烟草TM2 MAR序列作用机理研究及其应用
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摘要
核基质结合区(Matrix Attachment Regions,MARs)是基因组上通常富含A/T的能够将DNA或染色质附着到核基质上的DNA序列。通过与结合蛋白的互作,MARs在维持和/或修饰DNA或染色质结构及调控相关基因方面表达中发挥重要作用。
TM2是我们从烟草基因组中分离得到的一个MAR序列,在体外与核基质具有很强的结合能力,并且在水稻、烟草等转基因植株中对侧翼基因表达表现出很强的增强作用。为了进一步阐明TM2的表达调控机理,本研究对TM2在不同基因表达系统中调控侧翼基因表达的功能特点进行了详细分析,以探讨TM2可能的作用机制及其在植物基因工程中的应用。主要试验结果如下:
1.在烟草转基因植株和细胞悬浮系中,双端TM2序列均能显著提高侧翼表达盒中报告基因gusA的表达水平。细胞类型对转基因表达有一定影响,但不影响TM2的调控功能。MAR序列的串联重复能够增强其表达调控作用,但增强效应与串联拷贝数不成比例。
2.烟草TM2序列具有双向表达调控能力,且作用没有明显的序列方向性。无论在表达盒上游和下游,TM2均能提高侧翼基因的表达水平,表现为双向调控特性。尽管上游MAR表现出比下游MAR更强的调控作用,但双端TM2对于提高侧翼基因的表达无疑都是必要的。TM2在重组位点上正向插入和反向插入对其侧翼基因表达水平的增强作用没有显著影响,说明TM2的功能不受插入方向的影响。
3.烟草TM2能够改变侧翼基因的表达水平,但不改变其启动子的表达模式。启动子缺失分析表明,TM2对侧翼基因的表达增强作用要求启动子具有调控基础表达的必需元件。无论对于组成型CaMV 35S启动子还是光合组织特异的PNZIP启动子,TM2只改变启动子的调控水平,不改变启动子调控的基因表达模式。
4.TM2序列上的拓扑异构酶Ⅱ结合位点、DNA解旋结合位点和T-box均是功能元件。烟草TM2位点缺失分析表明,三种元件的缺失都会引起TM2侧翼基因表达水平的降低,是TM2 MAR的主要功能元件,但位点之间存在一定的功能冗余。
5.烟草TM2序列能够显著提高侧翼启动子区对核酸酶的敏感性。微球菌核酸酶敏感试验表明,TM2显著降低了转基因植株中CaMV 35S启动子的特异扩增水平,说明TM2能够使侧翼DNA结构松散,具有局部染色质开放能力。几个功能元件对于提高核酸酶敏感性起关键作用。
6.烟草TM2序列的功能不严格依赖核基质的存在,但需要在浓缩的DNA结构中才能发挥作用。在植物瞬时表达中,TM2没有明显的表达增强作用,但在酵母核外质粒表达系统中可以通过提高转录效率来增强侧翼基因的表达,几个功能元件在核外表达增强过程中同样发挥重要作用。
7.通过酵母单杂交分离到几个TM2序列的潜在结合蛋白,凝胶阻滞分析表明这些蛋白能够与TM2片段进行体外结合。多种侯选靶位点暗示TM2可能有多个核基质结合位点,也间接说明TM2作用机理的复杂性。
8.利用TM2序列和其他表达调控序列,构建了植物高效超表达载体和干涉表达载体,能够用于植物高效转化及转基因表达调控。利用In-Fusion Smart技术,可以将植物高效表达载体与cDNA池重组,用于大规模基因表达筛选。这些载体的构建可为植物基因功能分析提供有效的研究工具。
Matrix Attachment Regions (MARs) are the DNA sequences with rich A/T nucleotides that may be involved in anchoring DNA/chromatin to the nuclear matrix. By the interaction with the binding proteins, MARs play an important role in the maintance and modification of the DNA/chromatin structure and the regulation of the gene expression.
TM2 is a matrix attachment region isolated from the genomic DNA of tobacco, which can strongly bind to the nuclear matrix and significantly enhance the transgene expression in transgenic plants of rice and tobacco. To gain insights into the regulatory mechanism of TM2 by which transcription enhancement of transgene occurs, we give the detailed analysis of the expression variation of flanking transgenes drived by different promoters in different expression systems. We present the main results as follows:
1.The tandem repeats of TM2 sequence can enhance the transgene expression activation mediated from the flanking MAR in transformants, although this effect does not correspond with the copy number of the MARs. The average level of transgene expression in tobacco calli is markedly lower than that in plants, however, this difference from the cell development does not influnce the function of TM2.
2 . The TM2 bidirectionally regulated the flanking transgene expression without dependence on the sequence orientation on the integrating site. The 5′-TM2 and 3′-TM2 can both enhance the transgene expression, although the increasing distance of the MAR relative to the promoter might decrease the activation to a certain extent. This characterization indicates TM2 enhance the transgene expression in a bidirectional manner. The effect of location suggests both the 5′-TM2 and 3′-TM2 flanking the transgene in the construct are desirable for maximal enhancement of transgene expression. In addition, when the individual TM2 was constructed in the opposite direction relative to the transgene, either in the upstream or in the downstream of the cassette, the GUS assay does not show a significant difference between the constructs. These results indicate there is no direction effect of the TM2 sequence on transcription enhancement of the target gene expression.
3.The TM2 can change the expression lelvel of the flanking transgene rather than the expression pattern mediated from the promoter. The effect of TM2 on GUS expression in transgenic cells that harbored the CaMV 35S or PNZIP minipromoters suggests that transcription enhancement from the tobacco MAR requires the basic expression of reporter gene. Without the upstream enhancer elements of minipromoter the MAR present to be invalid.
4.The effect of the site-specific deletion of two unwinding sites, one topoisomerase II binding site and one T-box element in TM2 indicated that they are all functional elements. Deletion of any kind of elements always results in the decreasement of the flanking transgene expression. These four sites perform the vast majority of the enhancement mediated from TM2, although there is some functional redundancy in their contribution.
5.According to the micrococcal nuclease accessibility analysis, the CaMV 35S promoter adjacent to the TM2 was degraded more rapidly than the control without MAR. By contrast, the time-course digestion of the promoter linked to mutant MAR was similar with that of the control. Considering the increasing accessibility to micrococcal nuclease would result in the decrease of PCR products for the regions of interest, the difference revealed that TM2 plays a role in nucleosome remodeling of the promoter region. The deletion of the four sites determined the effect of TM2 on the micrococcal nuclease accessibility.
6.The transcription activation of flanking gene expression from the tobacco TM2 does not simply depend on the nuclear matrix but the condensed DNA structure. The MAR does not present any regulation ability in agrobacterium-mediated tobacco transient expression of the transgene expression. However, it can enhance the transcription efficiency so as to increase the his3 gene expression on plasmid expression vector out of the yeast nuclear. The above elements in TM2 also play important role in out-of-nuclear expression enhancement.
7.Several potential genes encoding TM2 sequence-binding proteins were screened from the cDNA pool by yeast one-hybrid method. These proteins show high affinity with the TM2 fragment by electrophoresis mobility shift assay. These potential multiple targets implicate the functional complexity of the TM2 MAR.
8.With TM2 and other regulation sequences, we construct the plant overexpression and RNAi vectors. These constructs can be used in high-efficient transformation and regulating gene expressions. The recombination between the high-efficient plant expression vector and the cDNA pool by the In-Fusion Smart method bring an important perspective to large-scale screening of genes. These constructs will provide efficient tools for function study of the plant genes.
TM2是我们从烟草基因组中分离得到的一个MAR序列,在体外与核基质具有很强的结合能力,并且在水稻、烟草等转基因植株中对侧翼基因表达表现出很强的增强作用。为了进一步阐明TM2的表达调控机理,本研究对TM2在不同基因表达系统中调控侧翼基因表达的功能特点进行了详细分析,以探讨TM2可能的作用机制及其在植物基因工程中的应用。主要试验结果如下:
1.在烟草转基因植株和细胞悬浮系中,双端TM2序列均能显著提高侧翼表达盒中报告基因gusA的表达水平。细胞类型对转基因表达有一定影响,但不影响TM2的调控功能。MAR序列的串联重复能够增强其表达调控作用,但增强效应与串联拷贝数不成比例。
2.烟草TM2序列具有双向表达调控能力,且作用没有明显的序列方向性。无论在表达盒上游和下游,TM2均能提高侧翼基因的表达水平,表现为双向调控特性。尽管上游MAR表现出比下游MAR更强的调控作用,但双端TM2对于提高侧翼基因的表达无疑都是必要的。TM2在重组位点上正向插入和反向插入对其侧翼基因表达水平的增强作用没有显著影响,说明TM2的功能不受插入方向的影响。
3.烟草TM2能够改变侧翼基因的表达水平,但不改变其启动子的表达模式。启动子缺失分析表明,TM2对侧翼基因的表达增强作用要求启动子具有调控基础表达的必需元件。无论对于组成型CaMV 35S启动子还是光合组织特异的PNZIP启动子,TM2只改变启动子的调控水平,不改变启动子调控的基因表达模式。
4.TM2序列上的拓扑异构酶Ⅱ结合位点、DNA解旋结合位点和T-box均是功能元件。烟草TM2位点缺失分析表明,三种元件的缺失都会引起TM2侧翼基因表达水平的降低,是TM2 MAR的主要功能元件,但位点之间存在一定的功能冗余。
5.烟草TM2序列能够显著提高侧翼启动子区对核酸酶的敏感性。微球菌核酸酶敏感试验表明,TM2显著降低了转基因植株中CaMV 35S启动子的特异扩增水平,说明TM2能够使侧翼DNA结构松散,具有局部染色质开放能力。几个功能元件对于提高核酸酶敏感性起关键作用。
6.烟草TM2序列的功能不严格依赖核基质的存在,但需要在浓缩的DNA结构中才能发挥作用。在植物瞬时表达中,TM2没有明显的表达增强作用,但在酵母核外质粒表达系统中可以通过提高转录效率来增强侧翼基因的表达,几个功能元件在核外表达增强过程中同样发挥重要作用。
7.通过酵母单杂交分离到几个TM2序列的潜在结合蛋白,凝胶阻滞分析表明这些蛋白能够与TM2片段进行体外结合。多种侯选靶位点暗示TM2可能有多个核基质结合位点,也间接说明TM2作用机理的复杂性。
8.利用TM2序列和其他表达调控序列,构建了植物高效超表达载体和干涉表达载体,能够用于植物高效转化及转基因表达调控。利用In-Fusion Smart技术,可以将植物高效表达载体与cDNA池重组,用于大规模基因表达筛选。这些载体的构建可为植物基因功能分析提供有效的研究工具。
Matrix Attachment Regions (MARs) are the DNA sequences with rich A/T nucleotides that may be involved in anchoring DNA/chromatin to the nuclear matrix. By the interaction with the binding proteins, MARs play an important role in the maintance and modification of the DNA/chromatin structure and the regulation of the gene expression.
TM2 is a matrix attachment region isolated from the genomic DNA of tobacco, which can strongly bind to the nuclear matrix and significantly enhance the transgene expression in transgenic plants of rice and tobacco. To gain insights into the regulatory mechanism of TM2 by which transcription enhancement of transgene occurs, we give the detailed analysis of the expression variation of flanking transgenes drived by different promoters in different expression systems. We present the main results as follows:
1.The tandem repeats of TM2 sequence can enhance the transgene expression activation mediated from the flanking MAR in transformants, although this effect does not correspond with the copy number of the MARs. The average level of transgene expression in tobacco calli is markedly lower than that in plants, however, this difference from the cell development does not influnce the function of TM2.
2 . The TM2 bidirectionally regulated the flanking transgene expression without dependence on the sequence orientation on the integrating site. The 5′-TM2 and 3′-TM2 can both enhance the transgene expression, although the increasing distance of the MAR relative to the promoter might decrease the activation to a certain extent. This characterization indicates TM2 enhance the transgene expression in a bidirectional manner. The effect of location suggests both the 5′-TM2 and 3′-TM2 flanking the transgene in the construct are desirable for maximal enhancement of transgene expression. In addition, when the individual TM2 was constructed in the opposite direction relative to the transgene, either in the upstream or in the downstream of the cassette, the GUS assay does not show a significant difference between the constructs. These results indicate there is no direction effect of the TM2 sequence on transcription enhancement of the target gene expression.
3.The TM2 can change the expression lelvel of the flanking transgene rather than the expression pattern mediated from the promoter. The effect of TM2 on GUS expression in transgenic cells that harbored the CaMV 35S or PNZIP minipromoters suggests that transcription enhancement from the tobacco MAR requires the basic expression of reporter gene. Without the upstream enhancer elements of minipromoter the MAR present to be invalid.
4.The effect of the site-specific deletion of two unwinding sites, one topoisomerase II binding site and one T-box element in TM2 indicated that they are all functional elements. Deletion of any kind of elements always results in the decreasement of the flanking transgene expression. These four sites perform the vast majority of the enhancement mediated from TM2, although there is some functional redundancy in their contribution.
5.According to the micrococcal nuclease accessibility analysis, the CaMV 35S promoter adjacent to the TM2 was degraded more rapidly than the control without MAR. By contrast, the time-course digestion of the promoter linked to mutant MAR was similar with that of the control. Considering the increasing accessibility to micrococcal nuclease would result in the decrease of PCR products for the regions of interest, the difference revealed that TM2 plays a role in nucleosome remodeling of the promoter region. The deletion of the four sites determined the effect of TM2 on the micrococcal nuclease accessibility.
6.The transcription activation of flanking gene expression from the tobacco TM2 does not simply depend on the nuclear matrix but the condensed DNA structure. The MAR does not present any regulation ability in agrobacterium-mediated tobacco transient expression of the transgene expression. However, it can enhance the transcription efficiency so as to increase the his3 gene expression on plasmid expression vector out of the yeast nuclear. The above elements in TM2 also play important role in out-of-nuclear expression enhancement.
7.Several potential genes encoding TM2 sequence-binding proteins were screened from the cDNA pool by yeast one-hybrid method. These proteins show high affinity with the TM2 fragment by electrophoresis mobility shift assay. These potential multiple targets implicate the functional complexity of the TM2 MAR.
8.With TM2 and other regulation sequences, we construct the plant overexpression and RNAi vectors. These constructs can be used in high-efficient transformation and regulating gene expressions. The recombination between the high-efficient plant expression vector and the cDNA pool by the In-Fusion Smart method bring an important perspective to large-scale screening of genes. These constructs will provide efficient tools for function study of the plant genes.
引文
张可伟,王健美,杨国栋,郭兴启,温孚江,崔德才,郑成超.(2002)强MAR的分离及其体内外功能鉴定。科学通报47:1527-1577
李旭刚,朱祯,徐军望,吴茜,徐鸿林. (2001)豌豆核基质结合区的分离及其在转基因烟草中的功能分析。中国科学C辑3:230-237
李旭刚,陈松彪,徐军望,刘翔,朱祯.(2002)玉米MAR序列的分离及其在转基因烟草中的功能研究。自然科学进展5:491-496
Abad PC, Lewis J, Mian IS, Knowles DW, Sturgis J, Badve S, Xie J, Lelièvre SA. (2007) NuMA influences higher order chromatin organization in human mammary epithelium. Mol Biol Cell 18:348-361
Adachi Y, Kas E, Laemmli UK. (1989) Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J 8:3997-4006
Akasaka K, Nishimura A, Takata K, Mitsunaga K, Mibuka F, Ueda H, Hirose S, Tsutsui K, Shimada H. (1999) Upstream element of the sea urchin arylsufatase gene serves as an insulator. Cell Mol Biol 45:555–565
Allen GC, Hall G Jr, Michalowski S, Newman W, Spiker S, Weissinger AK, Thompson WF. (1996) High-level transgene expression in plant cells:effects of a strong scaffold attachment region from tobacco. Plant Cell 8:899-913
Allen GC, Hall GE Jr, Childs LC, Weissinger AK, Spiker S, Thompson WF. (1993) Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. Plant Cell. 5:603-13
Allen GC, Spiker S, Thompson WF. (2000) Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol Biol 43:361-376
Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, and Kohwi-Shigematsu T. (2000) The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. Genes & Dev 14: 521-535
Amirand C, Viari A, Ballini JP, Rezaei H, Beaujean N, Jullien D, K?s E, Debey P. (1998) Three distinct sub-nuclear populations of HMG-I protein of different properties revealed by co-localization image analysis. J Cell Sci 111:3551-3561
Antes TJ,Namicu SJ,Fournier RE and Levy-Wilson B. (2001) The 5′-boundary of the human apolipoprotein B chromatin domain in intestinal cells. Biochemistry 40:6731-6742
Aravind L, Landsman D. (1998) AT-hook motifs identified in a wide variety of DNA-bindingproteins. Nucleic Acids Res 26:4413-4421
Avramova Z, Sanmiguel P, Georgieva E, Bennetzen JL. (1995) Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. Plant Cell 7:1667-1680
Banerjee S, Fisher O, Lohia A, Ankri S. (2005) Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR). Mol Biochem Parasitol 139:91-97
Banerjee S, Fisher O, Lohia A, Ankri S. (2005) Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR). Mol Biochem Parasitol139:91-97.
Belshaw NJ, Hakola S, Nevalanien, Penttil? M, Suominen P, Archer DB. (1997) Trichoderma reesei sequences that bind to the nuclear matrix enhance transformation frequency. Mol Gen Genet 256:18-27
Benfey PN, Ren L, Chua NH. (1990) Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. EMBO J 9:1685-1696
Berezney R and Coffey DS. (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1470
Bianchi ME, Agresti A. (2005) HMG proteins: Dynamic players in gene regulation and differentiation. Curr Opin Genet Dev 15: 496-506
Blatter EE, Ross W, Tang H, Gourse RL,Ebright RH. (1994) Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78:889-896
Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shgematsu T. (1992) Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255:195-197.
Bode J,Stengert-Iber,Kay V,Schlacker T and Dietz-Pfeilstetter A. (1996) Scaffold/ matrix- attached regions:topological switches with multiple regulatory functions. Crit Rev Eukaryot Gene Expr 6:115-138
Boulikas T. (1994) Transcription factor binding sites in the matrix attachment region (MAR) of the chicken alpha-globin gene. J Cell Biochem 55:513-529
Breyne P, Vanmontagu M, Depicker A, Gheysen G (1992) Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco. Plant Cell 4:463-471
Brouwer C, Bruce W, Maddock S, Avramova Z, Bowen B. (2002) Suppression of transgnene silencing by matrix attachment regions in maize: a dual role for the maize 5′-ADH1 matrix attachment region. Plant cell 14:2251-2264
Brummell DA, Balint-Kurti PJ, Harpster MH, Palys JM, Oeller PW, Gutterson N. (2003) Inverted repeat of a heterologous 3'-untranslated region for high-efficiency, high-throughput gene silencing.Plant J 33:793-800
Brunner E, Weitzel J, Heitmann B, Maurer T, Str?tling WH, Kalbitzer HR. (2000) Sequence-specific 1H, 13C, and 15N assignments of the MAR-binding domain of chicken MeCP2/ARBP. J Biomol NMR 17:175-176
Bustin M, Reeves R. (1996) High-mobility-group chromosomal proteins: Architectural components that facilitate chromatin function. Prog Nucleic Acid Res Mol Biol 54:35- 100
Byrd K, Corces VG. (2003)Visualization of chromatin domains created by the gypsy insulator of Drosophila. J. Cell Biol 162: 565-574
Cai S, Han HJ, Kohwi-Shigematsu T. (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat Genet 34:4-6
Chattopadhyay S, Kaul R, Charest A, Housman D, Chen J. (2000) SMAR1, a novel, alternatively spliced gene product, binds the Scaffold/Matrix-associated region at the T cell receptor beta locus. Genomics 68:93-96
Chattopadhyay S, Pavithra L. (2006) MARs and MARBPs: key modulators of gene regulation and disease manifestation. Subcell Biochem 41:213-230
Cheng ZQ, Targlli J, Wu R. (2001) Tobacco matrix attachment region sequence increased transgene expression levels in rice plants. Mol Breeding 7:317-327
Chua YL, Pwee KH, Kini RM (2001) DNA binding mediated by the wheat HMGa protein: a novel instance of selectivity against alternating GC sequence. Plant Mol Biol 46:193-204
Chuang CF, Meyerowitz EM. (2000) Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:4985-4990
Coleman HD, Ellis DD, Gilbert M, Mansfield SD. (2006) Up-regulation of sucrose synthase and UDP-glucose pyrophosphorylase impacts plant growth and metabolism. Plant Biotechnol J 4:87-101
Crichlow GV, Zhou H, Hsiao HH, Frederick KB, Debrosse M, Yang Y, Folta-Stogniew EJ, Chung HJ, Fan C, De la Cruz EM, Levens D, Lolis E, Braddock D. (2008) Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition. EMBO J27:277-289
Cunningham JM, Purucker ME, Jane SM, Safer B, Vanin EF, Ney PA, Lowrey CH, Nienhuis AW. (1994) The regulatory element 3' to the A gamma-globin gene binds to the nuclear matrix and interacts with special A-T-rich binding protein 1 (SATB1), an SAR/ MAR-associating region DNA binding protein. Blood 184:1298-1308
Curtis MD, Grossniklaus U. (2003) A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133:462-469
Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T. (2007) pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants.Plant Physiol 145:1272-1281
Dang Q, Auten J, and Plavec I. (2000) Human Beta Interferon Scaffold Attachment Region Inhibits De Novo Methylation and Confers Long-Term, Copy Number-Dependent Expression to a Retroviral Vector. J Virol 74: 2671- 2678
De Amicis F, Patti T, Marchetti S. (2007) Improvement of the pBI121 plant expression vector by leader replacement with a sequence combining a poly(CAA) and a CT motif. Transgenic Res 16:731-738
De Bolle MF, Butaye KM, Goderis IJ, Wouters PF, Jacobs A, DelauréSL, Depicker A, Cammue BP. (2007) The influence of matrix attachment regions on transgene expression in Arabidopsis thaliana wild type and gene silencing mutants. Plant Mol Biol 63:533-543
De Bolle MFC, Butaye KMJ, Coucke WJW, Goderis IJWM, Wouters PFJ, van Boxel N, Broekaert WF, Cammue BPA (2003) Analysis of the influence of promoter elements and a matrix attachment region on the inter-individual variation of transgene expression in populations of Arabidopsis thaliana. Plant Sci 165:169-179
Dickinson LA, Kohwi-Shigematsu T. (1995) Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential. Mol Cell Biol 15:456-465.
Dietz A, Kay V,Schlacker T, Landsmann J and Bode J. (1994) A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells. Nucleic Acids Res 22: 2744-2751
Dietz-Pfeilstetter A, Arndt N, Kay V, Bode J. (2003) Molecular structure and regulatory potential of a T-DNA integration site in petunia. Transgenic Res 12:83-99
Dobreva G, Dambacher J, Grosschedl R. (2003) SUMO modification of a novel MAR-binding protein, SATB2, modulates immunoglobulin mu gene expression. Genes Dev 17:3048- 3061
Fackelmayer FO, Dahm K, Renz A, Ramsperger U, Richter A. (1994) Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur J Biochem 221:749-757
Ferguson M, Henry PA, Currie RA. (2003) Histone deacetylase inhibition is associated with transcriptional repression of the Hmga2 gene. Nucleic Acids Res 131:3123-3133
Fiorini A, Gouveia Fde S, Fernandez MA. (2006) Scaffold/Matrix Attachment Regions and intrinsic DNA curvature. Biochemistry (Mosc) 71:481-488
Fisher O, Siman-Tov R, Ankri S. (2006) Pleiotropic phenotype in Entamoeba histolytica overexpressing DNA methyltransferase (Ehmeth). Mol Biochem Parasitol 147:48-54
Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K. (2004) Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces.Plant Mol Biol 56:225-239
Dickinson LA, Joh T, Kohwi Y and Kohwi-ShigematsuT. (1992) A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70: 631-645
Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K. (2004) Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol Biol 56:225-239
Fujiwara S, Matsuda N, Sato T, Sonobe S, Maeshima M. (2002) Molecular properties of a matrix attachment region-binding protein located in the nucleoli of tobacco cells. Plant Cell Physiol 43:1558-1567
Fukuda Y, Nishikawa S. (2003) Matrix attachment regions enhance transcription of a downstream transgene and the accessibility of its promoter region to Micrococcal nuclease. Plant Mol Biol 51:665-675
Fukuda Y. (1999) Characterization of matrix attachment sites in the upstream region of a tobacco chitinase gene. Plant Mol Biol 39:1051-1062
Gaal T, Ross W, Blatter EE, Tang H, Jia X, Krishnan VV, Assa-Munt N, Ebright RH, Gourse RL. (1996) DNA-binding determinants of theαsubunit of RNA polymerase: Novel DNA-binding domain architecture. Genes & Dev 10:16-26
Gallie DR. (1993) Posttranscriptional regulation of gene expression in plants. Ann Rev Plant Physiol Plant Mol Biol 44:77-105
Gallie DR. (2002) The 5′-leader of tobacco mosaic virus promotes translation through enhanced recruitment of eIF4F. Nucleic Acids Res 30:3401-3411
Gallie DR. (2002) The 5'-leader of tobacco mosaic virus promotes translation throughenhanced recruitment of eIF4F. Nucleic Acids Res 30:3401-3411
Gasser SM, Laemmli UK. (1986) Cohabitation of scaffold binding regions with upstream/ enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46:521-530
Gindullis F and Meier I. (1999) Matrix attachment region binding protein MFP1 is localized in discrete domains at the nuclear envelope. Plant Cell 11:1755-68
Gindullis F, Peffer NJ, Meier I. (1999) MAF1, a novel plant protein interacting with matrix attachment region binding protein MFP1, is located at the nuclear envelope. Plant Cell 11:1755-1768
Glazko GV, Koonin EV, Rogozin IB, Shabalina SA(.2003)A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 19:119-124
Gourse RL, Ross W, Gaal T. (2000) UPs and downs in bacterial transcription initiation: The role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37:687-695
Grasser KD, Krech AB, Feix G. (1994) The maize chromosomal HMGa protein recognises structural features of DNA and increases DNA flexibility. Plant J 6: 351–358
Grasser KD, Launholt D. (2006) Chromatin-associated architectural HMGA and HMGB proteins assist transcription factor function. In Regulation of Transcription in Plants, K.D. Grasser, ed. (Oxford, UK: Blackwell Publishing) pp 54–78.
Gross CA, Chan C, Dombroski A, Gruber T, Sharp M, Tupy J, Young B. (1998) The functional and regulatory roles of ? factors in transcription. Cold Spring Harbor Symp Quant Biol 63:141–155
Hall G Jr, Allen GC, Loer DS, Thompson WF, Spiker S. (1991) Nuclear scaffold and scaffold-attachment regions in higher plants. Proc Natl Acad Sci USA 88:9320-9324
Halweg C, Thompson WF and Spiker S. (2005) The Rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tabacco cells:a flow cytometrix study. Plant Cell 17:418-429
Han KH, Ma CP, Strauss SH. (1997) Matrix attachment regions (MARs) enhance transformation frequency and transgene expression in polar. Transgenic Res 6:415-420
Harpster MH, Townsend JA, Jones JD, Bedbrook J, Dunsmuir P. (1988) Relative strengths of the 35S cauliflower mosaic virus, 1', 2', and nopaline synthase promoters in transformed tobacco sugarbeet and oilseed rape callus tissue. Mol Gen Genet 212:182-190
Hatton D, Gray JC. (1999) Two MAR DNA-binding proteins of the pea nuclear matrix identify a new class of DNA-binding proteins. Plant J 18:417-429
Hayward RS, Igarashi K, Ishihama A. (1991) Functional specialization within theα-subunit of Escherichia coli RNA polymerase. J Mol Biol 221:23-29
Heitmann B, Maurer T, Weitzel JM, Str?tling WH, Kalbitzer HR, Brunner E. (2003) Solution structure of the matrix attachment region-binding domain of chicken MeCP2. Eur J Biochem 270:3263-3270
Heng HH, Goetze S, Ye CJ, Guo L, Stevens J B, Bremer SW, Wykes SM, Bode J, Krawetz SA. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J Cell Sci 117:999-1008
Heng HH, Krawetz SA, Lu W, Bremer S, Liu G and Ye CJ. (2001) Re-defining the chromatin loop domain. Cytogenet Cell Genet 93:155-161.
Hibino Y, Ohzeki H, Sugano N, Hiraga K. (2000b) Transcription modulation by a rat nuclear scaffold protein, P130, and a rat highly repetitive DNA component or various types of animal and plant matrix or scaffold attachment regions. Biochem Biophys Res Commun 279:282-287
Hibino Y. (2000a) Functional arrangement of genomic DNA and structure of nuclear matrix. Yakugaku Zasshi. 120:520-533
Hino S, Fan J, Taguwa S, Akasaka K, Matsuoka M. (2004) Sea urchin insulator protects lentiviral vector from silencing by maintaining active chromatin structure. Gene Ther 11:819–828
Hisada-Ishii S, Ebihara M, Kobayashi N, Kitagawa Y. (2007)Bipartite nuclear localization signal of matrin 3 is essential for vertebrate cells. Biochem Biophys Res Commun 354:72-76
Holmes-Davis R, Comai L. (2002) The matrix attachment regions (MARs) associated with the Heat Shock Cognate 80 gene (HSC80) of tomato represent specific regulatory elements. Mol Genet Genomics 266:891-898
Imbalzano AN, Kwon, H, Green, MR, Kingston RE. (1994) Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370:481–485
Izaurralde E, Kas E, Laemmli UK. (1989) Highly preferential nude H1 assembly on sacffold-associated regions. J Mol Biol 210: 573-585
Izaurralde E, Kas E, Laemmli UK. (1989) High perferential nucleation of histone H1 assembly on scaffold-associated regions. J Mol Biol 210:573-583
Izumikawa K, Yanagida M, Hayano T, Tachikawa H, Komatsu W, Shimamoto A, Futami K, Furuichi Y, Shinkawa T, Yamauchi Y, Isobe T, Takahashi N. (2008) Association of human DNA helicase RecQ5beta with RNA polymerase II and its possible role in transcription. Biochem J 413:505-516
Jackson DA. (1997) Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol Biol Rep 24: 209-220
Jackson DA, Dickinson P, Cook PR. (1990) The size of chromatin loops in Hela cell. EMBO J 9:567-571
Jefferson RA. (1987) Assaying chimeric genes in plants: the GUS gene fusion system. Plant Mol Biol Rep 5:387-405
Jeneke AC, Stehle IM, Herrmann F, Eisenberger T, Baiker A, Bode J, Fackelmayer FQ, Lipps HJ. (2004) Nuclear scaffold/matrix attached region modules linked to a transcription unit are sufficient for replication and maintenance of a mammalian episome. Proc Natl Acad Sci USA 101:11322-11327
Jeong SY, Peffer N, Meier I. (2004) Phosphorylation by protein kinase CKII modulates the DNA-binding activity of a chloroplast nucleoid-associated protein. Planta 219:298-302
Jeong SY, Rose A, Meier I. (2003) MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res 31:5175-5185
Jeong SY, Rose A, Meier I. (2003) MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res 31:5175-5185
Johns EW. (1982) The HMG Chromosomal Proteins. Academic Press, London Johnson CN and Levy LS. (2005) Matrix attachment regions as targets for retroviaral integration. J Virology 2:68-76
Kalos M and Fournier RE. (1995) Position-independent transgene expression mediated by boundary elements from apolipoprotein B chromatin domain. Mol Cell Bio 15:198-207
Karimi M, Inze D, Depicker A. (2002) GATEWAYTM vector for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193-195
Kas E, Izaurralde E and Laemmli UK. (1989) Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin. The role of oligo(dA).oligo(dT) tracts. J Mol Bio1210: 587-599
K?s E, Poljak L, Adachi Y and Laemmli UK (1993) A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin. EMBO J 12:115-126.
Kas E, Poljak L, Adachi Y, Laemmli UK. (1993) A model for chromatin opening: stimulation of topoisomerase-II and restriction enzyme cleavage of chromatin by distamycin. EMBO J 12: 115-126
Kas E, and Chasin LA. (1987) Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol 198:677-692
Kaul R, Mukherjee S, Ahmed F, Bhat MK, Chhipa R, Galande S, Chattopadhyay S. (2003) Direct interaction with and activation of p53 by SMAR1 retards cell-cycle progression at G2/M phase and delays tumor growth in mice. Int J Cancer 103:606-615.
Kaul-Ghanekar R, Jalota A, Pavithra L, Tucker P, Chattopadhyay S. (2004) SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRbeta enhancer (Ebeta). Nucleic Acids Res 32:4862-4875
Kawalleck P, Somssich IE, Feldbrügge M, Hahlbrock K, Weisshaar B. (1993) Polyubiquitin gene expression and structural properties of the ubi4-2 gene in Petroselinum crispum. Plant Mol Biol 21:673-684
Kerschen A, Napoli CA, Jorgensen RA,Muller AE. (2004) Effectiveness of RNA interference in transgenic plants. FEBS Lett 566:223-228
Kiledjian M, and Dreyfuss G. (1992) Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J 11:2655-2664
Kipp M, Gohring F, Ostendorp T, van Drunen CM, van Driel R, Przybylski M, Fackelmayer FO. (2000) SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA. Mol Cell Biol 20:7480-7489
Klosterman SJ, and Hadwiger LA. (2002) Plant HMG proteins bearing the AT-hook motif. Plant Sci 162: 855-866
Koch C, Str?tling WH. (2004) DNA binding of methyl-CpG-binding protein MeCP2 in human MCF7 cells. Biochemistry 43:5011-5021
Koga H, Deppert W. (2000) Identification of genomic DNA sequences bound by mutant p53 protein(Gly245-->Ser) in vivo. Oncogene 19:4178-83
Kohwi-Shigematsu T, Maass K, and Bode J. (1997) Athymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. Biochemistry 36: 12005-12010
Kozak M. (1991) Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem 266:19867–19870
Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR. (1994) Nucleosomedisruption and enhancement of activator binding by a human SW1/SNF complex. Nature 370:477–481
Laible G, Natt E, Seguin A, Doerner PW and Lamb CJ. (1994) A novel DNA-binding protein with histone H1 and high mobility group protein I/Y domains sandwiching a glutamine-rich tract interacts with an AT rich enhancer element of the bean PAL2 promoter.(unpublished): http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val= 555655
Larovaia OV, Akopov SB, Nikolaev LG, Sverdlov ED, Razin SV. (2005) Iuduction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix. Nucleic Acids Res 33:4157-4163
Lawit SJ, O'Grady K, Gurley WB, Czarnecka-Verner E. (2007) Yeast two-hybrid map of Arabidopsis TFIID. Plant Mol Biol 64:73-87
Lei JX, Liu QY, Sodja C, LeBlanc J, Ribecco-Lutkiewicz M, Smith B, Charlebois C, Walker PR, Sikorska M. (2005) S/MAR-binding properties of Sox2 and its involvement in apoptosis of human NT2 neural precursors. Cell Death Differ 12:1368-1377
Lei JX, Liu QY, Sodja C, LeBlanc J, Ribecco-Lutkiewicz M, Smith B, Charlebois C, Walker PR, Sikorska M. (2005) S/MAR-binding properties of Sox2 and its involvement in apoptosis of human NT2 neural precursors. Cell Death Differ.Nov 12:1368-1377
Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, Bird A. (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69:905-914
Li J, Brunner AM, Meilan R, Strauss SH. (2008) Matrix attachment region elements have small and variable effects on transgene expression and stability in field-grown Populus. Plant Biotechnol J 6:887-896
Li K, Cai R, Dai BB, Zhang XQ, Wang HJ, Ge SF, Xu WR, Lu J. (2007) SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron. Biochem Biophys Res Commun 356:6-12
Liebich I, Bode J, Reuter I, Wingender E (2002) Evaluation of sequence motifs found in scaffold/matrix-associated regions(S/MARs). Nucleic Acids Res 30:3433-3442
Lin HH, Hsu HL, Yeh NH. (2007) Apoptotic cleavage of NuMA at the C-terminal end is related to nuclear disruption and death amplification. J Biomed Sci 14:681-694
Liu JW, Tabe LM. (1998)The influences of two plant nuclear matrix attachment regions (MARs) on gene expression in transgenic plants. Plant Cell Physiol 39:115-23
Liu WM, Guerra-Vladusic FK, Kurakata S, Lupu R, Kohwi-Shigematsu T. (1999) HMG-I(Y)recognizes base-unpairing regions of matrix attachment sequences and its increased expression is directly linked to metastatic breast cancer phenotype. Cancer Res 59: 5695- 5703
Lobov IB, Tsutsui K, Mitchell AR, Podgornaya OI. (2001) Specificity of SAF-A and lamin B binding in vitro correlates with the satellite DNA bending state. J Cell Biochem 83: 218-229
Ludérus ME, de Graaf A, Mattia E, den Blaauwen JL, Grande MA, de Jong L, van Driel R. (1992) Binding of matrix attachment regions to lamin B1. Cell 70:949-959
Ludérus ME, den Blaauwen JL, de Smit OJ, Compton DA, van Driel R. (1994) Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove.Mol Cell Biol 14:6297-6305.
Makarevitch I and Somers DA. (2006) Association of Arabidopsis topoisomerase IIA cleavage sites with functional genomic elements and T-DNA loci. Plant journal 48: 697-709
Mankin S L,Allen G C,Phelan T,Spiker S, Thompson WF.(2003) Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3′MAR. Transgenic Res 12:3-12
Marsden MP, Laemmli UK. (1979) Metaphase chromosome structure: evidence for a radial loop model. Cell 17: 849-858
Martens JH, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A. (2002) Scaffold/Matrix Attachment Region Elements Interact with a p300-Scaffold Attachment Factor A Complex and Are Bound by Acetylated Nucleosomes. Mol Cell Biol 22: 2598-2606
McElroy D, Blowers AD, Jenes B, Wu R. (1991) Construction of expression vectors based on the rice actin 1 (Act1) 5' region for use in monocot transformation. Mol Gen Genet 231:150-160
Meehan RR, Lewis JD, Bird AP. (1992) Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA. Nucleic Acids Res 20: 5085-5092
Meier I, Phelan T, Gruissem W, Spiker S, Schneider D. (1996) MFP1, a novel plant filament-like protein with affinity for matrix attachment region DNA. Plant Cell 8:2105-2115
Michalowski SM, Allen GC, Hall GE Jr, Thompson WF, Spiker S. (1999) Characterization of randomly-obtained matrixattachment regions (MARs) from higher plants. Biochemistry 38: 12795-12804
Mirkovitch J, Mirault ME and Laemmli UK. (1984) Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39:223-232.
Mlynarova L, Jansen RC, Conner AJ, Stiekema WJ, and Nap JP. (1995) The MAR-Mediated Reduction in Position Effect Can Be Uncoupled from Copy Number- Dependent Expression in Transgenic Plants. Plant Cell 7: 599-609
Montazer-Torbati MB, Hue-Beauvais C, Droineau S, Ballester M, Coant N, Aujean E, Petitbarat M, Rijnkels M, Devinoy E. (2008) Epigenetic modifications and chromatin loop organization explain the different expression profiles of the Tbrg4, WAP and Ramp3 genes. Exp Cell Res 314:975-987
Moreira PN, Pérez-Crespo M, Ramírez MA, Pozueta J, Montoliu L, Gutiérrez-Adán A. (2007) Effect of transgene concentration, flanking matrix attachment regions, and RecA-coating on the efficiency of mouse transgenesis mediated by intracytoplasmic sperm injection. Biol Reprod 76:336-343
Morisawa G, Han-Yama A, Moda I, Tamai A, Iwabuchi M, Meshi T. (2000) AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12:1903-1916
Moritani K, Tagashira H, Shimotori T, Sakamoto N, Tanaka S, Takata K, Mitsunaga- Nakatsubo K, Bojiiwa Y, Yamamoto T, Shimada H, Akasaka K. (2004) A new G-stretch- DNA-binding protein, Unichrom, displays cell-cycle-dependent expression in sea urchin embryos. Dev Growth Differ 46:335-341
Murakami K, Fujita N, Ishihama A. (1996) Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element. EMBO J 15:4358-4367
Nabirochkin S, Ossokina M, Heidmann T. (1998) A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence. J Biol Chem 273: 2473- 2479
Nagata T, Nemoto Y, Hasezawa S. (1992) Tobacco BY-2 cell line as the Hela-cell in the cell biology of higher plants. Int Rev Cytool 132:1-30
Nagaya S, Yoshida K, Kato K, Akasaka K, Shinmyo A. (2001) An insulator element from the sea urchin Hemicentrotus pulcherri-mus suppresses variation in transgene expression in cultured tobacco cells. Mol Genet Genomics 265:405-413
Nakagomi K, Kohwi Y, Dickinson LA and Kohwi-Shigematsu T. (1994) A novel DNA- binding motif in the nuclear matrix attachment DNA-binding protein SATB1. Mol CellBiol 14:1852-1860
Nakayasu H and Berezney R. (1991) Nuclear matrins: identification of the major nuclear matrix proteins. Proc Natl Acad Sci USA 88: 10312–10316
Namciu SJ, Blochlinger KB, Fournier RE. (1998) Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol 18:2382-2391
Namciu SJ, Fournier RE. (2004) Human matrix attachment regions are necessary for the establishment but not the maintenance of transgene insulation in Drosophila melanogaster. Mol Cell Biol 24:10236-10245
Nap JP, van Spanje M, Dirkse WG, Baarda G, Mlynarova L, Loonen A, Grondhuis P, Stiekema WJ. (1993) Activity of the promoter of the Lhca3.St.1 gene, encoding the potato apoprotein 2 of the light-harvesting complex of Photosystem I, in transgenic potato and tobacco plants. Plant Mol Biol 23:605-612
Nayler O, Str?tling W, Bourquin JP, Stagljar I, Lindemann L, Jasper H, Hartmann AM, Fackelmayer FO, Ullrich A, Stamm S. (1998) SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements. Nucleic Acids Res 26:3542-3549
Nieto-Sotelo J, Ichida A, Quail PH. (1994) PF1: An A-T hook containing DNA binding protein from rice that interacts with a functionally defined d(AT)-rich element in the oat phytochrome A3 gene promoter. Plant Cell 6:287-301
Nikolaev LG, Tsevegiyn T, Akopov SB, Ashworth LK, Sverdlov ED. (1996) Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19. Nucleic Acids Res 24:1330-1336
Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FH. (2005) Structure of PTB bound to RNA: specific binding and implications for splicing regulation. 309:2054-2057
Obrdlik A, Kukalev A, Louvet E, Ostlund Farrants AK, Caputo L, Percipalle P. (2008) The histone acetyl transferase PCAF associates with actin and hnRNP U for RNA polymerase II transcription. Mol Cell Biol 28:6342-6357
Oh SJ, Jeong JS, Kim EH, Yi NR, Yi SI, Jang IC, Kim YS, Suh SC, Nahm BH, Kim JK (2005) Matrix attachment region from the chicken lysozyme locus reduces variability in transgene expression and confers copy number-dependence in transgenic rice plants. Plant Cell Rep 24:145-154
Onishi Y, Hanai S, Ohno T, Hara Y, Ishida N. (2008) Rhythmic SAF-A binding underliescircadian transcription of the Bmal1 gene. Mol Cell Biol 28:3477-3488
Orphanides G, Reinberg D. (2000) RNA polymerase II elongation through chromatin. Nature 407:471-475
Outchkourov NS, Peters J, de Jong J, Rademakers W, Jongsma MA. (2003) The promoter- terminator of chrysanthemum rbcS1 directs very high expression levels in plants. Planta 2216:1003-1012
Ow DW, Jacobs JD, Howell SH. (1987) Functional regions of the cauliflower mosaic virus 35S RNA promoter determined by use of the firefly luciferase gene as a reporter of promoter activity. Proc Natl Acad Sci USA 84:4870-4874
Park JY, Canam T, Kang KY, Ellis DD, Mansfield SD. (2008) Over-expression of an arabidopsis family A sucrose phosphate synthase (SPS) gene alters plant growth and fibre development. Transgenic Res 17:181-192
Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I. ( 2004) Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. Plant Cell 16:3260-3273
Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I. (2004) Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. Plant Cell 16:3260-3273
Pauli U, Chiu JF, Ditullio P, Kroeger P, Shalhoub V, Rowe T, Stein G, Stein J. (1989) Specific interactions of histone H1 and a 45 kilodalton nuclear protein with a putative matrix attachment site in the distal promoter region of a cell cycle-regulated human histone gene. J Cell Physiol 139:320-328
Paulson JR, Laemmli UK. (1977) The structure of histone-depleted metaphase chromosomes. Cell 12:817-828
Petersen K, Leah R, Knudsen S, Cameron-Mills V. (2002) Matrix attachment regions (MARs) enhance transformation frequencies and reduce variance of transgene expression in barley. Plant Mol Biol 49:45-58
Petrov A, Allinne J, Pirozhkova I, Laoudj D, Lipinski M, Vassetzky YS. (2008) A nuclear matrix attachment site in the 4q35 locus han an enhance-bloking activity in vivo: Implications for the facio-scapulo-humeral dystrophy. Genome Res 18:39-45
Phi-Van L and Stratling WH. (1996) Dissection of the ability of the chicken lysozyme gene 5′matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry 35:10735-10742
Phi-Van L, von Kries JP, Ostertag W, Str?tling WH. (1990) The chicken lysozyme 5' matrix attachment region increases transcription from a heterologous promoter in heterologous cells and dampens position effects on the expression of transfected genes. Mol Cell Biol 10:2302-2307
Pienta KJ, Getzenberg RH, Coffey DS. Cell structure and DNA organization. (1991) Crit Rev Eukaryotic Gene Expression 1:355-385
Poulsen C, Fluhr R, Kauffman JM, Boutry M and Chua NH. (1986) Characterization of an rbcS gene from Nicotiana plumbaginifolia and expression of an rbcS-CAT chimeric gene in homologous and heterologous nuclear background.Mo. Gen Genet 205:193-200
Rampalli S, Pavithra L, Bhatt A, Kundu TK, Chattopadhyay S. (2005) Tumor suppressor SMAR1 mediates cyclin D1 repression by recruitment of the SIN3/histone deacetylase 1 complex. Mol Cell Biol 25:8415-8429
Rampitsch C, Jordan MC, Cloutier S. (2000) A matrix attachment region is located upstream from the high-molecular-weight glutenin gene Bx7 in wheat (Triticum aestivum L.). Genome 43:483-486
Rao S, Procko E, Shannon MF. (2001) Chromatin remodelling, measured by a novel real-time polymerase chain reaction assay, across the proximal promoter region of the IL-2 gene. J Immunol 167:4494-4503
Reeves R, Adair JE. (2005) Role of high mobility group (HMG) chromatin proteins in DNA repair. DNA Repair (Amst) 4:926-38
Renz A, Fackelmayer FO. (1996) Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA. Nucleic Acids Res 24:843-849
Romig H, Fackelmayer FO, Renz A, Ramsperger U, Richter A. (1992) Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. EMBO J 11:3431-3440
Romig H, Ruff J, Fackelmayer FO, Patil MS, and Richter A. (1994) Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. Eur J Biochem 221:411-419
Ronai D, Berru M, Shulman MJ. (1999) Variegated expression of the endogenous immunoglobulin heavy-chain gene in the absence of the intronic locus control region. Mol Cell Biol 19:7031-7040
Rose A, Gindullis F, Meier I. (2003) A novel alpha-helical protein, specific to and highlyconserved in plants, is associated with the nuclear matrix fraction. J Exp Bot 54:1133-41
Ross W, Ernst A, Gourse RL. (2001) Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove. Genes Dev 15: 491- 506
Rudd S, Frisch M, Grote K, Meyers BC, Mayer K, Werner T. (2004) Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol 135:715-722
Samaniego R, de la Torre C, Moreno Díaz de la Espina S. (2008) Characterization, expression and subcellular distribution of a novel MFP1 (matrix attachment region-binding filament-like protein 1) in onion. Protoplasma 233:31-38
Samaniego R, Jeong SY, de la Torre C, Meier I, Moreno Díaz de la Espina S. (2006) CK2 phosphorylation weakens 90 kDa MFP1 association to the nuclear matrix in Allium cepa. J Exp Bot 57:113-24
Samaniego R, Jeong SY, Meier I, de la Espina SM. (2006) Dual location of MAR-binding, filament-like protein 1 in Arabidopsis,tobacco and tomato. Planta 223:1201-1206
Sander M, Hsieh T (1983) Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem 258:8421-8428
Samaniego R, Jeong SY, Meier I, de la Espina SM. (2006) Dual location of MAR-binding, filament-like protein 1 in Arabidopsis, tobacco, and tomato. Planta 223:1201-1206
Sass AV, Ruda VM, Akopov SB, Snezhkov EV, Nikolaev LG, Sverdlov ED. (2005) Regulatory potential of S/MAR elements in transient expression. Bioorg Khim 31:77-81
Shao X,Grishin NV. (2000) Common fold in helix–hairpin–helix proteins. Nucleic Acids Res 28:2643-2650
Shaposhnikov SA, Akopov SB, Chernov IP, Thomsen PD, Joergensen C, Collins AR, Frengen E, Nikolaev LG. (2007) A map of nuclear matrix attachment regions within the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1. Genomics 89: 354-361
Sidorenko L, Bruce W, Maddock S, Tagliani L, Li X, Daniels M, Peterson T. (2003)
Functional analysis of two matrix attachment region (MAR) elements in transgenic maize plants. Transgenic Res 12:137-154
Slatter RE, Dupree P, Gray JC. (1991) A scaffold-qssociated DNA region is located downstream of the Pea plastocyanin gene. Plant Cell 3:1239-1250
Sobol M, Gonzalez-Camacho F, Rodríguez-Vilari?o V, Kordyum E, Medina FJ. (2006) Subnucleolar location of fibrillarin and NopA64 in Lepidium sativum root meristematic cells is changed in altered gravity. Protoplasma 228:209-219
Spiker S and Thompson W F. (1996) Nuclear matrix attachment regions and transgene expression in plants. Plant Physiol 110:15-21
Spitzner JR, Muller MT. (1988) A consensus sequence for cleavage by vertebrate DNA topoismerase II. Nucleic Acids Res 16:5533-5556
Starr DB, Hawley DK. (1991) TFIID binds in the minor groove of the TATA box. Cell 67:1231-1240
Stokes DG and Perry RP. (1995) DNA-binding and chromatin localization properties of CHD1. Mol Cell Biol 15:2745-2753
Str?tling WH, Yu F. (1999) Origin and roles of nuclear matrix proteins. Specific functions of the MAR-binding protein MeCP2/ARBP.Crit Rev Eukaryot Gene Expr. 9:311-318
Tagashira H, Shimotori T, Sakamoto N, Katahira M, Miyanoiri Y, Yamamoto T, Mitsunaga- Nakatsubo K, Shimada H, Kusunoki S, Akasaka K.(2006)Unichrom, a novel nuclear matrix protein, binds to the Ars insulator and canonical MARs. Zoolog Sci 23:9-21
Taimen P, Bergh?ll H, Vainionp?? R, Kallajoki M. (2004) NuMA and nuclear lamins are cleaved during viral infection-inhibition of caspase activity prevents cleavage and rescues HeLa cells from measles virus-induced but not from rhinovirus 1B-induced cell death. Virology 320:85-98
Taimen P, Kallajoki M. (2003) NuMA and nuclear lamins behave differently in Fas-mediated apoptosis. J Cell Sci 116:571-583
Tajima S, Shinohara K, Fukumoto M, Zaitsu R, Miyagawa J, Hino S, Fan J, Akasaka K, Matsuoka M. (2006) Ars insulator identified in sea urchin possesses an activity to ensure the transgene expression in mouse cells. J Biochem 139:705-714
Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF. (2006) Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol 2:136-145
Thomas JO, Travers AA. (2001) HMG1 and 2, and related architectural DNA-binding proteins. Trends Biochem Sci 26:167-174
Torney F, Partier A, Says-Lesage V, Nadaud I, Barret P, Beckert M. (2004) Heritable transgene expression pattern imposed onto maize ubiquitin promoter by maize adh-1 matrix attachment regions: tissue and developmental specificity in maize transgenic plants.Plant Cell Rep 22:931-938
Tsutsui K, Okada S, Watarai S, Seki S, Yasuda T, Shohmori T. (1993) Identification and charaterization of a nuclear scaffold protein that bids the matrix attachment region DNA. J Biol Chem 268:12886-12894
ülker B, Allen GC, Thompson WF, Spiker S, Weissinger AK. (1999) A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants. The Plant Journal 18(3):253-263
Vain P, James A, Worland B, Snape W. (2002) Transgene behaviour across two generations in a large random population of transgenic rice plants produced by particle bombardment. Theor Appl Genet 105:878-889
Van der Geest AH, Hall GE Jr, Spiker S and Hall TC. (1994) Theβ-phaseolin gene is flanked by matrix attachment regions. Plant J 6:413-423
van der Geest AH, Hall TC (1997) Theβ-phaseolin 5′matrix attachment region acts as an enhancer facilitator. Plant Mol Biol 33:553-557
Van der Geest AH, Welter ME, Woosley AT, Pareddy DR, Pavelko SE, Skokut M, Ainley WMA. (2004) short synthetic MAR positively affects transgene expression in rice and Arabidopsis. Plant Biotechnol J 2:13-26
van Drunen CM, Oosterling RW, Keultjes GM, Weisbeek PJ, van Driel R, Smeekens SC. (1994) Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana. Nucleic Acids Res 25:3904-3911
Van Leeuwen W, Mlynarova L, Nap JP, van der Plas LH, van der Krol AR. (2001) The effect of MAR elements on variation in spatial and temporal regulation of transgene expression. Plant Mol Biol 47:543–554
Wang B, Dickinson LA, Koivunen E, Ruoslahti E, Kohwi-Shigematsu T. (1995) A novel matrix attachment region DNA binding motif identified using a random phage peptide library. J Biol Chem 270:23239-23242
Wang TY, Xue LX, Hou WH, Yang BS, Chai YR, Ji X, Wang YF. (2007) Increased expression of transgene in stably transformed cells of Dunaliella salina by matrix attachment regions. Appl Microbiol Biotechnol 76:651-657
Wang Z, Goldstein A, Zong RT, Lin D, Neufeld EJ, Scheuermann RH, Tucker PW. (1999) Cux/CDP homeoprotein is a component of NF-muNR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the bright transcription activator. Mol CellBiol 19:284-295.
Webster CI, Cooper MA, Packman LC, Williams DH, Gray JC. (2000) Kinetic analysis of high-mobility-group proteins HMG-1 and HMG-I/Y binding to cholesterol-tagged DNA on a supported lipid monolayer. Nucleic Acids Res 28:1618-1624
Webster CI, Packman LC, Gray JC. (2001) HMG-1 enhances HMG-I/Y binding to an A/T-rich enhancer element from the pea plastocyanin gene. Eur J Biochem 268: 3154-3162
Weitzel JM, Buhrmester H, and Stratling WH. (1997) Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG- binding protein MeCP2. Mol Cell Biol 17: 5656- 5666
Wong RW, Blobel G, Coutavas E. (2006) Rae1 interaction with NuMA is required for bipolar spindle formation.Proc Natl Acad Sci USA 103:19783-19787
Wu Q, Zhang W, Pwee KH, Kumar PP. (2003) Rice HMGB1 protein recognizes DNA structures and bends DNA efficiently. Arch Biochem Biophys 411:105-111
Xin L, Liu D P, Ling CC. (2003) A hypothesis for chromatin domain opening. Bioessays 25:507-514
Xue H, Yang Y T, Wu CA, Yang G.D, Zhang MM, Zheng CC. (2005) TM2, a novel strong matrix attachment region isolated from tobacco, increases transgene expression in transgenic rice calli and plants. Theor Appl Genet. 110:620-627
Yajima M, Kiyomoto M, Akasaka K. (2007) Ars insulator protects transgenes from long-term silencing in sea urchin larva. Dev Genes Evol 217:331-336
Yamaguchi H, Tateno M and Yamasaki K. (2006) Solution structure and DNA-binding mode of the matrix attachment region-binding domain of the transcriptional factor SATB1 that regulates the T-cell maturation. J Biol Chem 281:5319-5327
Yamasaki K, Akiba T, Yamasaki T and Harata K. (2007) Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1. Nucleic Acids Res 35: 5073-5084
Yan LY, Huang JC, Zhu ZY, Lei ZL, Shi LH, Nan CL, Zhao ZJ, Ouyang YC, Song XF, Sun QY, Chen DY. (2006) NuMA distribution and microtubule configuration in rabbit oocytes and cloned embryos.Reproduction 132:869-876.
Yanagisawa J, Ando J, Nakayama J, Kohwi Y, and Kohwi-Shigematsu T. (1996) A matrix attachment region (MAR)-binding activity due to a p114 kilodalton protein is found only in human breast carcinomas and not in normal and benign breast disease tissues. Cancer Res 56:457-462
Yang YT, Yang GD, Liu SJ, Guo XQ, Zheng CC. (2003) Isolation and functional analysis of a strong specific protmoter in photosynthetic tissues. Sci China Life C 46:652-660
Yasui D, Miyano M, Cai S, Varga-Weisz P, Kowhi-Shigematsu T. (2002) SATB1 targets chromatin remodeling to regulate genes over long distances. Nature 419:641-645
Youn BS, Lim CL, Shin MK, Hill JM, Kwon BS. (2002) An intronic silencer of the mouse perforin gene. Mol Cells 13:61-68
Chua YL, Pwee KH, Kini RM. (2001) DNA binding mediated by the wheat HMGa protein: a novel instance of selectivity against alternating GC sequence. Plant Mol Biol 46:193-204
Yugami M, Kabe Y, Yamaguchi Y, Wada T, Handa H. (2007) hnRNP-U enhances the expression of specific genes by stabilizing mRNA. FEBS Lett 581:1-7
Yukawa Y, Sugita M, Choisne N, Small I, Sugiura M. (2000) The TATA motif, the CAA motif and the poly(T) transcription termination motif are all important for transcription re-initiation on plant tRNA genes. Plant J 22:439-447
Zhang MM, Ji LS, Xue H, Yang YT, Wu CA, Zheng CC. (2007) High transformation frequency of tobacco and rice via Agrobacteriu-mediated gene transfer by flanking a tobacco matrix attachment region. Physiol Plantarum 120:644-651
Zhang W, Wu Q, Pwee KH, Jois SDS, Kini RM. (2003a) Characterization of the interaction of wheat HMGa with linear and four-way junction DNA. Biochemistry 42:6596–6607
Zhang W, Wu Q, Pwee KH, Kini RM. (2003b) Interaction of wheat high-mobility-group proteins with four-way-junction DNA and characterization of the structure and expression of HMGA gene. Arch Biochem Biophys 409:357-366
Zhao K, Kas E, Gonzalez E, Laemmli UK. (1993) SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J 12: 3237-3247
Zuo ZH, Li B, Wang CG, Cai JL, Chen YX. (2007) Increasing transient expression of CAT gene in Porphyra haitanensis by matrix attachment regions and 18S rDNA targeted homologous recombination. Aguacultrue Res 38:681-688
李旭刚,朱祯,徐军望,吴茜,徐鸿林. (2001)豌豆核基质结合区的分离及其在转基因烟草中的功能分析。中国科学C辑3:230-237
李旭刚,陈松彪,徐军望,刘翔,朱祯.(2002)玉米MAR序列的分离及其在转基因烟草中的功能研究。自然科学进展5:491-496
Abad PC, Lewis J, Mian IS, Knowles DW, Sturgis J, Badve S, Xie J, Lelièvre SA. (2007) NuMA influences higher order chromatin organization in human mammary epithelium. Mol Biol Cell 18:348-361
Adachi Y, Kas E, Laemmli UK. (1989) Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J 8:3997-4006
Akasaka K, Nishimura A, Takata K, Mitsunaga K, Mibuka F, Ueda H, Hirose S, Tsutsui K, Shimada H. (1999) Upstream element of the sea urchin arylsufatase gene serves as an insulator. Cell Mol Biol 45:555–565
Allen GC, Hall G Jr, Michalowski S, Newman W, Spiker S, Weissinger AK, Thompson WF. (1996) High-level transgene expression in plant cells:effects of a strong scaffold attachment region from tobacco. Plant Cell 8:899-913
Allen GC, Hall GE Jr, Childs LC, Weissinger AK, Spiker S, Thompson WF. (1993) Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. Plant Cell. 5:603-13
Allen GC, Spiker S, Thompson WF. (2000) Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol Biol 43:361-376
Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, and Kohwi-Shigematsu T. (2000) The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. Genes & Dev 14: 521-535
Amirand C, Viari A, Ballini JP, Rezaei H, Beaujean N, Jullien D, K?s E, Debey P. (1998) Three distinct sub-nuclear populations of HMG-I protein of different properties revealed by co-localization image analysis. J Cell Sci 111:3551-3561
Antes TJ,Namicu SJ,Fournier RE and Levy-Wilson B. (2001) The 5′-boundary of the human apolipoprotein B chromatin domain in intestinal cells. Biochemistry 40:6731-6742
Aravind L, Landsman D. (1998) AT-hook motifs identified in a wide variety of DNA-bindingproteins. Nucleic Acids Res 26:4413-4421
Avramova Z, Sanmiguel P, Georgieva E, Bennetzen JL. (1995) Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. Plant Cell 7:1667-1680
Banerjee S, Fisher O, Lohia A, Ankri S. (2005) Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR). Mol Biochem Parasitol 139:91-97
Banerjee S, Fisher O, Lohia A, Ankri S. (2005) Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR). Mol Biochem Parasitol139:91-97.
Belshaw NJ, Hakola S, Nevalanien, Penttil? M, Suominen P, Archer DB. (1997) Trichoderma reesei sequences that bind to the nuclear matrix enhance transformation frequency. Mol Gen Genet 256:18-27
Benfey PN, Ren L, Chua NH. (1990) Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. EMBO J 9:1685-1696
Berezney R and Coffey DS. (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1470
Bianchi ME, Agresti A. (2005) HMG proteins: Dynamic players in gene regulation and differentiation. Curr Opin Genet Dev 15: 496-506
Blatter EE, Ross W, Tang H, Gourse RL,Ebright RH. (1994) Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78:889-896
Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shgematsu T. (1992) Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255:195-197.
Bode J,Stengert-Iber,Kay V,Schlacker T and Dietz-Pfeilstetter A. (1996) Scaffold/ matrix- attached regions:topological switches with multiple regulatory functions. Crit Rev Eukaryot Gene Expr 6:115-138
Boulikas T. (1994) Transcription factor binding sites in the matrix attachment region (MAR) of the chicken alpha-globin gene. J Cell Biochem 55:513-529
Breyne P, Vanmontagu M, Depicker A, Gheysen G (1992) Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco. Plant Cell 4:463-471
Brouwer C, Bruce W, Maddock S, Avramova Z, Bowen B. (2002) Suppression of transgnene silencing by matrix attachment regions in maize: a dual role for the maize 5′-ADH1 matrix attachment region. Plant cell 14:2251-2264
Brummell DA, Balint-Kurti PJ, Harpster MH, Palys JM, Oeller PW, Gutterson N. (2003) Inverted repeat of a heterologous 3'-untranslated region for high-efficiency, high-throughput gene silencing.Plant J 33:793-800
Brunner E, Weitzel J, Heitmann B, Maurer T, Str?tling WH, Kalbitzer HR. (2000) Sequence-specific 1H, 13C, and 15N assignments of the MAR-binding domain of chicken MeCP2/ARBP. J Biomol NMR 17:175-176
Bustin M, Reeves R. (1996) High-mobility-group chromosomal proteins: Architectural components that facilitate chromatin function. Prog Nucleic Acid Res Mol Biol 54:35- 100
Byrd K, Corces VG. (2003)Visualization of chromatin domains created by the gypsy insulator of Drosophila. J. Cell Biol 162: 565-574
Cai S, Han HJ, Kohwi-Shigematsu T. (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat Genet 34:4-6
Chattopadhyay S, Kaul R, Charest A, Housman D, Chen J. (2000) SMAR1, a novel, alternatively spliced gene product, binds the Scaffold/Matrix-associated region at the T cell receptor beta locus. Genomics 68:93-96
Chattopadhyay S, Pavithra L. (2006) MARs and MARBPs: key modulators of gene regulation and disease manifestation. Subcell Biochem 41:213-230
Cheng ZQ, Targlli J, Wu R. (2001) Tobacco matrix attachment region sequence increased transgene expression levels in rice plants. Mol Breeding 7:317-327
Chua YL, Pwee KH, Kini RM (2001) DNA binding mediated by the wheat HMGa protein: a novel instance of selectivity against alternating GC sequence. Plant Mol Biol 46:193-204
Chuang CF, Meyerowitz EM. (2000) Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:4985-4990
Coleman HD, Ellis DD, Gilbert M, Mansfield SD. (2006) Up-regulation of sucrose synthase and UDP-glucose pyrophosphorylase impacts plant growth and metabolism. Plant Biotechnol J 4:87-101
Crichlow GV, Zhou H, Hsiao HH, Frederick KB, Debrosse M, Yang Y, Folta-Stogniew EJ, Chung HJ, Fan C, De la Cruz EM, Levens D, Lolis E, Braddock D. (2008) Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition. EMBO J27:277-289
Cunningham JM, Purucker ME, Jane SM, Safer B, Vanin EF, Ney PA, Lowrey CH, Nienhuis AW. (1994) The regulatory element 3' to the A gamma-globin gene binds to the nuclear matrix and interacts with special A-T-rich binding protein 1 (SATB1), an SAR/ MAR-associating region DNA binding protein. Blood 184:1298-1308
Curtis MD, Grossniklaus U. (2003) A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133:462-469
Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T. (2007) pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants.Plant Physiol 145:1272-1281
Dang Q, Auten J, and Plavec I. (2000) Human Beta Interferon Scaffold Attachment Region Inhibits De Novo Methylation and Confers Long-Term, Copy Number-Dependent Expression to a Retroviral Vector. J Virol 74: 2671- 2678
De Amicis F, Patti T, Marchetti S. (2007) Improvement of the pBI121 plant expression vector by leader replacement with a sequence combining a poly(CAA) and a CT motif. Transgenic Res 16:731-738
De Bolle MF, Butaye KM, Goderis IJ, Wouters PF, Jacobs A, DelauréSL, Depicker A, Cammue BP. (2007) The influence of matrix attachment regions on transgene expression in Arabidopsis thaliana wild type and gene silencing mutants. Plant Mol Biol 63:533-543
De Bolle MFC, Butaye KMJ, Coucke WJW, Goderis IJWM, Wouters PFJ, van Boxel N, Broekaert WF, Cammue BPA (2003) Analysis of the influence of promoter elements and a matrix attachment region on the inter-individual variation of transgene expression in populations of Arabidopsis thaliana. Plant Sci 165:169-179
Dickinson LA, Kohwi-Shigematsu T. (1995) Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential. Mol Cell Biol 15:456-465.
Dietz A, Kay V,Schlacker T, Landsmann J and Bode J. (1994) A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells. Nucleic Acids Res 22: 2744-2751
Dietz-Pfeilstetter A, Arndt N, Kay V, Bode J. (2003) Molecular structure and regulatory potential of a T-DNA integration site in petunia. Transgenic Res 12:83-99
Dobreva G, Dambacher J, Grosschedl R. (2003) SUMO modification of a novel MAR-binding protein, SATB2, modulates immunoglobulin mu gene expression. Genes Dev 17:3048- 3061
Fackelmayer FO, Dahm K, Renz A, Ramsperger U, Richter A. (1994) Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur J Biochem 221:749-757
Ferguson M, Henry PA, Currie RA. (2003) Histone deacetylase inhibition is associated with transcriptional repression of the Hmga2 gene. Nucleic Acids Res 131:3123-3133
Fiorini A, Gouveia Fde S, Fernandez MA. (2006) Scaffold/Matrix Attachment Regions and intrinsic DNA curvature. Biochemistry (Mosc) 71:481-488
Fisher O, Siman-Tov R, Ankri S. (2006) Pleiotropic phenotype in Entamoeba histolytica overexpressing DNA methyltransferase (Ehmeth). Mol Biochem Parasitol 147:48-54
Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K. (2004) Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces.Plant Mol Biol 56:225-239
Dickinson LA, Joh T, Kohwi Y and Kohwi-ShigematsuT. (1992) A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70: 631-645
Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K. (2004) Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol Biol 56:225-239
Fujiwara S, Matsuda N, Sato T, Sonobe S, Maeshima M. (2002) Molecular properties of a matrix attachment region-binding protein located in the nucleoli of tobacco cells. Plant Cell Physiol 43:1558-1567
Fukuda Y, Nishikawa S. (2003) Matrix attachment regions enhance transcription of a downstream transgene and the accessibility of its promoter region to Micrococcal nuclease. Plant Mol Biol 51:665-675
Fukuda Y. (1999) Characterization of matrix attachment sites in the upstream region of a tobacco chitinase gene. Plant Mol Biol 39:1051-1062
Gaal T, Ross W, Blatter EE, Tang H, Jia X, Krishnan VV, Assa-Munt N, Ebright RH, Gourse RL. (1996) DNA-binding determinants of theαsubunit of RNA polymerase: Novel DNA-binding domain architecture. Genes & Dev 10:16-26
Gallie DR. (1993) Posttranscriptional regulation of gene expression in plants. Ann Rev Plant Physiol Plant Mol Biol 44:77-105
Gallie DR. (2002) The 5′-leader of tobacco mosaic virus promotes translation through enhanced recruitment of eIF4F. Nucleic Acids Res 30:3401-3411
Gallie DR. (2002) The 5'-leader of tobacco mosaic virus promotes translation throughenhanced recruitment of eIF4F. Nucleic Acids Res 30:3401-3411
Gasser SM, Laemmli UK. (1986) Cohabitation of scaffold binding regions with upstream/ enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46:521-530
Gindullis F and Meier I. (1999) Matrix attachment region binding protein MFP1 is localized in discrete domains at the nuclear envelope. Plant Cell 11:1755-68
Gindullis F, Peffer NJ, Meier I. (1999) MAF1, a novel plant protein interacting with matrix attachment region binding protein MFP1, is located at the nuclear envelope. Plant Cell 11:1755-1768
Glazko GV, Koonin EV, Rogozin IB, Shabalina SA(.2003)A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 19:119-124
Gourse RL, Ross W, Gaal T. (2000) UPs and downs in bacterial transcription initiation: The role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37:687-695
Grasser KD, Krech AB, Feix G. (1994) The maize chromosomal HMGa protein recognises structural features of DNA and increases DNA flexibility. Plant J 6: 351–358
Grasser KD, Launholt D. (2006) Chromatin-associated architectural HMGA and HMGB proteins assist transcription factor function. In Regulation of Transcription in Plants, K.D. Grasser, ed. (Oxford, UK: Blackwell Publishing) pp 54–78.
Gross CA, Chan C, Dombroski A, Gruber T, Sharp M, Tupy J, Young B. (1998) The functional and regulatory roles of ? factors in transcription. Cold Spring Harbor Symp Quant Biol 63:141–155
Hall G Jr, Allen GC, Loer DS, Thompson WF, Spiker S. (1991) Nuclear scaffold and scaffold-attachment regions in higher plants. Proc Natl Acad Sci USA 88:9320-9324
Halweg C, Thompson WF and Spiker S. (2005) The Rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tabacco cells:a flow cytometrix study. Plant Cell 17:418-429
Han KH, Ma CP, Strauss SH. (1997) Matrix attachment regions (MARs) enhance transformation frequency and transgene expression in polar. Transgenic Res 6:415-420
Harpster MH, Townsend JA, Jones JD, Bedbrook J, Dunsmuir P. (1988) Relative strengths of the 35S cauliflower mosaic virus, 1', 2', and nopaline synthase promoters in transformed tobacco sugarbeet and oilseed rape callus tissue. Mol Gen Genet 212:182-190
Hatton D, Gray JC. (1999) Two MAR DNA-binding proteins of the pea nuclear matrix identify a new class of DNA-binding proteins. Plant J 18:417-429
Hayward RS, Igarashi K, Ishihama A. (1991) Functional specialization within theα-subunit of Escherichia coli RNA polymerase. J Mol Biol 221:23-29
Heitmann B, Maurer T, Weitzel JM, Str?tling WH, Kalbitzer HR, Brunner E. (2003) Solution structure of the matrix attachment region-binding domain of chicken MeCP2. Eur J Biochem 270:3263-3270
Heng HH, Goetze S, Ye CJ, Guo L, Stevens J B, Bremer SW, Wykes SM, Bode J, Krawetz SA. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J Cell Sci 117:999-1008
Heng HH, Krawetz SA, Lu W, Bremer S, Liu G and Ye CJ. (2001) Re-defining the chromatin loop domain. Cytogenet Cell Genet 93:155-161.
Hibino Y, Ohzeki H, Sugano N, Hiraga K. (2000b) Transcription modulation by a rat nuclear scaffold protein, P130, and a rat highly repetitive DNA component or various types of animal and plant matrix or scaffold attachment regions. Biochem Biophys Res Commun 279:282-287
Hibino Y. (2000a) Functional arrangement of genomic DNA and structure of nuclear matrix. Yakugaku Zasshi. 120:520-533
Hino S, Fan J, Taguwa S, Akasaka K, Matsuoka M. (2004) Sea urchin insulator protects lentiviral vector from silencing by maintaining active chromatin structure. Gene Ther 11:819–828
Hisada-Ishii S, Ebihara M, Kobayashi N, Kitagawa Y. (2007)Bipartite nuclear localization signal of matrin 3 is essential for vertebrate cells. Biochem Biophys Res Commun 354:72-76
Holmes-Davis R, Comai L. (2002) The matrix attachment regions (MARs) associated with the Heat Shock Cognate 80 gene (HSC80) of tomato represent specific regulatory elements. Mol Genet Genomics 266:891-898
Imbalzano AN, Kwon, H, Green, MR, Kingston RE. (1994) Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370:481–485
Izaurralde E, Kas E, Laemmli UK. (1989) Highly preferential nude H1 assembly on sacffold-associated regions. J Mol Biol 210: 573-585
Izaurralde E, Kas E, Laemmli UK. (1989) High perferential nucleation of histone H1 assembly on scaffold-associated regions. J Mol Biol 210:573-583
Izumikawa K, Yanagida M, Hayano T, Tachikawa H, Komatsu W, Shimamoto A, Futami K, Furuichi Y, Shinkawa T, Yamauchi Y, Isobe T, Takahashi N. (2008) Association of human DNA helicase RecQ5beta with RNA polymerase II and its possible role in transcription. Biochem J 413:505-516
Jackson DA. (1997) Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol Biol Rep 24: 209-220
Jackson DA, Dickinson P, Cook PR. (1990) The size of chromatin loops in Hela cell. EMBO J 9:567-571
Jefferson RA. (1987) Assaying chimeric genes in plants: the GUS gene fusion system. Plant Mol Biol Rep 5:387-405
Jeneke AC, Stehle IM, Herrmann F, Eisenberger T, Baiker A, Bode J, Fackelmayer FQ, Lipps HJ. (2004) Nuclear scaffold/matrix attached region modules linked to a transcription unit are sufficient for replication and maintenance of a mammalian episome. Proc Natl Acad Sci USA 101:11322-11327
Jeong SY, Peffer N, Meier I. (2004) Phosphorylation by protein kinase CKII modulates the DNA-binding activity of a chloroplast nucleoid-associated protein. Planta 219:298-302
Jeong SY, Rose A, Meier I. (2003) MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res 31:5175-5185
Jeong SY, Rose A, Meier I. (2003) MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res 31:5175-5185
Johns EW. (1982) The HMG Chromosomal Proteins. Academic Press, London Johnson CN and Levy LS. (2005) Matrix attachment regions as targets for retroviaral integration. J Virology 2:68-76
Kalos M and Fournier RE. (1995) Position-independent transgene expression mediated by boundary elements from apolipoprotein B chromatin domain. Mol Cell Bio 15:198-207
Karimi M, Inze D, Depicker A. (2002) GATEWAYTM vector for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193-195
Kas E, Izaurralde E and Laemmli UK. (1989) Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin. The role of oligo(dA).oligo(dT) tracts. J Mol Bio1210: 587-599
K?s E, Poljak L, Adachi Y and Laemmli UK (1993) A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin. EMBO J 12:115-126.
Kas E, Poljak L, Adachi Y, Laemmli UK. (1993) A model for chromatin opening: stimulation of topoisomerase-II and restriction enzyme cleavage of chromatin by distamycin. EMBO J 12: 115-126
Kas E, and Chasin LA. (1987) Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol 198:677-692
Kaul R, Mukherjee S, Ahmed F, Bhat MK, Chhipa R, Galande S, Chattopadhyay S. (2003) Direct interaction with and activation of p53 by SMAR1 retards cell-cycle progression at G2/M phase and delays tumor growth in mice. Int J Cancer 103:606-615.
Kaul-Ghanekar R, Jalota A, Pavithra L, Tucker P, Chattopadhyay S. (2004) SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRbeta enhancer (Ebeta). Nucleic Acids Res 32:4862-4875
Kawalleck P, Somssich IE, Feldbrügge M, Hahlbrock K, Weisshaar B. (1993) Polyubiquitin gene expression and structural properties of the ubi4-2 gene in Petroselinum crispum. Plant Mol Biol 21:673-684
Kerschen A, Napoli CA, Jorgensen RA,Muller AE. (2004) Effectiveness of RNA interference in transgenic plants. FEBS Lett 566:223-228
Kiledjian M, and Dreyfuss G. (1992) Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J 11:2655-2664
Kipp M, Gohring F, Ostendorp T, van Drunen CM, van Driel R, Przybylski M, Fackelmayer FO. (2000) SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA. Mol Cell Biol 20:7480-7489
Klosterman SJ, and Hadwiger LA. (2002) Plant HMG proteins bearing the AT-hook motif. Plant Sci 162: 855-866
Koch C, Str?tling WH. (2004) DNA binding of methyl-CpG-binding protein MeCP2 in human MCF7 cells. Biochemistry 43:5011-5021
Koga H, Deppert W. (2000) Identification of genomic DNA sequences bound by mutant p53 protein(Gly245-->Ser) in vivo. Oncogene 19:4178-83
Kohwi-Shigematsu T, Maass K, and Bode J. (1997) Athymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. Biochemistry 36: 12005-12010
Kozak M. (1991) Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem 266:19867–19870
Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR. (1994) Nucleosomedisruption and enhancement of activator binding by a human SW1/SNF complex. Nature 370:477–481
Laible G, Natt E, Seguin A, Doerner PW and Lamb CJ. (1994) A novel DNA-binding protein with histone H1 and high mobility group protein I/Y domains sandwiching a glutamine-rich tract interacts with an AT rich enhancer element of the bean PAL2 promoter.(unpublished): http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val= 555655
Larovaia OV, Akopov SB, Nikolaev LG, Sverdlov ED, Razin SV. (2005) Iuduction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix. Nucleic Acids Res 33:4157-4163
Lawit SJ, O'Grady K, Gurley WB, Czarnecka-Verner E. (2007) Yeast two-hybrid map of Arabidopsis TFIID. Plant Mol Biol 64:73-87
Lei JX, Liu QY, Sodja C, LeBlanc J, Ribecco-Lutkiewicz M, Smith B, Charlebois C, Walker PR, Sikorska M. (2005) S/MAR-binding properties of Sox2 and its involvement in apoptosis of human NT2 neural precursors. Cell Death Differ 12:1368-1377
Lei JX, Liu QY, Sodja C, LeBlanc J, Ribecco-Lutkiewicz M, Smith B, Charlebois C, Walker PR, Sikorska M. (2005) S/MAR-binding properties of Sox2 and its involvement in apoptosis of human NT2 neural precursors. Cell Death Differ.Nov 12:1368-1377
Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, Bird A. (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69:905-914
Li J, Brunner AM, Meilan R, Strauss SH. (2008) Matrix attachment region elements have small and variable effects on transgene expression and stability in field-grown Populus. Plant Biotechnol J 6:887-896
Li K, Cai R, Dai BB, Zhang XQ, Wang HJ, Ge SF, Xu WR, Lu J. (2007) SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron. Biochem Biophys Res Commun 356:6-12
Liebich I, Bode J, Reuter I, Wingender E (2002) Evaluation of sequence motifs found in scaffold/matrix-associated regions(S/MARs). Nucleic Acids Res 30:3433-3442
Lin HH, Hsu HL, Yeh NH. (2007) Apoptotic cleavage of NuMA at the C-terminal end is related to nuclear disruption and death amplification. J Biomed Sci 14:681-694
Liu JW, Tabe LM. (1998)The influences of two plant nuclear matrix attachment regions (MARs) on gene expression in transgenic plants. Plant Cell Physiol 39:115-23
Liu WM, Guerra-Vladusic FK, Kurakata S, Lupu R, Kohwi-Shigematsu T. (1999) HMG-I(Y)recognizes base-unpairing regions of matrix attachment sequences and its increased expression is directly linked to metastatic breast cancer phenotype. Cancer Res 59: 5695- 5703
Lobov IB, Tsutsui K, Mitchell AR, Podgornaya OI. (2001) Specificity of SAF-A and lamin B binding in vitro correlates with the satellite DNA bending state. J Cell Biochem 83: 218-229
Ludérus ME, de Graaf A, Mattia E, den Blaauwen JL, Grande MA, de Jong L, van Driel R. (1992) Binding of matrix attachment regions to lamin B1. Cell 70:949-959
Ludérus ME, den Blaauwen JL, de Smit OJ, Compton DA, van Driel R. (1994) Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove.Mol Cell Biol 14:6297-6305.
Makarevitch I and Somers DA. (2006) Association of Arabidopsis topoisomerase IIA cleavage sites with functional genomic elements and T-DNA loci. Plant journal 48: 697-709
Mankin S L,Allen G C,Phelan T,Spiker S, Thompson WF.(2003) Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3′MAR. Transgenic Res 12:3-12
Marsden MP, Laemmli UK. (1979) Metaphase chromosome structure: evidence for a radial loop model. Cell 17: 849-858
Martens JH, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A. (2002) Scaffold/Matrix Attachment Region Elements Interact with a p300-Scaffold Attachment Factor A Complex and Are Bound by Acetylated Nucleosomes. Mol Cell Biol 22: 2598-2606
McElroy D, Blowers AD, Jenes B, Wu R. (1991) Construction of expression vectors based on the rice actin 1 (Act1) 5' region for use in monocot transformation. Mol Gen Genet 231:150-160
Meehan RR, Lewis JD, Bird AP. (1992) Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA. Nucleic Acids Res 20: 5085-5092
Meier I, Phelan T, Gruissem W, Spiker S, Schneider D. (1996) MFP1, a novel plant filament-like protein with affinity for matrix attachment region DNA. Plant Cell 8:2105-2115
Michalowski SM, Allen GC, Hall GE Jr, Thompson WF, Spiker S. (1999) Characterization of randomly-obtained matrixattachment regions (MARs) from higher plants. Biochemistry 38: 12795-12804
Mirkovitch J, Mirault ME and Laemmli UK. (1984) Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39:223-232.
Mlynarova L, Jansen RC, Conner AJ, Stiekema WJ, and Nap JP. (1995) The MAR-Mediated Reduction in Position Effect Can Be Uncoupled from Copy Number- Dependent Expression in Transgenic Plants. Plant Cell 7: 599-609
Montazer-Torbati MB, Hue-Beauvais C, Droineau S, Ballester M, Coant N, Aujean E, Petitbarat M, Rijnkels M, Devinoy E. (2008) Epigenetic modifications and chromatin loop organization explain the different expression profiles of the Tbrg4, WAP and Ramp3 genes. Exp Cell Res 314:975-987
Moreira PN, Pérez-Crespo M, Ramírez MA, Pozueta J, Montoliu L, Gutiérrez-Adán A. (2007) Effect of transgene concentration, flanking matrix attachment regions, and RecA-coating on the efficiency of mouse transgenesis mediated by intracytoplasmic sperm injection. Biol Reprod 76:336-343
Morisawa G, Han-Yama A, Moda I, Tamai A, Iwabuchi M, Meshi T. (2000) AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12:1903-1916
Moritani K, Tagashira H, Shimotori T, Sakamoto N, Tanaka S, Takata K, Mitsunaga- Nakatsubo K, Bojiiwa Y, Yamamoto T, Shimada H, Akasaka K. (2004) A new G-stretch- DNA-binding protein, Unichrom, displays cell-cycle-dependent expression in sea urchin embryos. Dev Growth Differ 46:335-341
Murakami K, Fujita N, Ishihama A. (1996) Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element. EMBO J 15:4358-4367
Nabirochkin S, Ossokina M, Heidmann T. (1998) A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence. J Biol Chem 273: 2473- 2479
Nagata T, Nemoto Y, Hasezawa S. (1992) Tobacco BY-2 cell line as the Hela-cell in the cell biology of higher plants. Int Rev Cytool 132:1-30
Nagaya S, Yoshida K, Kato K, Akasaka K, Shinmyo A. (2001) An insulator element from the sea urchin Hemicentrotus pulcherri-mus suppresses variation in transgene expression in cultured tobacco cells. Mol Genet Genomics 265:405-413
Nakagomi K, Kohwi Y, Dickinson LA and Kohwi-Shigematsu T. (1994) A novel DNA- binding motif in the nuclear matrix attachment DNA-binding protein SATB1. Mol CellBiol 14:1852-1860
Nakayasu H and Berezney R. (1991) Nuclear matrins: identification of the major nuclear matrix proteins. Proc Natl Acad Sci USA 88: 10312–10316
Namciu SJ, Blochlinger KB, Fournier RE. (1998) Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol 18:2382-2391
Namciu SJ, Fournier RE. (2004) Human matrix attachment regions are necessary for the establishment but not the maintenance of transgene insulation in Drosophila melanogaster. Mol Cell Biol 24:10236-10245
Nap JP, van Spanje M, Dirkse WG, Baarda G, Mlynarova L, Loonen A, Grondhuis P, Stiekema WJ. (1993) Activity of the promoter of the Lhca3.St.1 gene, encoding the potato apoprotein 2 of the light-harvesting complex of Photosystem I, in transgenic potato and tobacco plants. Plant Mol Biol 23:605-612
Nayler O, Str?tling W, Bourquin JP, Stagljar I, Lindemann L, Jasper H, Hartmann AM, Fackelmayer FO, Ullrich A, Stamm S. (1998) SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements. Nucleic Acids Res 26:3542-3549
Nieto-Sotelo J, Ichida A, Quail PH. (1994) PF1: An A-T hook containing DNA binding protein from rice that interacts with a functionally defined d(AT)-rich element in the oat phytochrome A3 gene promoter. Plant Cell 6:287-301
Nikolaev LG, Tsevegiyn T, Akopov SB, Ashworth LK, Sverdlov ED. (1996) Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19. Nucleic Acids Res 24:1330-1336
Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FH. (2005) Structure of PTB bound to RNA: specific binding and implications for splicing regulation. 309:2054-2057
Obrdlik A, Kukalev A, Louvet E, Ostlund Farrants AK, Caputo L, Percipalle P. (2008) The histone acetyl transferase PCAF associates with actin and hnRNP U for RNA polymerase II transcription. Mol Cell Biol 28:6342-6357
Oh SJ, Jeong JS, Kim EH, Yi NR, Yi SI, Jang IC, Kim YS, Suh SC, Nahm BH, Kim JK (2005) Matrix attachment region from the chicken lysozyme locus reduces variability in transgene expression and confers copy number-dependence in transgenic rice plants. Plant Cell Rep 24:145-154
Onishi Y, Hanai S, Ohno T, Hara Y, Ishida N. (2008) Rhythmic SAF-A binding underliescircadian transcription of the Bmal1 gene. Mol Cell Biol 28:3477-3488
Orphanides G, Reinberg D. (2000) RNA polymerase II elongation through chromatin. Nature 407:471-475
Outchkourov NS, Peters J, de Jong J, Rademakers W, Jongsma MA. (2003) The promoter- terminator of chrysanthemum rbcS1 directs very high expression levels in plants. Planta 2216:1003-1012
Ow DW, Jacobs JD, Howell SH. (1987) Functional regions of the cauliflower mosaic virus 35S RNA promoter determined by use of the firefly luciferase gene as a reporter of promoter activity. Proc Natl Acad Sci USA 84:4870-4874
Park JY, Canam T, Kang KY, Ellis DD, Mansfield SD. (2008) Over-expression of an arabidopsis family A sucrose phosphate synthase (SPS) gene alters plant growth and fibre development. Transgenic Res 17:181-192
Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I. ( 2004) Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. Plant Cell 16:3260-3273
Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I. (2004) Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. Plant Cell 16:3260-3273
Pauli U, Chiu JF, Ditullio P, Kroeger P, Shalhoub V, Rowe T, Stein G, Stein J. (1989) Specific interactions of histone H1 and a 45 kilodalton nuclear protein with a putative matrix attachment site in the distal promoter region of a cell cycle-regulated human histone gene. J Cell Physiol 139:320-328
Paulson JR, Laemmli UK. (1977) The structure of histone-depleted metaphase chromosomes. Cell 12:817-828
Petersen K, Leah R, Knudsen S, Cameron-Mills V. (2002) Matrix attachment regions (MARs) enhance transformation frequencies and reduce variance of transgene expression in barley. Plant Mol Biol 49:45-58
Petrov A, Allinne J, Pirozhkova I, Laoudj D, Lipinski M, Vassetzky YS. (2008) A nuclear matrix attachment site in the 4q35 locus han an enhance-bloking activity in vivo: Implications for the facio-scapulo-humeral dystrophy. Genome Res 18:39-45
Phi-Van L and Stratling WH. (1996) Dissection of the ability of the chicken lysozyme gene 5′matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry 35:10735-10742
Phi-Van L, von Kries JP, Ostertag W, Str?tling WH. (1990) The chicken lysozyme 5' matrix attachment region increases transcription from a heterologous promoter in heterologous cells and dampens position effects on the expression of transfected genes. Mol Cell Biol 10:2302-2307
Pienta KJ, Getzenberg RH, Coffey DS. Cell structure and DNA organization. (1991) Crit Rev Eukaryotic Gene Expression 1:355-385
Poulsen C, Fluhr R, Kauffman JM, Boutry M and Chua NH. (1986) Characterization of an rbcS gene from Nicotiana plumbaginifolia and expression of an rbcS-CAT chimeric gene in homologous and heterologous nuclear background.Mo. Gen Genet 205:193-200
Rampalli S, Pavithra L, Bhatt A, Kundu TK, Chattopadhyay S. (2005) Tumor suppressor SMAR1 mediates cyclin D1 repression by recruitment of the SIN3/histone deacetylase 1 complex. Mol Cell Biol 25:8415-8429
Rampitsch C, Jordan MC, Cloutier S. (2000) A matrix attachment region is located upstream from the high-molecular-weight glutenin gene Bx7 in wheat (Triticum aestivum L.). Genome 43:483-486
Rao S, Procko E, Shannon MF. (2001) Chromatin remodelling, measured by a novel real-time polymerase chain reaction assay, across the proximal promoter region of the IL-2 gene. J Immunol 167:4494-4503
Reeves R, Adair JE. (2005) Role of high mobility group (HMG) chromatin proteins in DNA repair. DNA Repair (Amst) 4:926-38
Renz A, Fackelmayer FO. (1996) Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA. Nucleic Acids Res 24:843-849
Romig H, Fackelmayer FO, Renz A, Ramsperger U, Richter A. (1992) Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. EMBO J 11:3431-3440
Romig H, Ruff J, Fackelmayer FO, Patil MS, and Richter A. (1994) Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. Eur J Biochem 221:411-419
Ronai D, Berru M, Shulman MJ. (1999) Variegated expression of the endogenous immunoglobulin heavy-chain gene in the absence of the intronic locus control region. Mol Cell Biol 19:7031-7040
Rose A, Gindullis F, Meier I. (2003) A novel alpha-helical protein, specific to and highlyconserved in plants, is associated with the nuclear matrix fraction. J Exp Bot 54:1133-41
Ross W, Ernst A, Gourse RL. (2001) Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove. Genes Dev 15: 491- 506
Rudd S, Frisch M, Grote K, Meyers BC, Mayer K, Werner T. (2004) Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol 135:715-722
Samaniego R, de la Torre C, Moreno Díaz de la Espina S. (2008) Characterization, expression and subcellular distribution of a novel MFP1 (matrix attachment region-binding filament-like protein 1) in onion. Protoplasma 233:31-38
Samaniego R, Jeong SY, de la Torre C, Meier I, Moreno Díaz de la Espina S. (2006) CK2 phosphorylation weakens 90 kDa MFP1 association to the nuclear matrix in Allium cepa. J Exp Bot 57:113-24
Samaniego R, Jeong SY, Meier I, de la Espina SM. (2006) Dual location of MAR-binding, filament-like protein 1 in Arabidopsis,tobacco and tomato. Planta 223:1201-1206
Sander M, Hsieh T (1983) Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem 258:8421-8428
Samaniego R, Jeong SY, Meier I, de la Espina SM. (2006) Dual location of MAR-binding, filament-like protein 1 in Arabidopsis, tobacco, and tomato. Planta 223:1201-1206
Sass AV, Ruda VM, Akopov SB, Snezhkov EV, Nikolaev LG, Sverdlov ED. (2005) Regulatory potential of S/MAR elements in transient expression. Bioorg Khim 31:77-81
Shao X,Grishin NV. (2000) Common fold in helix–hairpin–helix proteins. Nucleic Acids Res 28:2643-2650
Shaposhnikov SA, Akopov SB, Chernov IP, Thomsen PD, Joergensen C, Collins AR, Frengen E, Nikolaev LG. (2007) A map of nuclear matrix attachment regions within the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1. Genomics 89: 354-361
Sidorenko L, Bruce W, Maddock S, Tagliani L, Li X, Daniels M, Peterson T. (2003)
Functional analysis of two matrix attachment region (MAR) elements in transgenic maize plants. Transgenic Res 12:137-154
Slatter RE, Dupree P, Gray JC. (1991) A scaffold-qssociated DNA region is located downstream of the Pea plastocyanin gene. Plant Cell 3:1239-1250
Sobol M, Gonzalez-Camacho F, Rodríguez-Vilari?o V, Kordyum E, Medina FJ. (2006) Subnucleolar location of fibrillarin and NopA64 in Lepidium sativum root meristematic cells is changed in altered gravity. Protoplasma 228:209-219
Spiker S and Thompson W F. (1996) Nuclear matrix attachment regions and transgene expression in plants. Plant Physiol 110:15-21
Spitzner JR, Muller MT. (1988) A consensus sequence for cleavage by vertebrate DNA topoismerase II. Nucleic Acids Res 16:5533-5556
Starr DB, Hawley DK. (1991) TFIID binds in the minor groove of the TATA box. Cell 67:1231-1240
Stokes DG and Perry RP. (1995) DNA-binding and chromatin localization properties of CHD1. Mol Cell Biol 15:2745-2753
Str?tling WH, Yu F. (1999) Origin and roles of nuclear matrix proteins. Specific functions of the MAR-binding protein MeCP2/ARBP.Crit Rev Eukaryot Gene Expr. 9:311-318
Tagashira H, Shimotori T, Sakamoto N, Katahira M, Miyanoiri Y, Yamamoto T, Mitsunaga- Nakatsubo K, Shimada H, Kusunoki S, Akasaka K.(2006)Unichrom, a novel nuclear matrix protein, binds to the Ars insulator and canonical MARs. Zoolog Sci 23:9-21
Taimen P, Bergh?ll H, Vainionp?? R, Kallajoki M. (2004) NuMA and nuclear lamins are cleaved during viral infection-inhibition of caspase activity prevents cleavage and rescues HeLa cells from measles virus-induced but not from rhinovirus 1B-induced cell death. Virology 320:85-98
Taimen P, Kallajoki M. (2003) NuMA and nuclear lamins behave differently in Fas-mediated apoptosis. J Cell Sci 116:571-583
Tajima S, Shinohara K, Fukumoto M, Zaitsu R, Miyagawa J, Hino S, Fan J, Akasaka K, Matsuoka M. (2006) Ars insulator identified in sea urchin possesses an activity to ensure the transgene expression in mouse cells. J Biochem 139:705-714
Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF. (2006) Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol 2:136-145
Thomas JO, Travers AA. (2001) HMG1 and 2, and related architectural DNA-binding proteins. Trends Biochem Sci 26:167-174
Torney F, Partier A, Says-Lesage V, Nadaud I, Barret P, Beckert M. (2004) Heritable transgene expression pattern imposed onto maize ubiquitin promoter by maize adh-1 matrix attachment regions: tissue and developmental specificity in maize transgenic plants.Plant Cell Rep 22:931-938
Tsutsui K, Okada S, Watarai S, Seki S, Yasuda T, Shohmori T. (1993) Identification and charaterization of a nuclear scaffold protein that bids the matrix attachment region DNA. J Biol Chem 268:12886-12894
ülker B, Allen GC, Thompson WF, Spiker S, Weissinger AK. (1999) A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants. The Plant Journal 18(3):253-263
Vain P, James A, Worland B, Snape W. (2002) Transgene behaviour across two generations in a large random population of transgenic rice plants produced by particle bombardment. Theor Appl Genet 105:878-889
Van der Geest AH, Hall GE Jr, Spiker S and Hall TC. (1994) Theβ-phaseolin gene is flanked by matrix attachment regions. Plant J 6:413-423
van der Geest AH, Hall TC (1997) Theβ-phaseolin 5′matrix attachment region acts as an enhancer facilitator. Plant Mol Biol 33:553-557
Van der Geest AH, Welter ME, Woosley AT, Pareddy DR, Pavelko SE, Skokut M, Ainley WMA. (2004) short synthetic MAR positively affects transgene expression in rice and Arabidopsis. Plant Biotechnol J 2:13-26
van Drunen CM, Oosterling RW, Keultjes GM, Weisbeek PJ, van Driel R, Smeekens SC. (1994) Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana. Nucleic Acids Res 25:3904-3911
Van Leeuwen W, Mlynarova L, Nap JP, van der Plas LH, van der Krol AR. (2001) The effect of MAR elements on variation in spatial and temporal regulation of transgene expression. Plant Mol Biol 47:543–554
Wang B, Dickinson LA, Koivunen E, Ruoslahti E, Kohwi-Shigematsu T. (1995) A novel matrix attachment region DNA binding motif identified using a random phage peptide library. J Biol Chem 270:23239-23242
Wang TY, Xue LX, Hou WH, Yang BS, Chai YR, Ji X, Wang YF. (2007) Increased expression of transgene in stably transformed cells of Dunaliella salina by matrix attachment regions. Appl Microbiol Biotechnol 76:651-657
Wang Z, Goldstein A, Zong RT, Lin D, Neufeld EJ, Scheuermann RH, Tucker PW. (1999) Cux/CDP homeoprotein is a component of NF-muNR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the bright transcription activator. Mol CellBiol 19:284-295.
Webster CI, Cooper MA, Packman LC, Williams DH, Gray JC. (2000) Kinetic analysis of high-mobility-group proteins HMG-1 and HMG-I/Y binding to cholesterol-tagged DNA on a supported lipid monolayer. Nucleic Acids Res 28:1618-1624
Webster CI, Packman LC, Gray JC. (2001) HMG-1 enhances HMG-I/Y binding to an A/T-rich enhancer element from the pea plastocyanin gene. Eur J Biochem 268: 3154-3162
Weitzel JM, Buhrmester H, and Stratling WH. (1997) Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG- binding protein MeCP2. Mol Cell Biol 17: 5656- 5666
Wong RW, Blobel G, Coutavas E. (2006) Rae1 interaction with NuMA is required for bipolar spindle formation.Proc Natl Acad Sci USA 103:19783-19787
Wu Q, Zhang W, Pwee KH, Kumar PP. (2003) Rice HMGB1 protein recognizes DNA structures and bends DNA efficiently. Arch Biochem Biophys 411:105-111
Xin L, Liu D P, Ling CC. (2003) A hypothesis for chromatin domain opening. Bioessays 25:507-514
Xue H, Yang Y T, Wu CA, Yang G.D, Zhang MM, Zheng CC. (2005) TM2, a novel strong matrix attachment region isolated from tobacco, increases transgene expression in transgenic rice calli and plants. Theor Appl Genet. 110:620-627
Yajima M, Kiyomoto M, Akasaka K. (2007) Ars insulator protects transgenes from long-term silencing in sea urchin larva. Dev Genes Evol 217:331-336
Yamaguchi H, Tateno M and Yamasaki K. (2006) Solution structure and DNA-binding mode of the matrix attachment region-binding domain of the transcriptional factor SATB1 that regulates the T-cell maturation. J Biol Chem 281:5319-5327
Yamasaki K, Akiba T, Yamasaki T and Harata K. (2007) Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1. Nucleic Acids Res 35: 5073-5084
Yan LY, Huang JC, Zhu ZY, Lei ZL, Shi LH, Nan CL, Zhao ZJ, Ouyang YC, Song XF, Sun QY, Chen DY. (2006) NuMA distribution and microtubule configuration in rabbit oocytes and cloned embryos.Reproduction 132:869-876.
Yanagisawa J, Ando J, Nakayama J, Kohwi Y, and Kohwi-Shigematsu T. (1996) A matrix attachment region (MAR)-binding activity due to a p114 kilodalton protein is found only in human breast carcinomas and not in normal and benign breast disease tissues. Cancer Res 56:457-462
Yang YT, Yang GD, Liu SJ, Guo XQ, Zheng CC. (2003) Isolation and functional analysis of a strong specific protmoter in photosynthetic tissues. Sci China Life C 46:652-660
Yasui D, Miyano M, Cai S, Varga-Weisz P, Kowhi-Shigematsu T. (2002) SATB1 targets chromatin remodeling to regulate genes over long distances. Nature 419:641-645
Youn BS, Lim CL, Shin MK, Hill JM, Kwon BS. (2002) An intronic silencer of the mouse perforin gene. Mol Cells 13:61-68
Chua YL, Pwee KH, Kini RM. (2001) DNA binding mediated by the wheat HMGa protein: a novel instance of selectivity against alternating GC sequence. Plant Mol Biol 46:193-204
Yugami M, Kabe Y, Yamaguchi Y, Wada T, Handa H. (2007) hnRNP-U enhances the expression of specific genes by stabilizing mRNA. FEBS Lett 581:1-7
Yukawa Y, Sugita M, Choisne N, Small I, Sugiura M. (2000) The TATA motif, the CAA motif and the poly(T) transcription termination motif are all important for transcription re-initiation on plant tRNA genes. Plant J 22:439-447
Zhang MM, Ji LS, Xue H, Yang YT, Wu CA, Zheng CC. (2007) High transformation frequency of tobacco and rice via Agrobacteriu-mediated gene transfer by flanking a tobacco matrix attachment region. Physiol Plantarum 120:644-651
Zhang W, Wu Q, Pwee KH, Jois SDS, Kini RM. (2003a) Characterization of the interaction of wheat HMGa with linear and four-way junction DNA. Biochemistry 42:6596–6607
Zhang W, Wu Q, Pwee KH, Kini RM. (2003b) Interaction of wheat high-mobility-group proteins with four-way-junction DNA and characterization of the structure and expression of HMGA gene. Arch Biochem Biophys 409:357-366
Zhao K, Kas E, Gonzalez E, Laemmli UK. (1993) SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J 12: 3237-3247
Zuo ZH, Li B, Wang CG, Cai JL, Chen YX. (2007) Increasing transient expression of CAT gene in Porphyra haitanensis by matrix attachment regions and 18S rDNA targeted homologous recombination. Aguacultrue Res 38:681-688