping. Integrative and Comparative Biology 44,266.
[72]Goldberg, M.W., and Allen, T.D. (1996). The nuclear pore complex and lamina: three-dimensional structures and interactions determined by field emission in-lens scanning electron microscopy. Journal of Molecular Biology 257,848-865.
[73]Goldberg, M.W., Wiese, C., Allen, T.D., and Wilson, K.L. (1997). Dimples, pores, star-rings, and thin rings on growing nuclear envelopes:evidence for structural intermediates in nuclear pore complex assembly. Journal of Cell Science 110 (Pt 4),409-420.
[74]Gong, Z., Dong, C.H., Lee, H., Zhu, J., Xiong, L., Gong, D., Stevenson, B., and Zhu, J.K. (2005). A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. The Plant Cell 17,256-267.
[75]Gould, P.D., Diaz, P., Hogben, C., Kusakina, J., Salem, R., Hartwell, J., and Hall, A. (2009). Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants. The Plant Journal 58,893-901.
[76]Green, R.M., Tingay, S., Wang, Z.Y., and Tobin, E.M. (2002). Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiology 129,576-584.
[77]Griffiths, J., Murase, K., Rieu, I., Zentella, R., Zhang, Z.L., Powers, S.J., Gong, F., Phillips, A.L., Hedden, P., Sun, T.P., and Thomas, S.G (2006). Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. The Plant Cell 18, 3399-3414.
[78]Grossman, E., Medalia, O., and Zwerger, M. (2012). Functional architecture of the nuclear pore complex. Annual Review of Biophysics 41,557-584.
[79]Groth, M., Takeda, N., Perry, J., Uchida, H., Draxl, S., Brachmann, A., Sato, S., Tabata, S., Kawaguchi, M., Wang, T.L., and Parniske, M. (2010). NENA, a Lotus japonicus homolog of See13, is required for rhizodermal infection by arbuscular mycorrhiza fungi and rhizobia but dispensable for cortical endosymbiotic development. The Plant Cell 22, 2509-2526.
[80]Guttinger, S., Laurell, E., and Kutay, U. (2009). Orchestrating nuclear envelope disassembly and reassembly during mitosis. Nature Reviews, Molecular Cell Biology 10, 178-191.
[81]Hall, A., Bastow, R.M., Davis, S.J., Hanano, S., McWatters, H.G., Hibberd, V., Doyle, M.R., Sung, S., Halliday, K.J., Amasino, R.M., and Millar, A.J. (2003). The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. The Plant Cell 15,2719-2729.
[82]Hanano, S., Domagalska, M.A., Nagy, F., and Davis, S.J. (2006). Multiple phytohormones influence distinct parameters of the plant circadian clock. Genes to cells 11,1381-1392.
[83]Harberd, N.P. (2003). Botany. Relieving DELLA restraint. Science 299,1853-1854.
[84]Harel, A., Chan, R.C., Lachish-Zalait, A., Zimmerman, E., Elbaum, M., and Forbes, D.J. (2003). Importin beta negatively regulates nuclear membrane fusion and nuclear pore complex assembly. Molecular Biology of the Cell 14,4387-4396.
[85]Harmer, S.L. (2009). The circadian system in higher plants. Annual Review of Plant Biology 60,357-377.
[86]Harmer, S.L., and Kay, S.A. (2005). Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis. The Plant Cell 17,1926-1940.
[87]Hazen, S.P., Schultz, T.F., Pruneda-Paz, J.L., Borevitz, J.O., Ecker, J.R., and Kay, S.A. (2005). LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America 102, 10387-10392.
[88]He, Y., Michaels, S.D., and Amasino, R.M. (2003). Regulation of flowering time by histone acetylation in Arabidopsis. Science 302,1751-1754.
[89]He, Y., Doyle, M.R., and Amasino, R.M. (2004). PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes & Development 18, 2774-2784.
[90]Heifer, A., Nusinow, D.A., Chow, B.Y., Gehrke, A.R., Bulyk, M.L., and Kay, S.A. (2011). LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Current Biology 21,126-133.
[91]Heo, J.B., and Sung, S. (2011). Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331,76-79.
[92]Herrero, E., and Davis, S.J. (2012). Time for a nuclear meeting:protein trafficking and chromatin dynamics intersect in the plant circadian system. Molecular Plant 5,554-565.
[93]Herrero, E., Kolmos, E., Bujdoso, N., Yuan, Y., Wang, M., Berns, M.C., Uhlworm, H., Coupland, G, Saini, R., Jaskolski, M., Webb, A., Goncalves, J., and Davis, S.J. (2012). EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. The Plant Cell 24,428-443.
[94]Hetzer, M.W., Walther, T.C., and Mattaj, I.W. (2005). Pushing the envelope:structure, function, and dynamics of the nuclear periphery. Annual Review of Cell and Developmental Biology 21,347-380.
[95]Hicks, K.A., Albertson, T.M., and Wagner, D.R. (2001). EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis. The Plant Cell 13,1281-1292.
[96]Hong, GJ., Xue, X.Y., Mao, Y.B., Wang, L.J., and Chen, X.Y. (2012). Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. The Plant Cell 24,2635-2648.
[97]Hong, S., Song, H.R., Lutz, K., Kerstetter, R.A., Michael, T.P., and McClung, C.R. (2010). Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107,21211-21216.
[98]Hornyik, C, Terzi, L.C., and Simpson, GG (2010). The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Developmental Cell 18,203-213.
[99]Hou, X., Lee, L.Y., Xia, K., Yan, Y., and Yu, H. (2010). DELLAs modulate jasmonate signaling via competitive binding to JAZs. Developmental Cell 19,884-894.
[100]Hsia, D.A., Tepper, C.G, Pochampalli, M.R., Hsia, E.Y., Izumiya, C., Huerta, S.B., Wright, M.E., Chen, H.W., Kung, H.J., and Izumiya, Y. (2010). KDM8, a H3K36me2 histone demethylase that acts in the cyclin Al coding region to regulate cancer cell proliferation. Proceedings of the National Academy of Sciences of the United States of America 107,9671-9676.
[101]Huang, W., Perez-Garcia, P., Pokhilko, A., Millar, A.J., Antoshechkin, I., Riechmann, J.L., and Mas, P. (2012). Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336,75-79.
[102]Huijser, P., and Schmid, M. (2011). The control of developmental phase transitions in plants. Development 138,4117-4129.
[103]Imaizumi, T. (2010). Arabidopsis circadian clock and photoperiodism:time to think about location. Current Opinion in Plant Biology 13,83-89.
[104]Imaizumi, T., Tran, H.G, Swartz, T.E., Briggs, W.R., and Kay, S.A. (2003). FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426,302-306.
[105]Imaizumi, T., Schultz, T.F., Harmon, F.G., Ho, L.A., and Kay, S.A. (2005). FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309, 293-297.
[106]Imlau, A., Truernit, E., and Sauer, N. (1999). Cell-to-cell and long-distance trafficking of the green fluorescent protein in the phloem and symplastic unloading of the protein into sink tissues. The Plant Cell 11,309-322.
[107]Inigo, S., Alvarez, M.J., Strasser, B., Califano, A., and Cerdan, P.D. (2012). PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis. The Plant Journal 69,601-612.
[108]Ishitani, M., Xiong, L., Lee, H., Stevenson, B., and Zhu, J.K. (1998). HOS1, a genetic locus involved in cold-responsive gene expression in arabidopsis. The Plant Cell 10, 1151-1161.
[109]Ito, S., Song, Y.H., Josephson-Day, A.R., Miller, R.J., Breton, G., Olmstead, R.G, and Imaizumi, T. (2012). FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 109,3582-3587.
[110]Jacob, Y., Mongkolsiriwatana, C., Veley, K.M., Kim, S.Y., and Michaels, S.D. (2007). The nuclear pore protein AtTPR is required for RNA homeostasis, flowering time, and auxin signaling. Plant Physiology 144,1383-1390.
[111]James, A.B., Syed, N.H., Bordage, S., Marshall, J., Nimmo, G.A., Jenkins, G.I., Herzyk, P., Brown, J.W., and Nimmo, H.G. (2012). Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. The Plant Cell 24,961-981.
[112]Jang, S., Marchal, V., Panigrahi, K.C., Wenkel, S., Soppe, W., Deng, X.W., Valverde, F., and Coupland, G. (2008). Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. The EMBO Journal 27, 1277-1288.
[113]Jeong, S.Y., Rose, A., Joseph, J., Dasso, M., and Meier, I. (2005). Plant-specific mitotic targeting of RanGAP requires a functional WPP domain. The Plant Journal 42,270-282.
[114]Jiang, D., Gu, X., and He, Y. (2009). Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. The Plant Cell 21,1733-1746.
[115]Johanson, U., West, J., Lister, C., Michaels, S., Amasino, R., and Dean, C. (2000). Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290,344-347.
[116]Jones, M.A., and Harmer, S. (2011). JMJD5 Functions in concert with TOC1 in the arabidopsis circadian system. Plant Signaling & Behavior 6,445-448.
[117]Jones, M.A., Covington, M.F., DiTacchio, L., Vollmers, C., Panda, S., and Harmer, S.L. (2010). Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proceedings of the National Academy of Sciences of the United States of America 107,21623-21628.
[118]Jung, J.H., Seo, P.J., Ahn, J.H., and Park, C.M. (2012a). Arabidopsis RNA-binding protein FCA regulates microRNA172 processing in thermosensory flowering. The Journal of Biological Chemistry 287,16007-16016.
[119]Jung, J.H., Ju, Y., Seo, P.J., Lee, J.H., and Park, C.M. (2012b). The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis. The Plant Journal 69,577-588.
[120]Jung, J.H., Seo, Y.H., Seo, P.J., Reyes, J.L., Yun, J., Chua, N.H., and Park, C.M. (2007). The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. The Plant Cell 19,2736-2748.
[121]Jung, J.H., Park, J.H., Lee, S., To, T.K., Kim, J.M., Seki, M., and Park, C.M. (2013). The Cold Signaling Attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 Activates FLOWERING LOCUS C Transcription via Chromatin Remodeling under Short-Term Cold Stress in Arabidopsis. The Plant Cell 25,4378-4390.
[122]Kanamori, N., Madsen, L.H., Radutoiu, S., Frantescu, M., Quistgaard, E.M., Miwa, H., Downie, J.A., James, E.K., Felle, H.H., Haaning, L.L., Jensen, T.H., Sato, S., Nakamura, Y., Tabata, S., Sandal, N., and Stougaard, J. (2006). A nucleoporin is required for induction of Ca2+spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proceedings of the National Academy of Sciences of the United States of America 103,359-364.
[123]Kiba, T., Henriques, R., Sakakibara, H., and Chua, N.H. (2007). Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. The Plant Cell 19,2516-2530.
[124]Kikis, E.A., Khanna, R., and Quail, P.H. (2005). ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY. The Plant Journal 44,300-313.
[125]Kim, D.H., Doyle, M.R., Sung, S., and Amasino, R.M. (2009). Vernalization:winter and the timing of flowering in plants. Annual Review of Cell and Developmental Biology 25, 277-299.
[126]Kim, H.J., Hyun, Y., Park, J.Y., Park, M.J., Park, M.K., Kim, M.D., Lee, M.H., Moon, J., Lee, I., and Kim, J. (2004). A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nature Genetics 36,167-171.
[127]Kim, J., Kim, Y., Yeom, M., Kim, J.H., and Nam, H.G (2008). FIONA1 is essential for regulating period length in the Arabidopsis circadian clock. The Plant Cell 20,307-319.
[128]Kim, J.J., Lee, J.H., Kim, W., Jung, H.S., Huijser, P., and Ann, J.H. (2012). The microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Plant Physiology 159,461-478.
[129]Kim, S., Choi, K., Park, C., Hwang, H.J., and Lee, I. (2006). SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C. The Plant Cell 18,2985-2998.
[130]Kim, W.Y., Fujiwara, S., Sun, S.S., Kim, J., Kim, Y., Han, L., David, K., Putterill, J., Nam, H.G, and Somers, D.E. (2007). ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature 449,356-360.
[131]Kiseleva, E., Rutherford, S., Cotter, L.M., Allen, T.D., and Goldberg, M.W. (2001). Steps of nuclear pore complex disassembly and reassembly during mitosis in early Drosophila embryos. Journal of Cell Science 114,3607-3618.
[132]Kobayashi, Y., and Weigel, D. (2007). Move on up, it's time for change--mobile signals controlling photoperiod-dependent flowering. Genes & Development 21,2371-2384.
[133]Koonin, E.V., and Aravind, L. (2009). Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 8,1984-1985.
[134]Kumar, S.V., Lucyshyn, D., Jaeger, K.E., Alos, E., Alvey, E., Harberd, N.P., and Wigge, P.A. (2012). Transcription factor PIF4 controls the thermosensory activation of flowering. Nature 484,242-245.
[135]Lau, O.S., Huang, X., Charron, J.B., Lee, J.H., Li, G., and Deng, X.W. (2011). Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Molecular Cell 43,703-712.
[136]Laubinger, S., Marchal, V., Le Gourrierec, J., Wenkel, S., Adrian, J., Jang, S., Kulajta, C., Braun, H., Coupland, G., and Hoecker, U. (2006). Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability. Development 133,3213-3222.
[137]Lazaro, A., Valverde, F., Pineiro, M., and Jarillo, J.A. (2012). The Arabidopsis E3 ubiquitin ligase HOS1 negatively regulates CONSTANS abundance in the photoperiodic control of flowering. The Plant Cell 24,982-999.
[138]Lee, H., Yoo, S.J., Lee, J.H., Kim, W., Yoo, S.K., Fitzgerald, H., Carrington, J.C., and Ahn, J.H. (2010). Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis. Nucleic Acids Research 38,3081-3093.
[139]Lee, I., Aukerman, M.J., Gore, S.L., Lohman, K.N., Michaels, S.D., Weaver, L.M., John, M.C., Feldmann, K.A., and Amasino, R.M. (1994). Isolation of LUMINIDEPENDENS:a gene involved in the control of flowering time in Arabidopsis. The Plant Cell 6,75-83.
[140]Lee, J.H., Yoo, S.J., Park, S.H., Hwang, I., Lee, J.S., and Ahn, J.H. (2007). Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes & Development 21,397-402.
[141]Lee, J.H., Kim, J.J., Kim, S.H., Cho, H.J., Kim, J., and Ahn, J.H. (2012). The E3 ubiquitin ligase HOS1 regulates low ambient temperature-responsive flowering in Arabidopsis thaliana. Plant & Cell Physiology 53,1802-1814.
[142]Lenhard, M., and Laux, T. (2003). Stem cell homeostasis in the Arabidopsis shoot meristem is regulated by intercellular movement of CLAVATA3 and its sequestration by CLAVATA1. Development 130,3163-3173.
[143]Levy, Y.Y., Mesnage, S., Mylne, J.S., Gendall, A.R., and Dean, C. (2002). Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297,243-246.
[144]Lian, H.L., He, S.B., Zhang, Y.C., Zhu, D.M., Zhang, J.Y., Jia, K.P., Sun, S.X., Li, L., and Yang, H.Q. (2011). Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism. Genes & Development 25,1023-1028.
[145]Lin, J.M., Kilman, V.L., Keegan, K., Paddock, B., Emery-Le, M., Rosbash, M., and Allada, R. (2002). A role for casein kinase 2alpha in the Drosophila circadian clock. Nature 420,816-820.
[146]Lincoln, C., Long, J., Yamaguchi, J., Serikawa, K., and Hake, S. (1994). Aknottedl-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. The Plant Cell 6,1859-1876.
[147]Liu, B., Zuo, Z., Liu, H., Liu, X., and Lin, C. (2011). Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light. Genes & Development 25, 1029-1034.
[148]Liu, F., Marquardt, S., Lister, C., Swiezewski, S., and Dean, C. (2010). Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327, 94-97.
[149]Liu, F., Quesada, V., Crevillen, P., Baurle, I., Swiezewski, S., and Dean, C. (2007). The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Molecular Cell 28,398-407.
[150]Liu, H., Yu, X., Li, K., Klejnot, J., Yang, H., Lisiero, D., and Lin, C. (2008a). Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322,1535-1539.
[151]Liu, L.J., Zhang, Y.C., Li, Q.H., Sang, Y., Mao, J., Lian, H.L., Wang, L., and Yang, H.Q. (2008b). COP 1-mediated ubiquitination of CONSTANS is implicated in cryptochrome regulation of flowering in Arabidopsis. The Plant Cell 20,292-306.
[152]Locke, J.C., Millar, A.J., and Turner, M.S. (2005). Modelling genetic networks with noisy and varied experimental data:the circadian clock in Arabidopsis thaliana. Journal of Theoretical Biology 234,383-393.
[153]Lu, Q., Tang, X., Tian, G., Wang, F., Liu, K., Nguyen, V., Kohalmi, S.E., Keller, W.A., Tsang, E.W., Harada, J.J., Rothstein, S.J., and Cui, Y. (2010). Arabidopsis homolog of the yeast TREX-2 mRNA export complex:components and anchoring nucleoporin. The Plant Journal 61,259-270.
[154]Lu, S.X., Knowles, S.M., Andronis, C., Ong, M.S., and Tobin, E.M. (2009). CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiology 150,834-843.
[155]Lu, S.X., Knowles, S.M., Webb, C.J., Celaya, R.B., Cha, C., Siu, J.P., and Tobin, E.M. (2011a). The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Plant Physiology 155,906-915.
[156]Lu, S.X., Liu, H., Knowles, S.M., Li, J., Ma, L., Tobin, E.M., and Lin, C. (2011b). A role for protein kinase casein kinase2 alpha-subunits in the Arabidopsis circadian clock. Plant Physiology 157,1537-1545.
[157]MacGregor, D.R., Gould, P., Foreman, J., Griffiths, J., Bird, S., Page, R., Stewart, K., Steel, G, Young, J., Paszkiewicz, K., Millar, A.J., Halliday, K.J., Hall, A.J., and Penfield, S. (2013). HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 is required for circadian periodicity through the promotion of nucleo-cytoplasmic mRNA export in Arabidopsis. The Plant Cell 25,4391-4404.
[158]Mahajan, R., Gerace, L., and Melchior, F. (1998). Molecular characterization of the SUMO-1 modification of RanGAPl and its role in nuclear envelope association. The Journal of Cell Biology 140,259-270.
[159]Mans, B.J., Anantharaman, V., Aravind, L., and Koonin, E.V. (2004). Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 3,1612-1637.
[160]Martin-Trillo, M., Lazaro, A., Poethig, R.S., Gomez-Mena, C., Pineiro, M.A., Martinez-Zapater, J.M., and Jarillo, J.A. (2006). EARLY IN SHORT DAYS 1 (ESDI) encodes ACTIN-RELATED PROTEIN 6 (AtARP6), a putative component of chromatin remodelling complexes that positively regulates FLC accumulation in Arabidopsis. Development 133,1241-1252.
[161]Mas, P. (2008). Circadian clock function in Arabidopsis thaliana:time beyond transcription. Trends in Cell Biology 18,273-281.
[162]Mas, P., Kim, W.Y., Somers, D.E., and Kay, S.A. (2003). Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426,567-570.
[163]Mathieu, J., Yant, L.J., Murdter, F., Kuttner, F., and Schmid, M. (2009). Repression of flowering by the miR172 target SMZ. PLoS Biology 7, e1000148.
[164]Matunis, M.J., Coutavas, E., and Blobel, G (1996). A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAPl between the cytosol and the nuclear pore complex. The Journal of Cell Biology 135,1457-1470.
[165]McClung, C.R. (2006). Plant circadian rhythms. The Plant Cell 18,792-803.
[166]McKim, S., and Hay, A. (2010). Patterning and evolution of floral structures-marking time. Current Opinion in Genetics & Development 20,448-453.
[167]Mehra, A., Shi, M., Baker, C.L., Colot, H.V., Loros, J.J., and Dunlap, J.C. (2009). A role for casein kinase 2 in the mechanism underlying circadian temperature compensation. Cell 137,749-760.
[168]Michael, T.P., and McClung, C.R. (2002). Phase-specific circadian clock regulatory elements in Arabidopsis. Plant Physiology 130,627-638.
[169]Michael, T.P., Salome, P.A., and McClung, C.R. (2003). Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proceedings of the National Academy of Sciences of the United States of America 100,6878-6883.
[170]Michaels, S.D., and Amasino, R.M. (1999). FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. The Plant Cell 11,949-956.
[171]Michaels, S.D., and Amasino, R.M. (2001). Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. The Plant Cell 13,935-941.
[172]Michaels, S.D., Bezerra, I.C., and Amasino, R.M. (2004). FRIGIDA-related genes are required for the winter-annual habit in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 101,3281-3285.
[173]Millar, A.J., Carre, I.A., Strayer, C.A., Chua, N.H., and Kay, S.A. (1995). Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267,1161-1163.
[174]Mizoguchi, T., Putterill, J., and Ohkoshi, Y. (2006). Kinase and phosphatase:the cog and spring of the circadian clock. International Review of Cytology 250,47-72.
[175]Mizoguchi, T., Wheatley, K., Hanzawa, Y., Wright, L., Mizoguchi, M., Song, H.R., Carre, I.A., and Coupland, G. (2002). LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Developmental Cell 2,629-641.
[176]Mizoguchi, T., Wright, L., Fujiwara, S., Cremer, F., Lee, K., Onouchi, H., Mouradov, A., Fowler, S., Kamada, H., Putterill, J., and Coupland, G. (2005). Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis. The Plant Cell 17,2255-2270.
[177]Moon, J., Suh, S.S., Lee, H., Choi, K.R., Hong, C.B., Paek, N.C., Kim, S.G, and Lee, I. (2003). The SOC1 MADS-box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis. The Plant Journal 35,613-623.
[178]Morris, K., Thornber, S., Codrai, L., Richardson, C., Craig, A., Sadanandom, A., Thomas, B., and Jackson, S. (2010). DAY NEUTRAL FLOWERING represses CONSTANS to prevent Arabidopsis flowering early in short days. The Plant Cell 22,1118-1128.
[179]Murase, K., Hirano, Y., Sun, T.P., and Hakoshima, T. (2008). Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 456,459-463.
[180]Murtas, G., Reeves, P.H., Fu, Y.F., Bancroft, I., Dean, C., and Coupland, G. (2003). A nuclear protease required for flowering-time regulation in Arabidopsis reduces the abundance of SMALL UBIQUITIN-RELATED MODIFIER conjugates. The Plant Cell 15,2308-2319.
[181]Mutasa-Gottgens, E., and Hedden, P. (2009). Gibberellin as a factor in floral regulatory networks. Journal of Experimental Botany 60,1979-1989.
[182]Muthuswamy, S., and Meier, I. (2011). Genetic and environmental changes in SUMO homeostasis lead to nuclear mRN A retention in plants. Planta 233,201-208.
[183]Mylne, J.S., Barrett, L., Tessadori, F., Mesnage, S., Johnson, L., Bernatavichute, Y.V., Jacobsen, S.E., Fransz, P., and Dean, C. (2006). LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN 1, is required for epigenetic silencing of FLC. Proceedings of the National Academy of Sciences of the United States of America 103,5012-5017.
[184]Nagel, D.H., and Kay, S.A. (2012). Complexity in the wiring and regulation of plant circadian networks. Current Biology 22, R648-657.
[185]Nakamichi, N. (2011). Molecular mechanisms underlying the Arabidopsis circadian clock. Plant & Cell Physiology 52,1709-1718.
[186]Ni, Z., Kim, E.D., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z.J. (2009). Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457, 327-331.
[187]Nilsen, T.W., and Graveley, B.R. (2010). Expansion of the eukaryotic proteome by alternative splicing. Nature 463,457-463.
[188]Noh, Y.S., and Amasino, R.M. (2003). PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. The Plant Cell 15,1671-1682.
[189]Noh, Y.S., Bizzell, C.M., Noh, B., Schomburg, F.M., and Amasino, R.M. (2004). EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. The Plant Journal 38,664-672.
[190]Nusinow, D.A., Helfer, A., Hamilton, E.E., King, J.J., Imaizumi, T., Schultz, T.F., Farre, E.M., and Kay, S.A. (2011). The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475,398-402.
[191]Oh, S., Zhang, H., Ludwig, P., and van Nocker, S. (2004). A mechanism related to the yeast transcriptional regulator Paflc is required for expression of the Arabidopsis FLC/MAF MADS box gene family. The Plant Cell 16,2940-2953.
[192]Onai, K., and Ishiura, M. (2005). PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes to Cells 10,963-972.
[193]Panda, S., Poirier, G.G, and Kay, S.A. (2002). tej defines a role for poly(ADP-ribosyl)ation in establishing period length of the arabidopsis circadian oscillator. Developmental Cell 3, 51-61.
[194]Pante, N., and Kann, M. (2002). Nuclear pore complex is able to transport macromolecules with diameters of about 39 nm. Molecular Biology of the Cell 13,425-434.
[195]Para, A., Farre, E.M., Imaizumi, T., Pruneda-Paz, J.L., Harmon, F.G, and Kay, S.A. (2007). PRR3 Is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. The Plant Cell 19,3462-3473.
[196]Park, B.S., Eo, H.J., Jang, I.C., Kang, H.G., Song, J.T., and Seo, H.S. (2010). Ubiquitination of LHY by SINAT5 regulates flowering time and is inhibited by DET1. Biochemical and Biophysical Research Communications 398,242-246.
[197]Park, D.H., Somers, D.E., Kim, Y.S., Choy, Y.H., Lim, H.K., Soh, M.S., Kim, H.J., Kay, S.A., and Nam, H.G. (1999). Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285,1579-1582.
[198]Parry, G., Ward, S., Cernac, A., Dharmasiri, S., and Estelle, M. (2006). The Arabidopsis SUPPRESSOR OF AUXIN RESISTANCE proteins are nucleoporins with an important role in hormone signaling and development. The Plant Cell 18,1590-1603.
[199]Peng, J., Carol, P., Richards, D.E., King, K.E., Cowling, R.J., Murphy, G.P., and Harberd, N.P. (1997). The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes & Development 11,3194-3205.
[200]Perales, M., and Mas, P. (2007). A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. The Plant Cell 19,2111-2123.
[201]Pien, S., Fleury, D., Mylne, J.S., Crevillen, P., Inze, D., Avramova, Z., Dean, C., and Grossniklaus, U. (2008). ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. The Plant Cell 20, 580-588.
[202]Pokhilko, A., Fernandez, A.P., Edwards, K.D., Southern, M.M., Halliday, K.J., and Millar, A.J. (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Molecular Systems Biology 8,574.
[203]Pokhilko, A., Hodge, S.K., Stratford, K., Knox, K., Edwards, K.D., Thomson, A.W., Mizuno, T., and Millar, A.J. (2010). Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Molecular Systems Biology 6, 416.
[204]Portoles, S., and Mas, P. (2010). The functional interplay between protein kinase CK2 and CCA1 transcriptional activity is essential for clock temperature compensation in Arabidopsis. PLoS Genetics 6, e1001201.
[205]Pruneda-Paz, J.L., and Kay, S.A. (2010). An expanding universe of circadian networks in higher plants. Trends in Plant Science 15,259-265.
[206]Pruneda-Paz, J.L., Breton, G., Para, A., and Kay, S.A. (2009). A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323, 1481-1485.
[207]Quesada, V., Macknight, R., Dean, C., and Simpson, G.G. (2003). Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. The EMBO Journal 22, 3142-3152.
[208]Rabut, G, Doye, V., and Ellenberg, J. (2004). Mapping the dynamic organization of the nuclear pore complex inside single living cells. Nature Cell Biology 6,1114-1121.
[209]Rawat, R., Takahashi, N., Hsu, P.Y., Jones, M.A., Schwartz, J., Salemi, M.R., Phinney, B.S., and Harmer, S.L. (2011). REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genetics 7, e1001350.
[210]Reeves, P.H., Murtas, G, Dash, S., and Coupland, G (2002). early in short days 4, a mutation in Arabidopsis that causes early flowering and reduces the mRNA abundance of the floral repressor FLC. Development 129,5349-5361.
[211]Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110,513-520.
[212]Richter, R., Behringer, C., Muller, I.K., and Schwechheimer, C. (2010). The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. Genes & Development 24,2093-2104.
[213]Ripoll, J.J., Rodriguez-Cazorla, E., Gonzalez-Reig, S., Andujar, A., Alonso-Cantabrana, H., Perez-Amador, M.A., Carbonell, J., Martinez-Laborda, A., and Vera, A. (2009). Antagonistic interactions between Arabidopsis K-homology domain genes uncover PEPPER as a positive regulator of the central floral repressor FLOWERING LOCUS C. Developmental Biology 333,251-262.
[214]Roberts, K., and Northcote, D.H. (1970). Structure of the nuclear pore in higher plants. Nature 228,385-386.
[215]Robles, L.M., Deslauriers, S.D., Alvarez, A.A., and Larsen, P.B. (2012). A loss-of-function mutation in the nucleoporin AtNUP160 indicates that normal auxin signalling is required for a proper ethylene response in Arabidopsis. Journal of Experimental Botany 63,2231-2241.
[216]Robson, F., Costa, M.M., Hepworth, S.R., Vizir, I., Pineiro, M., Reeves, P.H., Putterill, J., and Coupland, G. (2001). Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. The Plant Journal 28,619-631.
[217]Roenneberg, T., and Morse, D. (1993). Two circadian oscillators in one cell. Nature 362,3.
[218]Rose, A., and Meier, I. (2001). A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim. Proceedings of the National Academy of Sciences of the United States of America 98,15377-15382.
[219]Roth, C., and Wiermer, M. (2012). Nucleoporins Nup160 and Sehl are required for disease resistance in Arabidopsis. Plant Signaling & Behavior 7,1212-1214.
[220]Rout, M.P., Aitchison, J.D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B.T. (2000). The yeast nuclear pore complex:composition, architecture, and transport mechanism. The Journal of Cell Biology 148,635-651.
[221]Ryan, K.J., and Wente, S.R. (2000). The nuclear pore complex:a protein machine bridging the nucleus and cytoplasm. Current Opinion in Cell Biology 12,361-371.
[222]Ryan, K.J., McCaffery, J.M., and Wente, S.R. (2003). The Ran GTPase cycle is required for yeast nuclear pore complex assembly. The Journal of Cell Biology 160,1041-1053.
[223]Sai, J., and Johnson, C.H. (1999). Different circadian oscillators control Ca(2+) fluxes and lhcb gene expression. Proceedings of the National Academy of Sciences of the United States of America 96,11659-11663.
[224]Saito, K., Yoshikawa, M., Yano, K., Miwa, H., Uchida, H., Asamizu, E., Sato, S., Tabata, S., Imaizumi-Anraku, H., Umehara, Y., Kouchi, H., Murooka, Y., Szczyglowski, K., Downie, J.A., Parniske, M., Hayashi, M., and Kawaguchi, M. (2007). NUCLEOPORTN85 is required for calcium spiking, fungal and bacterial symbioses, and seed production in Lotus japonicus. The Plant Cell 19,610-624.
[225]Salome, P.A., Weigel, D., and McClung, C.R. (2010). The role of the Arabidopsis morning loop components CCA1, LHY, PRR7, and PRR9 in temperature compensation. The Plant Cell 22,3650-3661.
[226]Sanchez, S.E., Petrillo, E., Beckwith, E.J., Zhang, X., Rugnone, M.L., Hernando, C.E., Cuevas, J.C., Godoy Herz, M.A., Depetris-Chauvin, A., Simpson, C.G., Brown, J.W., Cerdan, P.D., Borevitz, J.O., Mas, P., Ceriani, M.F., Kornblihtt, A.R., and Yanovsky, M.J. (2010). A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature 468,112-116.
[227]Sawa, M., Nusinow, D.A., Kay, S.A., and Imaizumi, T. (2007). FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science 318, 261-265.
[228]Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carre, I.A., and Coupland, G (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93,1219-1229.
[229]Schmid, M., Uhlenhaut, N.H., Godard, F., Demar, M., Bressan, R., Weigel, D., and Lohmann, J.U. (2003). Dissection of floral induction pathways using global expression analysis. Development 130,6001-6012.
[230]Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M., and Weigel, D. (2005). Specific effects of microRNAs on the plant transcriptome. Developmental Cell 8,517-527.
[231]Schwartz, T. (2013). Functional insights from studies on the structure of the nuclear pore and coat protein complexes. Cold Spring Harbor Perspectives in Biology 5, a013375.
[232]Schwechheimer, C., and Willige, B.C. (2009). Shedding light on gibberellic acid signalling. Current Opinion in Plant Biology 12,57-62.
[233]Searle, I., He, Y., Turck, F., Vincent, C., Fornara, F., Krober, S., Amasino, R.A., and Coupland, G. (2006). The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes & Development 20,898-912.
[234]Seo, P.J., Ryu, J., Kang, S.K., and Park, C.M. (2011). Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis. The Plant Journal 65,418-429.
[235]Seo, P.J., Park, M.J., Lim, M.H., Kim, S.G, Lee, M., Baldwin, I.T., and Park, C.M. (2012). A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED 1 underlies the circadian clock regulation of temperature responses in Arabidopsis. The Plant Cell 24, 2427-2442.
[236]Sessions, A., Weigel, D., and Yanofsky, M.F. (1999). The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal expression in meristems and young primordia. The Plant Journal 20,259-263.
[237]Shen, L., Kang, Y.G, Liu, L., and Yu, H. (2011). The J-domain protein J3 mediates the integration of flowering signals in Arabidopsis. The Plant Cell 23,499-514.
[238]Shindo, C., Aranzana, M.J., Lister, C., Baxter, C., Nicholls, C., Nordborg, M., and Dean, C. (2005). Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiology 138,1163-1173.
[239]Simpson, G.G. (2004). The autonomous pathway:epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time. Current Opinion in Plant Biology 7, 570-574.
[240]Simpson, G.G., Dijkwel, P.P., Quesada, V., Henderson, I., and Dean, C. (2003). FY is an RNA 3'end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 113,777-787.
[241]Sivitz, A.B., Reinders, A., Johnson, M.E., Krentz, A.D., Grof, C.P., Perroux, J.M., and Ward, J.M. (2007). Arabidopsis sucrose transporter AtSUC9. High-affinity transport activity, intragenic control of expression, and early flowering mutant phenotype. Plant Physiology 143, 188-198.
[242]Smith, T.F., Gaitatzes, C., Saxena, K., and Neer, E.J. (1999). The WD repeat:a common architecture for diverse functions. Trends in Biochemical Sciences 24,181-185.
[243]Somers, D.E., and Quail, P.H. (1995). Temporal and spatial expression patterns of PHYA and PHYB genes in Arabidopsis. The Plant Journal 7,413-427.
[244]Somers, D.E., Webb, A.A., Pearson, M., and Kay, S.A. (1998). The short-period mutant, tocl-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana. Development 125,485-494.
[245]Song, H.R., and Carre, I.A. (2005). DET1 regulates the proteasomal degradation of LHY, a component of the Arabidopsis circadian clock. Plant Molecular Biology 57,761-771.
[246]Song, Y.H., Ito, S., and Imaizumi, T. (2013). Flowering time regulation:photoperiod-and temperature-sensing in leaves. Trends in Plant Science 18,575-583.
[247]Song, Y.H., Smith, R.W., To, B.J., Millar, A.J., and Imaizumi, T. (2012). FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering. Science 336, 1045-1049.
[248]Song, Y.H., Song, N.Y., Shin, S.Y., Kim, H.J., Yun, D.J., Lim, C.O., Lee, S.Y., Kang, K.Y., and Hong, J.C. (2008). Isolation of CONSTANS as a TGA4/OBF4 interacting protein. Molecules and Cells 25,559-565.
[249]Soppe, W.J., Bentsink, L., and Koornneef, M. (1999). The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana. Development 126, 4763-4770.
[250]Srikanth, A., and Schmid, M. (2011). Regulation of flowering time:all roads lead to Rome. Cellular and Molecular Life Sciences 68,2013-2037.
[251]Stoffler, D., Fahrenkrog, B., and Aebi, U. (1999). The nuclear pore complex:from molecular architecture to functional dynamics. Current Opinion in Cell Biology 11,391-401.
[252]Stoffler, D., Feja, B., Fahrenkrog, B., Walz, J., Typke, D., and Aebi, U. (2003). Cryo-electron tomography provides novel insights into nuclear pore architecture:implications for nucleocytoplasmic transport. Journal of Molecular Biology 328,119-130.
[253]Strasser, B., Alvarez, M.J., Califano, A., and Cerdan, P.D. (2009). A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature. The Plant Journal 58,629-640.
[254]Strayer, C., Oyama, T., Schultz, T.F., Raman, R., Somers, D.E., Mas, P., Panda, S., Kreps, J.A., and Kay, S.A. (2000). Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289,768-771.
[255]Sugano, S., Andronis, C., Ong, M.S., Green, R.M., and Tobin, E.M. (1999). The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 96,12362-12366.
[256]Sun, Q., Yoda, K., Suzuki, M., and Suzuki, H. (2003). Vascular tissue in the stem and roots of woody plants can conduct light. Journal of Experimental Botany 54,1627-1635.
[257]Sung, S., He, Y., Eshoo, T.W., Tamada, Y., Johnson, L., Nakahigashi, K., Goto, K., Jacobsen, S.E., and Amasino, R.M. (2006). Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nature Genetics 38,706-710.
[258]Swiezewski, S., Liu, F., Magusin, A., and Dean, C. (2009). Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462,799-802.
[259]Takada, S., and Goto, K. (2003). Terminal flower2, an Arabidopsis homolog of heterochromatin proteinl, counteracts the activation of flowering locus T by constans in the vascular tissues of leaves to regulate flowering time. The Plant Cell 15,2856-2865.
[260]Tamada, Y., Yun, J.Y., Woo, S.C., and Amasino, R.M. (2009). ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. The Plant Cell 21,3257-3269.
[261]Tamura, K., and Hara-Nishimura, I. (2012). The molecular architecture of the plant nuclear pore complex. Journal of Experimental Botany 64,823-832.
[262]Tamura, K., Fukao, Y., Iwamoto, M., Haraguchi, T., and Hara-Nishimura, I. (2010). Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. The Plant Cell 22,4084-4097.
[263]Thain, S.C., Hall, A., and Millar, A.J. (2000). Functional independence of circadian clocks that regulate plant gene expression. Current Biology 10,951-956.
[264]Thain, S.C., Murtas, G., Lynn, J.R., McGrath, R.B., and Millar, A.J. (2002). The circadian clock that controls gene expression in Arabidopsis is tissue specific. Plant Physiology 130, 102-110.
[265]Tiwari, S.B., Shen, Y., Chang, H.C., Hou, Y., Harris, A., Ma, S.F., McPartland, M., Hymus, GJ., Adam, L., Marion, C., Belachew, A., Repetti, P.P., Reuber, T.L., and Ratcliffe, O.J. (2010). The flowering time regulator CONSTANS is recruited to the FLOWERING LOCUS T promoter via a unique cis-element. The New Phytologist 187, 57-66.
[266]Todesco, M., Rubio-Somoza, I., Paz-Ares, J., and Weigel, D. (2010). A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genetics 6, e1001031.
[267]Torti, S., Fornara, F., Vincent, C., Andres, F., Nordstrom, K., Gobel, U., Knoll, D., Schoof, H., and Coupland, G (2012). Analysis of the Arabidopsis shoot meristem transcriptome during floral transition identifies distinct regulatory patterns and a leucine-rich repeat protein that promotes flowering. The Plant Cell 24,444-462.
[268]Tran, E.J,, and Wente, S.R. (2006). Dynamic nuclear pore complexes:life on the edge. Cell 125,1041-1053.
[269]Troncoso-Ponce, M.A., and Mas, P. (2012). Newly described components and regulatory mechanisms of circadian clock function in Arabidopsis thaliana. Molecular Plant 5,545-553.
[270]Tsuchiya, Y., Akashi, M., Matsuda, M., Goto, K., Miyata, Y., Node, K., and Nishida, E. (2009). Involvement of the protein kinase CK2 in the regulation of mammalian circadian rhythms. Science Signaling 2, ra26.
[271]Valverde, F., Mouradov, A., Soppe, W., Ravenscroft, D., Samach, A., and Coupland, G. (2004). Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 303,1003-1006.
[272]Wahl, V., Ponnu, J., Schlereth, A., Arrivault, S., Langenecker, T., Franke, A., Feil, R., Lunn, J.E., Stitt, M., and Schmid, M. (2013). Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science 339,704-707.
[273]Walther, T.C., Askjaer, P., Gentzel, M., Habermann, A., Griffiths, G, Wilm, M., Mattaj, I.W., and Hetzer, M. (2003). RanGTP mediates nuclear pore complex assembly. Nature 424, 689-694.
[274]Wang, J.W., Czech, B., and Weigel, D. (2009). miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138,738-749.
[275]Wang, L., Fujiwara, S., and Somers, D.E. (2010). PRR5 regulates phosphorylation, nuclear import and sub nuclear localization of TOC1 in the Arabidopsis circadian clock. The EMBO Journal 29,1903-1915.
[276]Wang, Y., Wu, J.F., Nakamichi, N., Sakakibara, H., Nam, H.G, and Wu, S.H. (2011). LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 form a positive feedback regulatory loop in the Arabidopsis circadian clock. The Plant Cell 23,486-498.
[277]Wang, Z.Y., and Tobin, E.M. (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93,1207-1217.
[278]Wang, Z.Y., Kenigsbuch, D., Sun, L., Harel, E., Ong, M.S., and Tobin, E.M. (1997). A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. The Plant Cell 9,491-507.
[279]Wenden, B., Toner, D.L., Hodge, S.K., Grima, R., and Millar, A.J. (2012). Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proceedings of the National Academy of Sciences of the United States of America 109,6757-6762.
[280]Wiermer, M., Cheng, Y.T., Imkampe, J., Li, M., Wang, D., Lipka, V., and Li, X. (2012). Putative members of the Arabidopsis Nup107-16 nuclear pore sub-complex contribute to pathogen defense. The Plant Journal 70,796-808.
[281]Wilson, R.N., Heckman, J.W., and Somerville, C.R. (1992). Gibberellin Is Required for Flowering in Arabidopsis thaliana under Short Days. Plant Physiology 100,403-408.
[282]Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V., and Provart, N.J. (2007). An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PloS One 2, e718.
[283]Wood, C.C., Robertson, M., Tanner, G., Peacock, W.J., Dennis, E.S., and Helliwell, C.A. (2006). The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proceedings of the National Academy of Sciences of the United States of America 103,14631-14636.
[284]Wu, G., and Poethig, R.S. (2006). Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133,3539-3547.
[285]Wu, G., Park, M.Y., Conway, S.R., Wang, J.W., Weigel, D., and Poethig, R.S. (2009). The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138,750-759.
[286]Wu, J.F., Wang, Y., and Wu, S.H. (2008). Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering. Plant Physiology 148,948-959.
[287]Xu, X., Hotta, C.T., Dodd, A.N., Love, J., Sharrock, R., Lee, Y.W., Xie, Q., Johnson, C.H., and Webb, A.A. (2007a). Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis. The Plant Cell 19,3474-3490.
[288]Xu, X.M., Meulia, T., and Meier, I. (2007b). Anchorage of plant RanGAP to the nuclear envelope involves novel nuclear-pore-associated proteins. Current Biology 17,1157-1163.
[289]Xu, X.M., Rose, A., Muthuswamy, S., Jeong, S.Y., Venkatakrishnan, S., Zhao, Q., and Meier, I. (2007c). NUCLEAR PORE ANCHOR, the Arabidopsis homolog of Tpr/Mlpl/Mlp2/megator, is involved in mRNA export and SUMO homeostasis and affects diverse aspects of plant development. The Plant Cell 19,1537-1548.
[290]Yamaguchi, A., Wu, M.F., Yang, L., Wu, G., Poethig, R.S., and Wagner, D. (2009). The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Developmental Cell 17,268-278.
[291]Yamamoto, Y.T., Taylor, C.G, Acedo, GN., Cheng, C.L., and Conkling, M.A. (1991). Characterization of cis-acting sequences regulating root-specific gene expression in tobacco. The Plant Cell 3,371-382.
[292]Yang, D.L., Yao, J., Mei, C.S., Tong, X.H., Zeng, L.J., Li, Q., Xiao, L.T., Sun, T.P., Li, J., Deng, X.W., Lee, C.M., Thomashow, M.F., Yang, Y., He, Z., and He, S.Y. (2012). Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proceedings of the National Academy of Sciences of the United States of America 109, E1192-1200.
[293]Yang, L., Xu, M., Koo, Y., He, J., and Poethig, R.S. (2013). Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156Aand MIR156C. eLife 2, e00260.
[294]Yang, Y.D., Elamawi, R., Bubeck, J., Pepperkok, R., Ritzenthaler, C, and Robinson, D.G (2005). Dynamics of COPII vesicles and the Golgi apparatus in cultured Nicotiana tabacum BY-2 cells provides evidence for transient association of Golgi stacks with endoplasmic reticulum exit sites. The Plant Cell 17,1513-1531.
[295]Yasui, Y., Mukougawa, K., Uemoto, M., Yokofuji, A., Suzuri, R., Nishitani, A., and Kohchi, T. (2012). The phytochrome-interacting vascular plant one-zinc fingerl and VOZ2 redundantly regulate flowering in Arabidopsis. The Plant Cell 24,3248-3263.
[296]Yerushalmi, S., and Green, R.M. (2009). Evidence for the adaptive significance of circadian rhythms. Ecology Letters 12,970-981.
[297]Yoo, B.Y., and Bayley, S.T. (1967). The structure of pores in isolated pea nuclei. Journal of Ultrastructure Research 18,651-660.
[298]Yu, S., Galvao, V.C., Zhang, Y.C., Horrer, D., Zhang, T.Q., Hao, Y.H., Feng, Y.Q., Wang, S., Schmid, M., and Wang, J.W. (2012). Gibberellin regulates the Arabidopsis floral transition through miRl 56-targeted SQUAMOSA promoter binding-like transcription factors. The Plant Cell 24,3320-3332.
[299]Yu, S., Cao, L., Zhou, C.M., Zhang, T.Q., Lian, H., Sun, Y., Wu, J., Huang, J., Wang, G, and Wang, J.W. (2013). Sugar is an endogenous cue for juvenile-to-adult phase transition in plants. eLife 2, e00269.
[300]Zhang, C., Hutchins, J.R., Muhlhausser, P., Kutay, U., and Clarke, P.R. (2002). Role of importin-beta in the control of nuclear envelope assembly by Ran. Current Biology 12, 498-502.
[301]Zhang, H., and van Nocker, S. (2002). The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C. The Plant Journal 31,663-673.
[302]Zhang, H., Ransom, C., Ludwig, P., and van Nocker, S. (2003). Genetic analysis of early flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for expression of the flowering-time switch flowering locus C. Genetics 164, 347-358.
[303]Zhang, Y., and Li, X. (2005). A putative nucleoporin 96 Is required for both basal defense and constitutive resistance responses mediated by suppressor of npr 1-1,constitutive 1. The Plant Cell 17,1306-1316.
[304]Zhao, Q., and Meier, I. (2011). Identification and characterization of the Arabidopsis FG-repeat nucleoporin Nup62. Plant Signaling & Behavior 6,330-334.
[305]Zuo, Z., Liu, H., Liu, B., Liu, X., and Lin, C. (2011). Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in Arabidopsis. Current Biology 21,841-847.
[2]Adrian, J., Farrona, S., Reimer, J.J., Albani, M.C., Coupland, G., and Turck, F. (2010). cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. The Plant Cell 22,1425-1440.
[3]Alabadi, D., Oyama, T., Yanovsky, M.J., Harmon, F.G., Mas, P., and Kay, S.A. (2001). Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293,880-883.
[4]Alber, F., Dokudovskaya, S., Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B.T., Sali, A., and Rout, M.P. (2007). The molecular architecture of the nuclear pore complex. Nature 450,695-701.
[5]Allen, J.L., and Douglas, M.G (1989). Organization of the nuclear pore complex in Saccharomyces cerevisiae. Journal of Ultrastructure and Molecular Structure Research 102, 95-108.
[6]An, H., Roussot, C., Suarez-Lopez, P., Corbesier, L., Vincent, C., Pineiro, M., Hepworth, S., Mouradov, A., Justin, S., Turnbull, C., and Coupland, G. (2004). CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development 131,3615-3626.
[7]Andres, F., and Coupland, G. (2012). The genetic basis of flowering responses to seasonal cues. Nature reviews. Genetics 13,627-639.
[8]Anwer, M.U., and Davis, S.J. (2013). An overview of natural variation studies in the Arabidopsis thaliana circadian clock. Seminars in Cell & Developmental Biology 24, 422-429.
[9]Askjaer, P., Galy, V., Hannak, E., and Mattaj, I.W. (2002). Ran GTPase cycle and importins alpha and beta are essential for spindle formation and nuclear envelope assembly in living Caenorhabditis elegans embryos. Molecular Biology of the Cell 13,4355-4370.
[10]Ausin, I., Alonso-Blanco, C., Jarillo, J.A., Ruiz-Garcia, L., and Martinez-Zapater, J.M. (2004). Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nature Genetics 36,162-166.
[11]Balasubramanian, S., Sureshkumar, S., Lempe, J., and Weigel, D. (2006). Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genetics 2, e106.
[12]Baudry, A., Ito, S., Song, Y.H., Strait, A.A., Kiba, T., Lu, S., Henriques, R., Pruneda-Paz, J.L., Chua, N.H., Tobin, E.M., Kay, S.A., and Imaizumi, T. (2010). F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. The Plant Cell 22,606-622.
[13]Baurle, I., and Dean, C. (2008). Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets. PloS One 3, e2733.
[14]Bell-Pedersen, D., Cassone, V.M., Earnest, D.J., Golden, S.S., Hardin, P.E., Thomas, T.L., and Zoran, M.J. (2005). Circadian rhythms from multiple oscillators:lessons from diverse organisms. Nature Reviews, Genetics 6,544-556.
[15]Bilokapic, S., and Schwartz, T.U. (2012). Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex. Proceedings of the National Academy of Sciences of the United States of America 109,15241-15246.
[16]Blazquez, M.A., Ahn, J.H., and Weigel, D. (2003). A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nature Genetics 33,168-171.
[17]Blazquez, M.A., Green, R., Nilsson, O., Sussman, M.R., and Weigel, D. (1998). Gibberellins promote flowering of arabidopsis by activating the LEAFY promoter. The Plant Cell 10,791-800.
[18]Bodoor, K., Shaikh, S., Salina, D., Raharjo, W.H., Bastos, R., Lohka, M., and Burke, B. (1999). Sequential recruitment of NPC proteins to the nuclear periphery at the end of mitosis. Journal of Cell Science 112,2253-2264.
[19]Boikoglou, E., Ma, Z., von Korff, M., Davis, A.M., Nagy, F., and Davis, S.J. (2011). Environmental memory from a circadian oscillator:the Arabidopsis thaliana clock differentially integrates perception of photic vs. thermal entrainment. Genetics 189,655-664.
[20]Boruc, J., Zhou, X., and Meier, I. (2012). Dynamics of the plant nuclear envelope and nuclear pore. Plant Physiology 158,78-86.
[21]Braud, C., Zheng, W., and Xiao, W. (2012). LONO1 encoding a nucleoporin is required for embryogenesis and seed viability in Arabidopsis. Plant Physiology 160,823-836.
[22]Bustamante, J.O., Michelette, E.R., Geibel, J.P., Dean, D.A., Hanover, J.A., and McDonnell, T.J. (2000). Calcium, ATP and nuclear pore channel gating. Pflugers Archiv 439, 433-444.
[23]Cardon, G., Hohmann, S., Klein, J., Nettesheim, K., Saedler, H., and Huijser, P. (1999). Molecular characterisation of the Arabidopsis SBP-box genes. Gene 237,91-104.
[24]Castillejo, C., and Pelaz, S. (2008). The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering. Current Biology 18,1338-1343.
[25]Cavalier-Smith, T. (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematic and Evolutionary Microbiology 52,297-354.
[26]Cheng, Y.T., Germain, H., Wiermer, M., Bi, D., Xu, F., Garcia, A.V., Wirthmueller, L., Despres, C., Parker, J.E., Zhang, Y., and Li, X. (2009). Nuclear pore complex component MOS7/Nup88 is required for innate immunity and nuclear accumulation of defense regulators in Arabidopsis. The Plant Cell 21,2503-2516.
[27]Cho, H.J., Kim, J.J., Lee, J.H., Kim, W., Jung, J.H., Park, C.M., and Ahn, J.H. (2012). SHORT VEGETATIVE PHASE (SVP) protein negatively regulates miR172 transcription via direct binding to the pri-miR172a promoter in Arabidopsis. FEBS Letters 586,2332-2337.
[28]Chow, B.Y., Heifer, A., Nusinow, D.A., and Kay, S.A. (2012). ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock. Plant Signaling & Behavior 7,170-173.
[29]Clarke, P.R., and Zhang, C. (2004). Spatial and temporal control of nuclear envelope assembly by Ran GTPase. Symposia of the Society for Experimental Biology,193-204.
[30]Colot, H.V., Loros, J.J., and Dunlap, J.C. (2005). Temperature-modulated alternative splicing and promoter use in the Circadian clock gene frequency. Molecular Biology of the Cell 16,5563-5571.
[31]Corbesier, L., Lejeune, P., and Bernier, G (1998). The role of carbohydrates in the induction of flowering in Arabidopsis thaliana:comparison between the wild type and a starchless mutant. Planta 206,131-137.
[32]Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., Giakountis, A., Farrona, S., Gissot, L., Turnbull, C., and Coupland, G. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316, 1030-1033.
[33]Cronshaw, J.M., Krutchinsky, A.N., Zhang, W., Chait, B.T., and Matunis, M.J. (2002). Proteomic analysis of the mammalian nuclear pore complex. The Journal of Cell Biology 158, 915-927.
[34]D'Angelo, M.A., and Hetzer, M.W. (2008). Structure, dynamics and function of nuclear pore complexes. Trends Cell Biol 18,456-466.
[35]Dai, S., Wei, X., Pei, L., Thompson, R.L., Liu, Y., Heard, J.E., Ruff, T.G, and Beachy, R.N. (2011). BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock. The Plant Cell 23,961-972.
[36]Daigle, N., Beaudouin, J., Hartnell, L., Imreh, G., Hallberg, E., Lippincott-Schwartz, J., and Ellenberg, J. (2001). Nuclear pore complexes form immobile networks and have a very low turnover in live mammalian cells. The Journal of Cell Biology 154,71-84.
[37]Daniel, X., Sugano, S., and Tobin, E.M. (2004). CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 101,3292-3297.
[38]Danker, T., and Oberleithner, H. (2000). Nuclear pore function viewed with atomic force microscopy. Pflugers Archiv 439,671-681.
[39]Darrah, C., Taylor, B.L., Edwards, K.D., Brown, P.E., Hall, A., and McWatters, H.G (2006). Analysis of phase of LUCIFERASE expression reveals novel circadian quantitative trait loci in Arabidopsis. Plant Physiology 140,1464-1474.
[40]David, K.M., Armbruster, U., Tama, N., and Putterill, J. (2006). Arabidopsis GIGANTEA protein is post-transcriptionally regulated by light and dark. FEBS Letters 580,1193-1197.
[41]Davis, S.J., and Millar, A.J. (2001). Watching the hands of the Arabidopsis biological clock. Genome Biology 2, Reviews 1008.1-Reviews1008.3.
[42]de Lucas, M., Daviere, J.M., Rodriguez-Falcon, M., Pontin, M., Iglesias-Pedraz, J.M., Lorrain, S., Fankhauser, C., Blazquez, M.A., Titarenko, E., and Prat, S. (2008). A molecular framework for light and gibberellin control of cell elongation. Nature 451,480-484.
[43]De Lucia, F., Crevillen, P., Jones, A.M., Greb, T., and Dean, C. (2008). A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proceedings of the National Academy of Sciences of the United States of America 105, 16831-16836.
[44]Deal, R.B., Kandasamy, M.K., McKinney, E.C., and Meagher, R.B. (2005). The nuclear actin-related protein ARP6 is a pleiotropic developmental regulator required for the maintenance of FLOWERING LOCUS C expression and repression of flowering in Arabidopsis. The Plant Cell 17,2633-2646.
[45]Deng, X., Gu, L., Liu, C., Lu, T., Lu, F., Lu, Z., Cui, P., Pei, Y., Wang, B., Hu, S., and Cao, X. (2010). Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America 107,19114-19119.
[46]Devlin, P.F., and Kay, S.A. (2000). Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. The Plant Cell 12,2499-2510.
[47]Diernfellner, A., Colot, H.V., Dintsis, O., Loros, J.J., Dunlap, J.C., and Brunner, M. (2007). Long and short isoforms of Neurospora clock protein FRQ support temperature-compensated circadian rhythms. FEBS Letters 581,5759-5764.
[48]Dill, A., Jung, H.S., and Sun, T.P. (2001). The DELLA motif is essential for gibberellin-induced degradation of RGA. Proceedings of the National Academy of Sciences of the United States of America 98,14162-14167.
[49]Ding, Z., Doyle, M.R., Amasino, R.M., and Davis, S.J. (2007). A complex genetic interaction between Arabidopsis thaliana TOC1 and CCA1/LHY in driving the circadian clock and in output regulation. Genetics 176,1501-1510.
[50]Dixon, L.E., Knox, K., Kozma-Bognar, L., Southern, M.M., Pokhilko, A., and Millar, A.J. (2011). Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis. Current Biology 21,120-125.
[51]Dong, C.H., Agarwal, M., Zhang, Y., Xie, Q., and Zhu, J.K. (2006a). The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proceedings of the National Academy of Sciences of the United States of America 103,8281-8286.
[52]Dong, C.H., Hu, X., Tang, W., Zheng, X., Kim, Y.S., Lee, B.H., and Zhu, J.K. (2006b). A putative Arabidopsis nucleoporin, AtNUP160, is critical for RNA export and required for plant tolerance to cold stress. Molecular and Cellular Biology 26,9533-9543.
[53]Doyle, M.R., Bizzell, CM., Keller, M.R., Michaels, S.D., Song, J., Noh, Y.S., and Amasino, R.M. (2005). HUA2 is required for the expression of floral repressors in Arabidopsis thaliana. The Plant Journal 41,376-385.
[54]Doyle, M.R., Davis, S.J., Bastow, R.M., McWatters, H.G., Kozma-Bognar, L., Nagy, F., Millar, A.J,, and Amasino, R.M. (2002). The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419,74-77.
[55]Enninga, J., Levay, A., and Fontoura, B.M. (2003). Sec13 shuttles between the nucleus and the cytoplasm and stably interacts with Nup96 at the nuclear pore complex. Molecular and Cellular Biology 23,7271-7284.
[56]Eriksson, S., Bohlenius, H., Moritz, T., and Nilsson, O. (2006). GA4 is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation. The Plant Cell 18,2172-2181.
[57]Fahrenkrog, B., and Aebi, U. (2003). The nuclear pore complex:nucleocytoplasmic transport and beyond. Nature reviews. Molecular Cell Biology 4,757-766.
[58]Fahrenkrog, B., Koser, J., and Aebi, U. (2004). The nuclear pore complex:a jack of all trades? Trends in Biochemical Sciences 29,175-182.
[59]Farinas, B., and Mas, P. (2011). Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. The Plant Journal 66,318-329.
[60]Farre, E.M., Harmer, S.L., Harmon, F.G., Yanovsky, M.J., and Kay, S.A. (2005). Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Current Biology 15,47-54.
[61]Ferrandez-Ayela, A., Alonso-Peral, M.M., Sanchez-Garcia, A.B., Micol-Ponce, R., Perez-Perez, J.M., Micol, J.L., and Ponce, M.R. (2013). Arabidopsis TRANSCURVATA1 encodes NUP58, a component of the nucleopore central channel. PloS One 8, e67661.
[62]Filichkin, S.A., Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E., Wong, W.K., and Mockler, T.C. (2010). Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Research 20,45-58.
[63]Fiserova, J., Kiseleva, E., and Goldberg, M.W. (2009). Nuclear envelope and nuclear pore complex structure and organization in tobacco BY-2 cells. The Plant Journal 59,243-255.
[64]Fontoura, B.M., Blobel, G, and Matunis, M.J. (1999). A conserved biogenesis pathway for nucleoporins:proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96. The Journal of Cell Biology 144,1097-1112.
[65]Fornara, F., de Montaigu, A., and Coupland, G (2010). SnapShot:Control of flowering in Arabidopsis. Cell 141,550,550.e1-550.e2.
[66]Fornara, F., Panigrahi, K.C., Gissot, L., Sauerbrunn, N., Ruhl, M., Jarillo, J.A., and Coupland, G (2009). Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Developmental Cell 17,75-86.
[67]Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A., and Paz-Ares, J. (2007). Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics 39,1033-1037.
[68]Fujiwara, S., Wang, L., Han, L., Suh, S.S., Salome, P.A., McClung, C.R., and Somers, D.E. (2008). Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins. The Journal of Biological Chemistry 283,23073-23083.
[69]Fukuda, H., Nakamichi, N., Hisatsune, M., Murase, H., and Mizuno, T. (2007). Synchronization of plant circadian oscillators with a phase delay effect of the vein network. Physical Review Letters 99,098102.
[70]Gendron, J.M., Pruneda-Paz, J.L., Doherty, C.J., Gross, A.M., Kang, S.E., and Kay, S.A. (2012). Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proceedings of the National Academy of Sciences of the United States of America 109, 3167-3172.
[71]Giebultowicz, J. (2004). Chronobiology:biological timekeeping. Integrative and Comparative Biology 44,266.
[72]Goldberg, M.W., and Allen, T.D. (1996). The nuclear pore complex and lamina: three-dimensional structures and interactions determined by field emission in-lens scanning electron microscopy. Journal of Molecular Biology 257,848-865.
[73]Goldberg, M.W., Wiese, C., Allen, T.D., and Wilson, K.L. (1997). Dimples, pores, star-rings, and thin rings on growing nuclear envelopes:evidence for structural intermediates in nuclear pore complex assembly. Journal of Cell Science 110 (Pt 4),409-420.
[74]Gong, Z., Dong, C.H., Lee, H., Zhu, J., Xiong, L., Gong, D., Stevenson, B., and Zhu, J.K. (2005). A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. The Plant Cell 17,256-267.
[75]Gould, P.D., Diaz, P., Hogben, C., Kusakina, J., Salem, R., Hartwell, J., and Hall, A. (2009). Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants. The Plant Journal 58,893-901.
[76]Green, R.M., Tingay, S., Wang, Z.Y., and Tobin, E.M. (2002). Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiology 129,576-584.
[77]Griffiths, J., Murase, K., Rieu, I., Zentella, R., Zhang, Z.L., Powers, S.J., Gong, F., Phillips, A.L., Hedden, P., Sun, T.P., and Thomas, S.G (2006). Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. The Plant Cell 18, 3399-3414.
[78]Grossman, E., Medalia, O., and Zwerger, M. (2012). Functional architecture of the nuclear pore complex. Annual Review of Biophysics 41,557-584.
[79]Groth, M., Takeda, N., Perry, J., Uchida, H., Draxl, S., Brachmann, A., Sato, S., Tabata, S., Kawaguchi, M., Wang, T.L., and Parniske, M. (2010). NENA, a Lotus japonicus homolog of See13, is required for rhizodermal infection by arbuscular mycorrhiza fungi and rhizobia but dispensable for cortical endosymbiotic development. The Plant Cell 22, 2509-2526.
[80]Guttinger, S., Laurell, E., and Kutay, U. (2009). Orchestrating nuclear envelope disassembly and reassembly during mitosis. Nature Reviews, Molecular Cell Biology 10, 178-191.
[81]Hall, A., Bastow, R.M., Davis, S.J., Hanano, S., McWatters, H.G., Hibberd, V., Doyle, M.R., Sung, S., Halliday, K.J., Amasino, R.M., and Millar, A.J. (2003). The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. The Plant Cell 15,2719-2729.
[82]Hanano, S., Domagalska, M.A., Nagy, F., and Davis, S.J. (2006). Multiple phytohormones influence distinct parameters of the plant circadian clock. Genes to cells 11,1381-1392.
[83]Harberd, N.P. (2003). Botany. Relieving DELLA restraint. Science 299,1853-1854.
[84]Harel, A., Chan, R.C., Lachish-Zalait, A., Zimmerman, E., Elbaum, M., and Forbes, D.J. (2003). Importin beta negatively regulates nuclear membrane fusion and nuclear pore complex assembly. Molecular Biology of the Cell 14,4387-4396.
[85]Harmer, S.L. (2009). The circadian system in higher plants. Annual Review of Plant Biology 60,357-377.
[86]Harmer, S.L., and Kay, S.A. (2005). Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis. The Plant Cell 17,1926-1940.
[87]Hazen, S.P., Schultz, T.F., Pruneda-Paz, J.L., Borevitz, J.O., Ecker, J.R., and Kay, S.A. (2005). LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America 102, 10387-10392.
[88]He, Y., Michaels, S.D., and Amasino, R.M. (2003). Regulation of flowering time by histone acetylation in Arabidopsis. Science 302,1751-1754.
[89]He, Y., Doyle, M.R., and Amasino, R.M. (2004). PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes & Development 18, 2774-2784.
[90]Heifer, A., Nusinow, D.A., Chow, B.Y., Gehrke, A.R., Bulyk, M.L., and Kay, S.A. (2011). LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Current Biology 21,126-133.
[91]Heo, J.B., and Sung, S. (2011). Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331,76-79.
[92]Herrero, E., and Davis, S.J. (2012). Time for a nuclear meeting:protein trafficking and chromatin dynamics intersect in the plant circadian system. Molecular Plant 5,554-565.
[93]Herrero, E., Kolmos, E., Bujdoso, N., Yuan, Y., Wang, M., Berns, M.C., Uhlworm, H., Coupland, G, Saini, R., Jaskolski, M., Webb, A., Goncalves, J., and Davis, S.J. (2012). EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. The Plant Cell 24,428-443.
[94]Hetzer, M.W., Walther, T.C., and Mattaj, I.W. (2005). Pushing the envelope:structure, function, and dynamics of the nuclear periphery. Annual Review of Cell and Developmental Biology 21,347-380.
[95]Hicks, K.A., Albertson, T.M., and Wagner, D.R. (2001). EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis. The Plant Cell 13,1281-1292.
[96]Hong, GJ., Xue, X.Y., Mao, Y.B., Wang, L.J., and Chen, X.Y. (2012). Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. The Plant Cell 24,2635-2648.
[97]Hong, S., Song, H.R., Lutz, K., Kerstetter, R.A., Michael, T.P., and McClung, C.R. (2010). Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107,21211-21216.
[98]Hornyik, C, Terzi, L.C., and Simpson, GG (2010). The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Developmental Cell 18,203-213.
[99]Hou, X., Lee, L.Y., Xia, K., Yan, Y., and Yu, H. (2010). DELLAs modulate jasmonate signaling via competitive binding to JAZs. Developmental Cell 19,884-894.
[100]Hsia, D.A., Tepper, C.G, Pochampalli, M.R., Hsia, E.Y., Izumiya, C., Huerta, S.B., Wright, M.E., Chen, H.W., Kung, H.J., and Izumiya, Y. (2010). KDM8, a H3K36me2 histone demethylase that acts in the cyclin Al coding region to regulate cancer cell proliferation. Proceedings of the National Academy of Sciences of the United States of America 107,9671-9676.
[101]Huang, W., Perez-Garcia, P., Pokhilko, A., Millar, A.J., Antoshechkin, I., Riechmann, J.L., and Mas, P. (2012). Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336,75-79.
[102]Huijser, P., and Schmid, M. (2011). The control of developmental phase transitions in plants. Development 138,4117-4129.
[103]Imaizumi, T. (2010). Arabidopsis circadian clock and photoperiodism:time to think about location. Current Opinion in Plant Biology 13,83-89.
[104]Imaizumi, T., Tran, H.G, Swartz, T.E., Briggs, W.R., and Kay, S.A. (2003). FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426,302-306.
[105]Imaizumi, T., Schultz, T.F., Harmon, F.G., Ho, L.A., and Kay, S.A. (2005). FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309, 293-297.
[106]Imlau, A., Truernit, E., and Sauer, N. (1999). Cell-to-cell and long-distance trafficking of the green fluorescent protein in the phloem and symplastic unloading of the protein into sink tissues. The Plant Cell 11,309-322.
[107]Inigo, S., Alvarez, M.J., Strasser, B., Califano, A., and Cerdan, P.D. (2012). PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis. The Plant Journal 69,601-612.
[108]Ishitani, M., Xiong, L., Lee, H., Stevenson, B., and Zhu, J.K. (1998). HOS1, a genetic locus involved in cold-responsive gene expression in arabidopsis. The Plant Cell 10, 1151-1161.
[109]Ito, S., Song, Y.H., Josephson-Day, A.R., Miller, R.J., Breton, G., Olmstead, R.G, and Imaizumi, T. (2012). FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 109,3582-3587.
[110]Jacob, Y., Mongkolsiriwatana, C., Veley, K.M., Kim, S.Y., and Michaels, S.D. (2007). The nuclear pore protein AtTPR is required for RNA homeostasis, flowering time, and auxin signaling. Plant Physiology 144,1383-1390.
[111]James, A.B., Syed, N.H., Bordage, S., Marshall, J., Nimmo, G.A., Jenkins, G.I., Herzyk, P., Brown, J.W., and Nimmo, H.G. (2012). Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. The Plant Cell 24,961-981.
[112]Jang, S., Marchal, V., Panigrahi, K.C., Wenkel, S., Soppe, W., Deng, X.W., Valverde, F., and Coupland, G. (2008). Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. The EMBO Journal 27, 1277-1288.
[113]Jeong, S.Y., Rose, A., Joseph, J., Dasso, M., and Meier, I. (2005). Plant-specific mitotic targeting of RanGAP requires a functional WPP domain. The Plant Journal 42,270-282.
[114]Jiang, D., Gu, X., and He, Y. (2009). Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. The Plant Cell 21,1733-1746.
[115]Johanson, U., West, J., Lister, C., Michaels, S., Amasino, R., and Dean, C. (2000). Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290,344-347.
[116]Jones, M.A., and Harmer, S. (2011). JMJD5 Functions in concert with TOC1 in the arabidopsis circadian system. Plant Signaling & Behavior 6,445-448.
[117]Jones, M.A., Covington, M.F., DiTacchio, L., Vollmers, C., Panda, S., and Harmer, S.L. (2010). Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proceedings of the National Academy of Sciences of the United States of America 107,21623-21628.
[118]Jung, J.H., Seo, P.J., Ahn, J.H., and Park, C.M. (2012a). Arabidopsis RNA-binding protein FCA regulates microRNA172 processing in thermosensory flowering. The Journal of Biological Chemistry 287,16007-16016.
[119]Jung, J.H., Ju, Y., Seo, P.J., Lee, J.H., and Park, C.M. (2012b). The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis. The Plant Journal 69,577-588.
[120]Jung, J.H., Seo, Y.H., Seo, P.J., Reyes, J.L., Yun, J., Chua, N.H., and Park, C.M. (2007). The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. The Plant Cell 19,2736-2748.
[121]Jung, J.H., Park, J.H., Lee, S., To, T.K., Kim, J.M., Seki, M., and Park, C.M. (2013). The Cold Signaling Attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 Activates FLOWERING LOCUS C Transcription via Chromatin Remodeling under Short-Term Cold Stress in Arabidopsis. The Plant Cell 25,4378-4390.
[122]Kanamori, N., Madsen, L.H., Radutoiu, S., Frantescu, M., Quistgaard, E.M., Miwa, H., Downie, J.A., James, E.K., Felle, H.H., Haaning, L.L., Jensen, T.H., Sato, S., Nakamura, Y., Tabata, S., Sandal, N., and Stougaard, J. (2006). A nucleoporin is required for induction of Ca2+spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proceedings of the National Academy of Sciences of the United States of America 103,359-364.
[123]Kiba, T., Henriques, R., Sakakibara, H., and Chua, N.H. (2007). Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. The Plant Cell 19,2516-2530.
[124]Kikis, E.A., Khanna, R., and Quail, P.H. (2005). ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY. The Plant Journal 44,300-313.
[125]Kim, D.H., Doyle, M.R., Sung, S., and Amasino, R.M. (2009). Vernalization:winter and the timing of flowering in plants. Annual Review of Cell and Developmental Biology 25, 277-299.
[126]Kim, H.J., Hyun, Y., Park, J.Y., Park, M.J., Park, M.K., Kim, M.D., Lee, M.H., Moon, J., Lee, I., and Kim, J. (2004). A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nature Genetics 36,167-171.
[127]Kim, J., Kim, Y., Yeom, M., Kim, J.H., and Nam, H.G (2008). FIONA1 is essential for regulating period length in the Arabidopsis circadian clock. The Plant Cell 20,307-319.
[128]Kim, J.J., Lee, J.H., Kim, W., Jung, H.S., Huijser, P., and Ann, J.H. (2012). The microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Plant Physiology 159,461-478.
[129]Kim, S., Choi, K., Park, C., Hwang, H.J., and Lee, I. (2006). SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C. The Plant Cell 18,2985-2998.
[130]Kim, W.Y., Fujiwara, S., Sun, S.S., Kim, J., Kim, Y., Han, L., David, K., Putterill, J., Nam, H.G, and Somers, D.E. (2007). ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. Nature 449,356-360.
[131]Kiseleva, E., Rutherford, S., Cotter, L.M., Allen, T.D., and Goldberg, M.W. (2001). Steps of nuclear pore complex disassembly and reassembly during mitosis in early Drosophila embryos. Journal of Cell Science 114,3607-3618.
[132]Kobayashi, Y., and Weigel, D. (2007). Move on up, it's time for change--mobile signals controlling photoperiod-dependent flowering. Genes & Development 21,2371-2384.
[133]Koonin, E.V., and Aravind, L. (2009). Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 8,1984-1985.
[134]Kumar, S.V., Lucyshyn, D., Jaeger, K.E., Alos, E., Alvey, E., Harberd, N.P., and Wigge, P.A. (2012). Transcription factor PIF4 controls the thermosensory activation of flowering. Nature 484,242-245.
[135]Lau, O.S., Huang, X., Charron, J.B., Lee, J.H., Li, G., and Deng, X.W. (2011). Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Molecular Cell 43,703-712.
[136]Laubinger, S., Marchal, V., Le Gourrierec, J., Wenkel, S., Adrian, J., Jang, S., Kulajta, C., Braun, H., Coupland, G., and Hoecker, U. (2006). Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability. Development 133,3213-3222.
[137]Lazaro, A., Valverde, F., Pineiro, M., and Jarillo, J.A. (2012). The Arabidopsis E3 ubiquitin ligase HOS1 negatively regulates CONSTANS abundance in the photoperiodic control of flowering. The Plant Cell 24,982-999.
[138]Lee, H., Yoo, S.J., Lee, J.H., Kim, W., Yoo, S.K., Fitzgerald, H., Carrington, J.C., and Ahn, J.H. (2010). Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis. Nucleic Acids Research 38,3081-3093.
[139]Lee, I., Aukerman, M.J., Gore, S.L., Lohman, K.N., Michaels, S.D., Weaver, L.M., John, M.C., Feldmann, K.A., and Amasino, R.M. (1994). Isolation of LUMINIDEPENDENS:a gene involved in the control of flowering time in Arabidopsis. The Plant Cell 6,75-83.
[140]Lee, J.H., Yoo, S.J., Park, S.H., Hwang, I., Lee, J.S., and Ahn, J.H. (2007). Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes & Development 21,397-402.
[141]Lee, J.H., Kim, J.J., Kim, S.H., Cho, H.J., Kim, J., and Ahn, J.H. (2012). The E3 ubiquitin ligase HOS1 regulates low ambient temperature-responsive flowering in Arabidopsis thaliana. Plant & Cell Physiology 53,1802-1814.
[142]Lenhard, M., and Laux, T. (2003). Stem cell homeostasis in the Arabidopsis shoot meristem is regulated by intercellular movement of CLAVATA3 and its sequestration by CLAVATA1. Development 130,3163-3173.
[143]Levy, Y.Y., Mesnage, S., Mylne, J.S., Gendall, A.R., and Dean, C. (2002). Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297,243-246.
[144]Lian, H.L., He, S.B., Zhang, Y.C., Zhu, D.M., Zhang, J.Y., Jia, K.P., Sun, S.X., Li, L., and Yang, H.Q. (2011). Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism. Genes & Development 25,1023-1028.
[145]Lin, J.M., Kilman, V.L., Keegan, K., Paddock, B., Emery-Le, M., Rosbash, M., and Allada, R. (2002). A role for casein kinase 2alpha in the Drosophila circadian clock. Nature 420,816-820.
[146]Lincoln, C., Long, J., Yamaguchi, J., Serikawa, K., and Hake, S. (1994). Aknottedl-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. The Plant Cell 6,1859-1876.
[147]Liu, B., Zuo, Z., Liu, H., Liu, X., and Lin, C. (2011). Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light. Genes & Development 25, 1029-1034.
[148]Liu, F., Marquardt, S., Lister, C., Swiezewski, S., and Dean, C. (2010). Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327, 94-97.
[149]Liu, F., Quesada, V., Crevillen, P., Baurle, I., Swiezewski, S., and Dean, C. (2007). The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Molecular Cell 28,398-407.
[150]Liu, H., Yu, X., Li, K., Klejnot, J., Yang, H., Lisiero, D., and Lin, C. (2008a). Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322,1535-1539.
[151]Liu, L.J., Zhang, Y.C., Li, Q.H., Sang, Y., Mao, J., Lian, H.L., Wang, L., and Yang, H.Q. (2008b). COP 1-mediated ubiquitination of CONSTANS is implicated in cryptochrome regulation of flowering in Arabidopsis. The Plant Cell 20,292-306.
[152]Locke, J.C., Millar, A.J., and Turner, M.S. (2005). Modelling genetic networks with noisy and varied experimental data:the circadian clock in Arabidopsis thaliana. Journal of Theoretical Biology 234,383-393.
[153]Lu, Q., Tang, X., Tian, G., Wang, F., Liu, K., Nguyen, V., Kohalmi, S.E., Keller, W.A., Tsang, E.W., Harada, J.J., Rothstein, S.J., and Cui, Y. (2010). Arabidopsis homolog of the yeast TREX-2 mRNA export complex:components and anchoring nucleoporin. The Plant Journal 61,259-270.
[154]Lu, S.X., Knowles, S.M., Andronis, C., Ong, M.S., and Tobin, E.M. (2009). CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiology 150,834-843.
[155]Lu, S.X., Knowles, S.M., Webb, C.J., Celaya, R.B., Cha, C., Siu, J.P., and Tobin, E.M. (2011a). The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Plant Physiology 155,906-915.
[156]Lu, S.X., Liu, H., Knowles, S.M., Li, J., Ma, L., Tobin, E.M., and Lin, C. (2011b). A role for protein kinase casein kinase2 alpha-subunits in the Arabidopsis circadian clock. Plant Physiology 157,1537-1545.
[157]MacGregor, D.R., Gould, P., Foreman, J., Griffiths, J., Bird, S., Page, R., Stewart, K., Steel, G, Young, J., Paszkiewicz, K., Millar, A.J., Halliday, K.J., Hall, A.J., and Penfield, S. (2013). HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 is required for circadian periodicity through the promotion of nucleo-cytoplasmic mRNA export in Arabidopsis. The Plant Cell 25,4391-4404.
[158]Mahajan, R., Gerace, L., and Melchior, F. (1998). Molecular characterization of the SUMO-1 modification of RanGAPl and its role in nuclear envelope association. The Journal of Cell Biology 140,259-270.
[159]Mans, B.J., Anantharaman, V., Aravind, L., and Koonin, E.V. (2004). Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle 3,1612-1637.
[160]Martin-Trillo, M., Lazaro, A., Poethig, R.S., Gomez-Mena, C., Pineiro, M.A., Martinez-Zapater, J.M., and Jarillo, J.A. (2006). EARLY IN SHORT DAYS 1 (ESDI) encodes ACTIN-RELATED PROTEIN 6 (AtARP6), a putative component of chromatin remodelling complexes that positively regulates FLC accumulation in Arabidopsis. Development 133,1241-1252.
[161]Mas, P. (2008). Circadian clock function in Arabidopsis thaliana:time beyond transcription. Trends in Cell Biology 18,273-281.
[162]Mas, P., Kim, W.Y., Somers, D.E., and Kay, S.A. (2003). Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426,567-570.
[163]Mathieu, J., Yant, L.J., Murdter, F., Kuttner, F., and Schmid, M. (2009). Repression of flowering by the miR172 target SMZ. PLoS Biology 7, e1000148.
[164]Matunis, M.J., Coutavas, E., and Blobel, G (1996). A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAPl between the cytosol and the nuclear pore complex. The Journal of Cell Biology 135,1457-1470.
[165]McClung, C.R. (2006). Plant circadian rhythms. The Plant Cell 18,792-803.
[166]McKim, S., and Hay, A. (2010). Patterning and evolution of floral structures-marking time. Current Opinion in Genetics & Development 20,448-453.
[167]Mehra, A., Shi, M., Baker, C.L., Colot, H.V., Loros, J.J., and Dunlap, J.C. (2009). A role for casein kinase 2 in the mechanism underlying circadian temperature compensation. Cell 137,749-760.
[168]Michael, T.P., and McClung, C.R. (2002). Phase-specific circadian clock regulatory elements in Arabidopsis. Plant Physiology 130,627-638.
[169]Michael, T.P., Salome, P.A., and McClung, C.R. (2003). Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proceedings of the National Academy of Sciences of the United States of America 100,6878-6883.
[170]Michaels, S.D., and Amasino, R.M. (1999). FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. The Plant Cell 11,949-956.
[171]Michaels, S.D., and Amasino, R.M. (2001). Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. The Plant Cell 13,935-941.
[172]Michaels, S.D., Bezerra, I.C., and Amasino, R.M. (2004). FRIGIDA-related genes are required for the winter-annual habit in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 101,3281-3285.
[173]Millar, A.J., Carre, I.A., Strayer, C.A., Chua, N.H., and Kay, S.A. (1995). Circadian clock mutants in Arabidopsis identified by luciferase imaging. Science 267,1161-1163.
[174]Mizoguchi, T., Putterill, J., and Ohkoshi, Y. (2006). Kinase and phosphatase:the cog and spring of the circadian clock. International Review of Cytology 250,47-72.
[175]Mizoguchi, T., Wheatley, K., Hanzawa, Y., Wright, L., Mizoguchi, M., Song, H.R., Carre, I.A., and Coupland, G. (2002). LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Developmental Cell 2,629-641.
[176]Mizoguchi, T., Wright, L., Fujiwara, S., Cremer, F., Lee, K., Onouchi, H., Mouradov, A., Fowler, S., Kamada, H., Putterill, J., and Coupland, G. (2005). Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis. The Plant Cell 17,2255-2270.
[177]Moon, J., Suh, S.S., Lee, H., Choi, K.R., Hong, C.B., Paek, N.C., Kim, S.G, and Lee, I. (2003). The SOC1 MADS-box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis. The Plant Journal 35,613-623.
[178]Morris, K., Thornber, S., Codrai, L., Richardson, C., Craig, A., Sadanandom, A., Thomas, B., and Jackson, S. (2010). DAY NEUTRAL FLOWERING represses CONSTANS to prevent Arabidopsis flowering early in short days. The Plant Cell 22,1118-1128.
[179]Murase, K., Hirano, Y., Sun, T.P., and Hakoshima, T. (2008). Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 456,459-463.
[180]Murtas, G., Reeves, P.H., Fu, Y.F., Bancroft, I., Dean, C., and Coupland, G. (2003). A nuclear protease required for flowering-time regulation in Arabidopsis reduces the abundance of SMALL UBIQUITIN-RELATED MODIFIER conjugates. The Plant Cell 15,2308-2319.
[181]Mutasa-Gottgens, E., and Hedden, P. (2009). Gibberellin as a factor in floral regulatory networks. Journal of Experimental Botany 60,1979-1989.
[182]Muthuswamy, S., and Meier, I. (2011). Genetic and environmental changes in SUMO homeostasis lead to nuclear mRN A retention in plants. Planta 233,201-208.
[183]Mylne, J.S., Barrett, L., Tessadori, F., Mesnage, S., Johnson, L., Bernatavichute, Y.V., Jacobsen, S.E., Fransz, P., and Dean, C. (2006). LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN 1, is required for epigenetic silencing of FLC. Proceedings of the National Academy of Sciences of the United States of America 103,5012-5017.
[184]Nagel, D.H., and Kay, S.A. (2012). Complexity in the wiring and regulation of plant circadian networks. Current Biology 22, R648-657.
[185]Nakamichi, N. (2011). Molecular mechanisms underlying the Arabidopsis circadian clock. Plant & Cell Physiology 52,1709-1718.
[186]Ni, Z., Kim, E.D., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z.J. (2009). Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457, 327-331.
[187]Nilsen, T.W., and Graveley, B.R. (2010). Expansion of the eukaryotic proteome by alternative splicing. Nature 463,457-463.
[188]Noh, Y.S., and Amasino, R.M. (2003). PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. The Plant Cell 15,1671-1682.
[189]Noh, Y.S., Bizzell, C.M., Noh, B., Schomburg, F.M., and Amasino, R.M. (2004). EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. The Plant Journal 38,664-672.
[190]Nusinow, D.A., Helfer, A., Hamilton, E.E., King, J.J., Imaizumi, T., Schultz, T.F., Farre, E.M., and Kay, S.A. (2011). The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475,398-402.
[191]Oh, S., Zhang, H., Ludwig, P., and van Nocker, S. (2004). A mechanism related to the yeast transcriptional regulator Paflc is required for expression of the Arabidopsis FLC/MAF MADS box gene family. The Plant Cell 16,2940-2953.
[192]Onai, K., and Ishiura, M. (2005). PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes to Cells 10,963-972.
[193]Panda, S., Poirier, G.G, and Kay, S.A. (2002). tej defines a role for poly(ADP-ribosyl)ation in establishing period length of the arabidopsis circadian oscillator. Developmental Cell 3, 51-61.
[194]Pante, N., and Kann, M. (2002). Nuclear pore complex is able to transport macromolecules with diameters of about 39 nm. Molecular Biology of the Cell 13,425-434.
[195]Para, A., Farre, E.M., Imaizumi, T., Pruneda-Paz, J.L., Harmon, F.G, and Kay, S.A. (2007). PRR3 Is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. The Plant Cell 19,3462-3473.
[196]Park, B.S., Eo, H.J., Jang, I.C., Kang, H.G., Song, J.T., and Seo, H.S. (2010). Ubiquitination of LHY by SINAT5 regulates flowering time and is inhibited by DET1. Biochemical and Biophysical Research Communications 398,242-246.
[197]Park, D.H., Somers, D.E., Kim, Y.S., Choy, Y.H., Lim, H.K., Soh, M.S., Kim, H.J., Kay, S.A., and Nam, H.G. (1999). Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285,1579-1582.
[198]Parry, G., Ward, S., Cernac, A., Dharmasiri, S., and Estelle, M. (2006). The Arabidopsis SUPPRESSOR OF AUXIN RESISTANCE proteins are nucleoporins with an important role in hormone signaling and development. The Plant Cell 18,1590-1603.
[199]Peng, J., Carol, P., Richards, D.E., King, K.E., Cowling, R.J., Murphy, G.P., and Harberd, N.P. (1997). The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes & Development 11,3194-3205.
[200]Perales, M., and Mas, P. (2007). A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. The Plant Cell 19,2111-2123.
[201]Pien, S., Fleury, D., Mylne, J.S., Crevillen, P., Inze, D., Avramova, Z., Dean, C., and Grossniklaus, U. (2008). ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. The Plant Cell 20, 580-588.
[202]Pokhilko, A., Fernandez, A.P., Edwards, K.D., Southern, M.M., Halliday, K.J., and Millar, A.J. (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Molecular Systems Biology 8,574.
[203]Pokhilko, A., Hodge, S.K., Stratford, K., Knox, K., Edwards, K.D., Thomson, A.W., Mizuno, T., and Millar, A.J. (2010). Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Molecular Systems Biology 6, 416.
[204]Portoles, S., and Mas, P. (2010). The functional interplay between protein kinase CK2 and CCA1 transcriptional activity is essential for clock temperature compensation in Arabidopsis. PLoS Genetics 6, e1001201.
[205]Pruneda-Paz, J.L., and Kay, S.A. (2010). An expanding universe of circadian networks in higher plants. Trends in Plant Science 15,259-265.
[206]Pruneda-Paz, J.L., Breton, G., Para, A., and Kay, S.A. (2009). A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323, 1481-1485.
[207]Quesada, V., Macknight, R., Dean, C., and Simpson, G.G. (2003). Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. The EMBO Journal 22, 3142-3152.
[208]Rabut, G, Doye, V., and Ellenberg, J. (2004). Mapping the dynamic organization of the nuclear pore complex inside single living cells. Nature Cell Biology 6,1114-1121.
[209]Rawat, R., Takahashi, N., Hsu, P.Y., Jones, M.A., Schwartz, J., Salemi, M.R., Phinney, B.S., and Harmer, S.L. (2011). REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genetics 7, e1001350.
[210]Reeves, P.H., Murtas, G, Dash, S., and Coupland, G (2002). early in short days 4, a mutation in Arabidopsis that causes early flowering and reduces the mRNA abundance of the floral repressor FLC. Development 129,5349-5361.
[211]Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110,513-520.
[212]Richter, R., Behringer, C., Muller, I.K., and Schwechheimer, C. (2010). The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. Genes & Development 24,2093-2104.
[213]Ripoll, J.J., Rodriguez-Cazorla, E., Gonzalez-Reig, S., Andujar, A., Alonso-Cantabrana, H., Perez-Amador, M.A., Carbonell, J., Martinez-Laborda, A., and Vera, A. (2009). Antagonistic interactions between Arabidopsis K-homology domain genes uncover PEPPER as a positive regulator of the central floral repressor FLOWERING LOCUS C. Developmental Biology 333,251-262.
[214]Roberts, K., and Northcote, D.H. (1970). Structure of the nuclear pore in higher plants. Nature 228,385-386.
[215]Robles, L.M., Deslauriers, S.D., Alvarez, A.A., and Larsen, P.B. (2012). A loss-of-function mutation in the nucleoporin AtNUP160 indicates that normal auxin signalling is required for a proper ethylene response in Arabidopsis. Journal of Experimental Botany 63,2231-2241.
[216]Robson, F., Costa, M.M., Hepworth, S.R., Vizir, I., Pineiro, M., Reeves, P.H., Putterill, J., and Coupland, G. (2001). Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. The Plant Journal 28,619-631.
[217]Roenneberg, T., and Morse, D. (1993). Two circadian oscillators in one cell. Nature 362,3.
[218]Rose, A., and Meier, I. (2001). A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim. Proceedings of the National Academy of Sciences of the United States of America 98,15377-15382.
[219]Roth, C., and Wiermer, M. (2012). Nucleoporins Nup160 and Sehl are required for disease resistance in Arabidopsis. Plant Signaling & Behavior 7,1212-1214.
[220]Rout, M.P., Aitchison, J.D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B.T. (2000). The yeast nuclear pore complex:composition, architecture, and transport mechanism. The Journal of Cell Biology 148,635-651.
[221]Ryan, K.J., and Wente, S.R. (2000). The nuclear pore complex:a protein machine bridging the nucleus and cytoplasm. Current Opinion in Cell Biology 12,361-371.
[222]Ryan, K.J., McCaffery, J.M., and Wente, S.R. (2003). The Ran GTPase cycle is required for yeast nuclear pore complex assembly. The Journal of Cell Biology 160,1041-1053.
[223]Sai, J., and Johnson, C.H. (1999). Different circadian oscillators control Ca(2+) fluxes and lhcb gene expression. Proceedings of the National Academy of Sciences of the United States of America 96,11659-11663.
[224]Saito, K., Yoshikawa, M., Yano, K., Miwa, H., Uchida, H., Asamizu, E., Sato, S., Tabata, S., Imaizumi-Anraku, H., Umehara, Y., Kouchi, H., Murooka, Y., Szczyglowski, K., Downie, J.A., Parniske, M., Hayashi, M., and Kawaguchi, M. (2007). NUCLEOPORTN85 is required for calcium spiking, fungal and bacterial symbioses, and seed production in Lotus japonicus. The Plant Cell 19,610-624.
[225]Salome, P.A., Weigel, D., and McClung, C.R. (2010). The role of the Arabidopsis morning loop components CCA1, LHY, PRR7, and PRR9 in temperature compensation. The Plant Cell 22,3650-3661.
[226]Sanchez, S.E., Petrillo, E., Beckwith, E.J., Zhang, X., Rugnone, M.L., Hernando, C.E., Cuevas, J.C., Godoy Herz, M.A., Depetris-Chauvin, A., Simpson, C.G., Brown, J.W., Cerdan, P.D., Borevitz, J.O., Mas, P., Ceriani, M.F., Kornblihtt, A.R., and Yanovsky, M.J. (2010). A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature 468,112-116.
[227]Sawa, M., Nusinow, D.A., Kay, S.A., and Imaizumi, T. (2007). FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science 318, 261-265.
[228]Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carre, I.A., and Coupland, G (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93,1219-1229.
[229]Schmid, M., Uhlenhaut, N.H., Godard, F., Demar, M., Bressan, R., Weigel, D., and Lohmann, J.U. (2003). Dissection of floral induction pathways using global expression analysis. Development 130,6001-6012.
[230]Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M., and Weigel, D. (2005). Specific effects of microRNAs on the plant transcriptome. Developmental Cell 8,517-527.
[231]Schwartz, T. (2013). Functional insights from studies on the structure of the nuclear pore and coat protein complexes. Cold Spring Harbor Perspectives in Biology 5, a013375.
[232]Schwechheimer, C., and Willige, B.C. (2009). Shedding light on gibberellic acid signalling. Current Opinion in Plant Biology 12,57-62.
[233]Searle, I., He, Y., Turck, F., Vincent, C., Fornara, F., Krober, S., Amasino, R.A., and Coupland, G. (2006). The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes & Development 20,898-912.
[234]Seo, P.J., Ryu, J., Kang, S.K., and Park, C.M. (2011). Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis. The Plant Journal 65,418-429.
[235]Seo, P.J., Park, M.J., Lim, M.H., Kim, S.G, Lee, M., Baldwin, I.T., and Park, C.M. (2012). A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED 1 underlies the circadian clock regulation of temperature responses in Arabidopsis. The Plant Cell 24, 2427-2442.
[236]Sessions, A., Weigel, D., and Yanofsky, M.F. (1999). The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal expression in meristems and young primordia. The Plant Journal 20,259-263.
[237]Shen, L., Kang, Y.G, Liu, L., and Yu, H. (2011). The J-domain protein J3 mediates the integration of flowering signals in Arabidopsis. The Plant Cell 23,499-514.
[238]Shindo, C., Aranzana, M.J., Lister, C., Baxter, C., Nicholls, C., Nordborg, M., and Dean, C. (2005). Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiology 138,1163-1173.
[239]Simpson, G.G. (2004). The autonomous pathway:epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time. Current Opinion in Plant Biology 7, 570-574.
[240]Simpson, G.G., Dijkwel, P.P., Quesada, V., Henderson, I., and Dean, C. (2003). FY is an RNA 3'end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 113,777-787.
[241]Sivitz, A.B., Reinders, A., Johnson, M.E., Krentz, A.D., Grof, C.P., Perroux, J.M., and Ward, J.M. (2007). Arabidopsis sucrose transporter AtSUC9. High-affinity transport activity, intragenic control of expression, and early flowering mutant phenotype. Plant Physiology 143, 188-198.
[242]Smith, T.F., Gaitatzes, C., Saxena, K., and Neer, E.J. (1999). The WD repeat:a common architecture for diverse functions. Trends in Biochemical Sciences 24,181-185.
[243]Somers, D.E., and Quail, P.H. (1995). Temporal and spatial expression patterns of PHYA and PHYB genes in Arabidopsis. The Plant Journal 7,413-427.
[244]Somers, D.E., Webb, A.A., Pearson, M., and Kay, S.A. (1998). The short-period mutant, tocl-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana. Development 125,485-494.
[245]Song, H.R., and Carre, I.A. (2005). DET1 regulates the proteasomal degradation of LHY, a component of the Arabidopsis circadian clock. Plant Molecular Biology 57,761-771.
[246]Song, Y.H., Ito, S., and Imaizumi, T. (2013). Flowering time regulation:photoperiod-and temperature-sensing in leaves. Trends in Plant Science 18,575-583.
[247]Song, Y.H., Smith, R.W., To, B.J., Millar, A.J., and Imaizumi, T. (2012). FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering. Science 336, 1045-1049.
[248]Song, Y.H., Song, N.Y., Shin, S.Y., Kim, H.J., Yun, D.J., Lim, C.O., Lee, S.Y., Kang, K.Y., and Hong, J.C. (2008). Isolation of CONSTANS as a TGA4/OBF4 interacting protein. Molecules and Cells 25,559-565.
[249]Soppe, W.J., Bentsink, L., and Koornneef, M. (1999). The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana. Development 126, 4763-4770.
[250]Srikanth, A., and Schmid, M. (2011). Regulation of flowering time:all roads lead to Rome. Cellular and Molecular Life Sciences 68,2013-2037.
[251]Stoffler, D., Fahrenkrog, B., and Aebi, U. (1999). The nuclear pore complex:from molecular architecture to functional dynamics. Current Opinion in Cell Biology 11,391-401.
[252]Stoffler, D., Feja, B., Fahrenkrog, B., Walz, J., Typke, D., and Aebi, U. (2003). Cryo-electron tomography provides novel insights into nuclear pore architecture:implications for nucleocytoplasmic transport. Journal of Molecular Biology 328,119-130.
[253]Strasser, B., Alvarez, M.J., Califano, A., and Cerdan, P.D. (2009). A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature. The Plant Journal 58,629-640.
[254]Strayer, C., Oyama, T., Schultz, T.F., Raman, R., Somers, D.E., Mas, P., Panda, S., Kreps, J.A., and Kay, S.A. (2000). Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289,768-771.
[255]Sugano, S., Andronis, C., Ong, M.S., Green, R.M., and Tobin, E.M. (1999). The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 96,12362-12366.
[256]Sun, Q., Yoda, K., Suzuki, M., and Suzuki, H. (2003). Vascular tissue in the stem and roots of woody plants can conduct light. Journal of Experimental Botany 54,1627-1635.
[257]Sung, S., He, Y., Eshoo, T.W., Tamada, Y., Johnson, L., Nakahigashi, K., Goto, K., Jacobsen, S.E., and Amasino, R.M. (2006). Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nature Genetics 38,706-710.
[258]Swiezewski, S., Liu, F., Magusin, A., and Dean, C. (2009). Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462,799-802.
[259]Takada, S., and Goto, K. (2003). Terminal flower2, an Arabidopsis homolog of heterochromatin proteinl, counteracts the activation of flowering locus T by constans in the vascular tissues of leaves to regulate flowering time. The Plant Cell 15,2856-2865.
[260]Tamada, Y., Yun, J.Y., Woo, S.C., and Amasino, R.M. (2009). ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. The Plant Cell 21,3257-3269.
[261]Tamura, K., and Hara-Nishimura, I. (2012). The molecular architecture of the plant nuclear pore complex. Journal of Experimental Botany 64,823-832.
[262]Tamura, K., Fukao, Y., Iwamoto, M., Haraguchi, T., and Hara-Nishimura, I. (2010). Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. The Plant Cell 22,4084-4097.
[263]Thain, S.C., Hall, A., and Millar, A.J. (2000). Functional independence of circadian clocks that regulate plant gene expression. Current Biology 10,951-956.
[264]Thain, S.C., Murtas, G., Lynn, J.R., McGrath, R.B., and Millar, A.J. (2002). The circadian clock that controls gene expression in Arabidopsis is tissue specific. Plant Physiology 130, 102-110.
[265]Tiwari, S.B., Shen, Y., Chang, H.C., Hou, Y., Harris, A., Ma, S.F., McPartland, M., Hymus, GJ., Adam, L., Marion, C., Belachew, A., Repetti, P.P., Reuber, T.L., and Ratcliffe, O.J. (2010). The flowering time regulator CONSTANS is recruited to the FLOWERING LOCUS T promoter via a unique cis-element. The New Phytologist 187, 57-66.
[266]Todesco, M., Rubio-Somoza, I., Paz-Ares, J., and Weigel, D. (2010). A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genetics 6, e1001031.
[267]Torti, S., Fornara, F., Vincent, C., Andres, F., Nordstrom, K., Gobel, U., Knoll, D., Schoof, H., and Coupland, G (2012). Analysis of the Arabidopsis shoot meristem transcriptome during floral transition identifies distinct regulatory patterns and a leucine-rich repeat protein that promotes flowering. The Plant Cell 24,444-462.
[268]Tran, E.J,, and Wente, S.R. (2006). Dynamic nuclear pore complexes:life on the edge. Cell 125,1041-1053.
[269]Troncoso-Ponce, M.A., and Mas, P. (2012). Newly described components and regulatory mechanisms of circadian clock function in Arabidopsis thaliana. Molecular Plant 5,545-553.
[270]Tsuchiya, Y., Akashi, M., Matsuda, M., Goto, K., Miyata, Y., Node, K., and Nishida, E. (2009). Involvement of the protein kinase CK2 in the regulation of mammalian circadian rhythms. Science Signaling 2, ra26.
[271]Valverde, F., Mouradov, A., Soppe, W., Ravenscroft, D., Samach, A., and Coupland, G. (2004). Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 303,1003-1006.
[272]Wahl, V., Ponnu, J., Schlereth, A., Arrivault, S., Langenecker, T., Franke, A., Feil, R., Lunn, J.E., Stitt, M., and Schmid, M. (2013). Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science 339,704-707.
[273]Walther, T.C., Askjaer, P., Gentzel, M., Habermann, A., Griffiths, G, Wilm, M., Mattaj, I.W., and Hetzer, M. (2003). RanGTP mediates nuclear pore complex assembly. Nature 424, 689-694.
[274]Wang, J.W., Czech, B., and Weigel, D. (2009). miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138,738-749.
[275]Wang, L., Fujiwara, S., and Somers, D.E. (2010). PRR5 regulates phosphorylation, nuclear import and sub nuclear localization of TOC1 in the Arabidopsis circadian clock. The EMBO Journal 29,1903-1915.
[276]Wang, Y., Wu, J.F., Nakamichi, N., Sakakibara, H., Nam, H.G, and Wu, S.H. (2011). LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 form a positive feedback regulatory loop in the Arabidopsis circadian clock. The Plant Cell 23,486-498.
[277]Wang, Z.Y., and Tobin, E.M. (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93,1207-1217.
[278]Wang, Z.Y., Kenigsbuch, D., Sun, L., Harel, E., Ong, M.S., and Tobin, E.M. (1997). A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. The Plant Cell 9,491-507.
[279]Wenden, B., Toner, D.L., Hodge, S.K., Grima, R., and Millar, A.J. (2012). Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proceedings of the National Academy of Sciences of the United States of America 109,6757-6762.
[280]Wiermer, M., Cheng, Y.T., Imkampe, J., Li, M., Wang, D., Lipka, V., and Li, X. (2012). Putative members of the Arabidopsis Nup107-16 nuclear pore sub-complex contribute to pathogen defense. The Plant Journal 70,796-808.
[281]Wilson, R.N., Heckman, J.W., and Somerville, C.R. (1992). Gibberellin Is Required for Flowering in Arabidopsis thaliana under Short Days. Plant Physiology 100,403-408.
[282]Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V., and Provart, N.J. (2007). An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PloS One 2, e718.
[283]Wood, C.C., Robertson, M., Tanner, G., Peacock, W.J., Dennis, E.S., and Helliwell, C.A. (2006). The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proceedings of the National Academy of Sciences of the United States of America 103,14631-14636.
[284]Wu, G., and Poethig, R.S. (2006). Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133,3539-3547.
[285]Wu, G., Park, M.Y., Conway, S.R., Wang, J.W., Weigel, D., and Poethig, R.S. (2009). The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138,750-759.
[286]Wu, J.F., Wang, Y., and Wu, S.H. (2008). Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering. Plant Physiology 148,948-959.
[287]Xu, X., Hotta, C.T., Dodd, A.N., Love, J., Sharrock, R., Lee, Y.W., Xie, Q., Johnson, C.H., and Webb, A.A. (2007a). Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis. The Plant Cell 19,3474-3490.
[288]Xu, X.M., Meulia, T., and Meier, I. (2007b). Anchorage of plant RanGAP to the nuclear envelope involves novel nuclear-pore-associated proteins. Current Biology 17,1157-1163.
[289]Xu, X.M., Rose, A., Muthuswamy, S., Jeong, S.Y., Venkatakrishnan, S., Zhao, Q., and Meier, I. (2007c). NUCLEAR PORE ANCHOR, the Arabidopsis homolog of Tpr/Mlpl/Mlp2/megator, is involved in mRNA export and SUMO homeostasis and affects diverse aspects of plant development. The Plant Cell 19,1537-1548.
[290]Yamaguchi, A., Wu, M.F., Yang, L., Wu, G., Poethig, R.S., and Wagner, D. (2009). The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Developmental Cell 17,268-278.
[291]Yamamoto, Y.T., Taylor, C.G, Acedo, GN., Cheng, C.L., and Conkling, M.A. (1991). Characterization of cis-acting sequences regulating root-specific gene expression in tobacco. The Plant Cell 3,371-382.
[292]Yang, D.L., Yao, J., Mei, C.S., Tong, X.H., Zeng, L.J., Li, Q., Xiao, L.T., Sun, T.P., Li, J., Deng, X.W., Lee, C.M., Thomashow, M.F., Yang, Y., He, Z., and He, S.Y. (2012). Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proceedings of the National Academy of Sciences of the United States of America 109, E1192-1200.
[293]Yang, L., Xu, M., Koo, Y., He, J., and Poethig, R.S. (2013). Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156Aand MIR156C. eLife 2, e00260.
[294]Yang, Y.D., Elamawi, R., Bubeck, J., Pepperkok, R., Ritzenthaler, C, and Robinson, D.G (2005). Dynamics of COPII vesicles and the Golgi apparatus in cultured Nicotiana tabacum BY-2 cells provides evidence for transient association of Golgi stacks with endoplasmic reticulum exit sites. The Plant Cell 17,1513-1531.
[295]Yasui, Y., Mukougawa, K., Uemoto, M., Yokofuji, A., Suzuri, R., Nishitani, A., and Kohchi, T. (2012). The phytochrome-interacting vascular plant one-zinc fingerl and VOZ2 redundantly regulate flowering in Arabidopsis. The Plant Cell 24,3248-3263.
[296]Yerushalmi, S., and Green, R.M. (2009). Evidence for the adaptive significance of circadian rhythms. Ecology Letters 12,970-981.
[297]Yoo, B.Y., and Bayley, S.T. (1967). The structure of pores in isolated pea nuclei. Journal of Ultrastructure Research 18,651-660.
[298]Yu, S., Galvao, V.C., Zhang, Y.C., Horrer, D., Zhang, T.Q., Hao, Y.H., Feng, Y.Q., Wang, S., Schmid, M., and Wang, J.W. (2012). Gibberellin regulates the Arabidopsis floral transition through miRl 56-targeted SQUAMOSA promoter binding-like transcription factors. The Plant Cell 24,3320-3332.
[299]Yu, S., Cao, L., Zhou, C.M., Zhang, T.Q., Lian, H., Sun, Y., Wu, J., Huang, J., Wang, G, and Wang, J.W. (2013). Sugar is an endogenous cue for juvenile-to-adult phase transition in plants. eLife 2, e00269.
[300]Zhang, C., Hutchins, J.R., Muhlhausser, P., Kutay, U., and Clarke, P.R. (2002). Role of importin-beta in the control of nuclear envelope assembly by Ran. Current Biology 12, 498-502.
[301]Zhang, H., and van Nocker, S. (2002). The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C. The Plant Journal 31,663-673.
[302]Zhang, H., Ransom, C., Ludwig, P., and van Nocker, S. (2003). Genetic analysis of early flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for expression of the flowering-time switch flowering locus C. Genetics 164, 347-358.
[303]Zhang, Y., and Li, X. (2005). A putative nucleoporin 96 Is required for both basal defense and constitutive resistance responses mediated by suppressor of npr 1-1,constitutive 1. The Plant Cell 17,1306-1316.
[304]Zhao, Q., and Meier, I. (2011). Identification and characterization of the Arabidopsis FG-repeat nucleoporin Nup62. Plant Signaling & Behavior 6,330-334.
[305]Zuo, Z., Liu, H., Liu, B., Liu, X., and Lin, C. (2011). Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in Arabidopsis. Current Biology 21,841-847.