Tudor结构域蛋白识别甲基化精氨酸蛋白的分子机理研究
|
摘要
蛋白质的翻译后修饰是表观遗传学的重要研究内容之一,它与DNA的甲基化修饰以及非编码RNA调控是表观遗传学中调节基因表达的主要机制。目前,关于蛋白质翻译后修饰的研究主要集中在蛋白质翻译后修饰的修饰酶“WRITERS",识别蛋白"READERS"以及修饰标志去除酶"EREASERS”等方面,并且乙酰化修饰,磷酸化修饰和甲基化赖氨酸修饰标志的识别蛋白的结构特点和结合机理已经有很多报道。目前,关于甲基化精氨酸修饰标志的修饰酶已经被报道10余年,但是甲基化精氨酸修饰标志的结合机理还一直未能阐明。
Tudor domain containing proteins (TDRDs)是目前发现的一类可以识别结合甲基化精氨酸修饰标志的蛋白家族。因此,本论文系统地分析了整个TDRDs蛋白家族不同Tudor结构域识别结合甲基化精氨酸修饰蛋白的特异性,并通过氨基酸序列比对,点突变实验,FP/ITC结合实验和X-ray晶体结构阐述了Tudor结构域蛋白识别结合甲基化精氨酸蛋白的结构特点和结合方式。
我们通过免疫印迹,FP和ITC实验证实,与其他的TDRDs蛋白相似,SND1蛋白能够在生殖细胞内表达,并且能够通过识别对称双甲基化精氨酸标志结合生殖细胞内的PIWIL1/Miwi蛋白。为了进一步研究SND1蛋白识别结合甲基化精氨酸蛋白的分子机理,我们解析了分辨率分别为1.77A的SND1蛋白与PIWIL1_R4me2s多肽的复合物结构和1.85A的SND1蛋白与PIWIL1_R14me2s多肽的复合物晶体结构。这两种复合物晶体结构表明,SND1蛋白的延伸Tudor结构域主要通过cation-π,疏水作用,范德华力以及氢键与甲基化PIWIL1多肽相互作用从而形成了稳定的复合物结构,并且组成SND1蛋白延伸Tudor结构域的典型的Tudor结构域和第五个SN结构域对于SND1蛋白结合甲基化PIWIL1多肽都是必不可少的。此外,SND1蛋白的延伸Tudor结构域形成一个宽的、带有负电的芳香结合槽,这个结合槽能够从不同的方向结合不同的甲基化PIWIL1多肽。通过上述结果,我们首次阐明了Tudor结构域蛋白识别结合甲基化精氨酸修饰蛋白的识别结合机理,这就为进一步研究甲基化精氨酸修饰蛋白和SND1蛋白的生理功能奠定了重要的结构基础。
TDRD3蛋白是目前发现的唯一一个能够识别结合甲基化精氨酸组蛋白的Tudor结构域蛋白,并且它的Tudor结构域与SMN蛋白和SPF30蛋白的udor结构域具有很高的保守性。我们通过FP和ITC结合实验发现,虽然它们具有相似的Tudor结构域结构,但却具有不同的结合特异性。TDRD3蛋白优先结合非对称甲基化精氨酸蛋白,而SMN蛋白能够结合各种含有甲基化精氨酸修饰标志的蛋白,SPF30蛋白只可以很弱的结合具有GAR重复序列的甲基化精氨酸修饰蛋白。同时,我们还发现,与SND1蛋白不同,TDRD3蛋白和SMN蛋白典型的Tudor结构域就足够识别并结合甲基化精氨酸蛋白。在此基础上,我们解析了分辨率为1.9A的TDRD3蛋白和小分子PG4的复合物结构。通过复合物结构,我们发现小分子PG4类似甲基化精氨酸修饰侧链结合于TDRD3蛋白的芳香结合槽内。
在SND1蛋白和TDRD3蛋白的研究基础上,我们系统地研究了TDRDs蛋白家族的不同Tudor结构域的结合特异性。通过FP结合实验,我们发现TDRDs蛋白优先结合PIWIL1多肽,但是它们的结合特异性却具有很大的区别。例如,TDRD1、TDRD7、TDRD9和SND1蛋白的Tudor结构域优先结合对称双甲基PIWILl多肽；TDRD3和TDRD4蛋白优先结合非对称双甲基PIWIL1多肽；TDRKH (TDRD2)蛋白的Tudor结构域优先结合非甲级化的PIWIL1多肽。此外,我们还发现在一些多Tudor结构域的TDRDs蛋白中,如TDRD1和TDRD4蛋白,并不是每一个Tudor结构域都具有结合甲基化精氨酸多肽的能力。此外,利用点突变生物学和氨基酸序列比对预测了各种Tudor结构域蛋白结合甲基化精氨酸蛋白的结构特点。我们对TDRDs蛋白家族的不同Tudor结构域的系统性研究为进一步研究Tudor结构域蛋白结合甲基化精氨酸修饰的结构特点以及TDRDs蛋白的在生物体内,尤其是生殖细胞内的生物功能提供了重要的理论基础。
Post-translational modifications (PTMs) of histones are important epigenetic modifications, which, together with DNA modifications and non-coding RNAs, form the cornerstones of chromatin biology and epigenetics. The enzymes responsible for bringing about steady-state balance of PTMs and the PTM recognition proteins, which are referred to WRITERS, ERASERS and READERS, have attracted lots of attention. By means of X-ray crystallography and NMR techniques, the molecular mechanims of histone and protein modifications (acetylation, phosphorylation and lysine methyllation) and their recogniztion have been reported. Although the enzymes responsible for arginine methylation have been known for over10years, but the binding mechanism of the methylarginine recognition is still elusive.
Recently, it was reported that the Tudor domain containing proteins (TDRDs), including TDRD1to TDRD12, comprise a family of proteins which can read the methylarginine marks. Hence, here we systematically analyzed the binding specificity of the Tudor domains of the TDRD proteins against a family of methylarginine peptides, and elaborated the binding mechanism of the Tudor domain proteins by structural studies coupled with binding assays, sequence alignment, and mutagenesis.
We established that, like other germ-line Tudor domain proteins, the ancestral staphylococcal nuclease domain-containing1(SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells in mouse. We also found that human SND1protein binds PIWIL1in an arginine methylation-dependent manner with a preference for symmetrically dimethylated arginine. In order to further study how SND1recognize methylarginine marks, we investigated the crystal structures of the human SND1extended Tudor domain in complex with symmetrically dimethylated arginine peptides PIWIL1_R4me2s and PIWIL1_R14me2s with the resolution of1.77A and1.85A, respectively. Both complex structures show that the extended Tudor domain of SND1protein binds the peptides through cation-π, hydrophobic, van der Waals, and hydrogen bond interactions. Moreover, we found that both the entire Tudor domain and a bifurcated SN domain are required for the binding, and the canonical Tudor domain alone is insufficient for methylarginine ligand binding. Our crystal structures also show that the intact SND1extended Tudor domain forms a wide and negatively charged binding groove, which can accommodate distinct symmetrically dimethylated arginine peptides from PIWIL1in different orientations. This analysis explains how SND1preferentially recognizes symmetrical dimethylarginine via an aromatic cage and conserved hydrogen bonds, and provides a general paradigm for the binding mechanisms of methylarginine containing peptides by extended Tudor domains, and also provides important information for the further study of the functions of SND1and methylarginine containing proteins.
TDRD3(Tudor domain containing protein3) is the only identified protein, which could bind methylarginine marks on histones. In addition, it is also found that the Tudor domain of TDRD3is highly homologous to those of the SMN and SPF30proteins. Through a series of FP and ITC experiments, we found that they preferentially bind different methylarginine marks. For example, TDRD3preferentially recognizes asymmetrical dimethylated arginine mark, while SMN is a very promiscuous effector molecule, which recognizes different arginine containing sequence motifs and preferentially binds symmetrical dimethylated arginine, and SPF30is the weakest methylarginine binder, which only binds the GAR motif sequences. Interestingly, our data also showed that the canonical Tudor domain alone is sufficient for methylarginine ligand binding for the TDRD3and SMN protein, which is very different from the Tudor domain of SND1. Furthermore, we also reported the high-resolution crystal structures of the Tudor domain of TDRD3in complex with one small molecule PG4at1.9A, in which the small molecule PG4occupies the aromatic cage of TDRD3, mimicking the methylarginine residue.
Guided by our understandings gained from the SND1and TDRD3studies, we systematically studied the binding affinities of the Tudor domains from other TDRD family members with methylarginine peptides. Our results showed that these Tudor domains exhibit distinct binding specificities. For example, TDRD1, TDRD7, TDRD9and SND1proteins preferentially bind to symmetrically dimethylated arginine PIWIL1peptides, TDRD3and TDRD4preferentially bind to asymmetrically dimethylated arginine PIWIL1peptides, and TDRKH (TDRD2) preferentially binds to unmodified PIWIL1peptides. Furthermore, we also found that only a subset of Tudor domains can recognize methylarginined peptides in the multiple Tudor domain proteins. These discoveries lay an important foundation for the futuer function study of the methylarginined marks and TDRDs.
Tudor domain containing proteins (TDRDs)是目前发现的一类可以识别结合甲基化精氨酸修饰标志的蛋白家族。因此,本论文系统地分析了整个TDRDs蛋白家族不同Tudor结构域识别结合甲基化精氨酸修饰蛋白的特异性,并通过氨基酸序列比对,点突变实验,FP/ITC结合实验和X-ray晶体结构阐述了Tudor结构域蛋白识别结合甲基化精氨酸蛋白的结构特点和结合方式。
我们通过免疫印迹,FP和ITC实验证实,与其他的TDRDs蛋白相似,SND1蛋白能够在生殖细胞内表达,并且能够通过识别对称双甲基化精氨酸标志结合生殖细胞内的PIWIL1/Miwi蛋白。为了进一步研究SND1蛋白识别结合甲基化精氨酸蛋白的分子机理,我们解析了分辨率分别为1.77A的SND1蛋白与PIWIL1_R4me2s多肽的复合物结构和1.85A的SND1蛋白与PIWIL1_R14me2s多肽的复合物晶体结构。这两种复合物晶体结构表明,SND1蛋白的延伸Tudor结构域主要通过cation-π,疏水作用,范德华力以及氢键与甲基化PIWIL1多肽相互作用从而形成了稳定的复合物结构,并且组成SND1蛋白延伸Tudor结构域的典型的Tudor结构域和第五个SN结构域对于SND1蛋白结合甲基化PIWIL1多肽都是必不可少的。此外,SND1蛋白的延伸Tudor结构域形成一个宽的、带有负电的芳香结合槽,这个结合槽能够从不同的方向结合不同的甲基化PIWIL1多肽。通过上述结果,我们首次阐明了Tudor结构域蛋白识别结合甲基化精氨酸修饰蛋白的识别结合机理,这就为进一步研究甲基化精氨酸修饰蛋白和SND1蛋白的生理功能奠定了重要的结构基础。
TDRD3蛋白是目前发现的唯一一个能够识别结合甲基化精氨酸组蛋白的Tudor结构域蛋白,并且它的Tudor结构域与SMN蛋白和SPF30蛋白的udor结构域具有很高的保守性。我们通过FP和ITC结合实验发现,虽然它们具有相似的Tudor结构域结构,但却具有不同的结合特异性。TDRD3蛋白优先结合非对称甲基化精氨酸蛋白,而SMN蛋白能够结合各种含有甲基化精氨酸修饰标志的蛋白,SPF30蛋白只可以很弱的结合具有GAR重复序列的甲基化精氨酸修饰蛋白。同时,我们还发现,与SND1蛋白不同,TDRD3蛋白和SMN蛋白典型的Tudor结构域就足够识别并结合甲基化精氨酸蛋白。在此基础上,我们解析了分辨率为1.9A的TDRD3蛋白和小分子PG4的复合物结构。通过复合物结构,我们发现小分子PG4类似甲基化精氨酸修饰侧链结合于TDRD3蛋白的芳香结合槽内。
在SND1蛋白和TDRD3蛋白的研究基础上,我们系统地研究了TDRDs蛋白家族的不同Tudor结构域的结合特异性。通过FP结合实验,我们发现TDRDs蛋白优先结合PIWIL1多肽,但是它们的结合特异性却具有很大的区别。例如,TDRD1、TDRD7、TDRD9和SND1蛋白的Tudor结构域优先结合对称双甲基PIWILl多肽；TDRD3和TDRD4蛋白优先结合非对称双甲基PIWIL1多肽；TDRKH (TDRD2)蛋白的Tudor结构域优先结合非甲级化的PIWIL1多肽。此外,我们还发现在一些多Tudor结构域的TDRDs蛋白中,如TDRD1和TDRD4蛋白,并不是每一个Tudor结构域都具有结合甲基化精氨酸多肽的能力。此外,利用点突变生物学和氨基酸序列比对预测了各种Tudor结构域蛋白结合甲基化精氨酸蛋白的结构特点。我们对TDRDs蛋白家族的不同Tudor结构域的系统性研究为进一步研究Tudor结构域蛋白结合甲基化精氨酸修饰的结构特点以及TDRDs蛋白的在生物体内,尤其是生殖细胞内的生物功能提供了重要的理论基础。
Post-translational modifications (PTMs) of histones are important epigenetic modifications, which, together with DNA modifications and non-coding RNAs, form the cornerstones of chromatin biology and epigenetics. The enzymes responsible for bringing about steady-state balance of PTMs and the PTM recognition proteins, which are referred to WRITERS, ERASERS and READERS, have attracted lots of attention. By means of X-ray crystallography and NMR techniques, the molecular mechanims of histone and protein modifications (acetylation, phosphorylation and lysine methyllation) and their recogniztion have been reported. Although the enzymes responsible for arginine methylation have been known for over10years, but the binding mechanism of the methylarginine recognition is still elusive.
Recently, it was reported that the Tudor domain containing proteins (TDRDs), including TDRD1to TDRD12, comprise a family of proteins which can read the methylarginine marks. Hence, here we systematically analyzed the binding specificity of the Tudor domains of the TDRD proteins against a family of methylarginine peptides, and elaborated the binding mechanism of the Tudor domain proteins by structural studies coupled with binding assays, sequence alignment, and mutagenesis.
We established that, like other germ-line Tudor domain proteins, the ancestral staphylococcal nuclease domain-containing1(SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells in mouse. We also found that human SND1protein binds PIWIL1in an arginine methylation-dependent manner with a preference for symmetrically dimethylated arginine. In order to further study how SND1recognize methylarginine marks, we investigated the crystal structures of the human SND1extended Tudor domain in complex with symmetrically dimethylated arginine peptides PIWIL1_R4me2s and PIWIL1_R14me2s with the resolution of1.77A and1.85A, respectively. Both complex structures show that the extended Tudor domain of SND1protein binds the peptides through cation-π, hydrophobic, van der Waals, and hydrogen bond interactions. Moreover, we found that both the entire Tudor domain and a bifurcated SN domain are required for the binding, and the canonical Tudor domain alone is insufficient for methylarginine ligand binding. Our crystal structures also show that the intact SND1extended Tudor domain forms a wide and negatively charged binding groove, which can accommodate distinct symmetrically dimethylated arginine peptides from PIWIL1in different orientations. This analysis explains how SND1preferentially recognizes symmetrical dimethylarginine via an aromatic cage and conserved hydrogen bonds, and provides a general paradigm for the binding mechanisms of methylarginine containing peptides by extended Tudor domains, and also provides important information for the further study of the functions of SND1and methylarginine containing proteins.
TDRD3(Tudor domain containing protein3) is the only identified protein, which could bind methylarginine marks on histones. In addition, it is also found that the Tudor domain of TDRD3is highly homologous to those of the SMN and SPF30proteins. Through a series of FP and ITC experiments, we found that they preferentially bind different methylarginine marks. For example, TDRD3preferentially recognizes asymmetrical dimethylated arginine mark, while SMN is a very promiscuous effector molecule, which recognizes different arginine containing sequence motifs and preferentially binds symmetrical dimethylated arginine, and SPF30is the weakest methylarginine binder, which only binds the GAR motif sequences. Interestingly, our data also showed that the canonical Tudor domain alone is sufficient for methylarginine ligand binding for the TDRD3and SMN protein, which is very different from the Tudor domain of SND1. Furthermore, we also reported the high-resolution crystal structures of the Tudor domain of TDRD3in complex with one small molecule PG4at1.9A, in which the small molecule PG4occupies the aromatic cage of TDRD3, mimicking the methylarginine residue.
Guided by our understandings gained from the SND1and TDRD3studies, we systematically studied the binding affinities of the Tudor domains from other TDRD family members with methylarginine peptides. Our results showed that these Tudor domains exhibit distinct binding specificities. For example, TDRD1, TDRD7, TDRD9and SND1proteins preferentially bind to symmetrically dimethylated arginine PIWIL1peptides, TDRD3and TDRD4preferentially bind to asymmetrically dimethylated arginine PIWIL1peptides, and TDRKH (TDRD2) preferentially binds to unmodified PIWIL1peptides. Furthermore, we also found that only a subset of Tudor domains can recognize methylarginined peptides in the multiple Tudor domain proteins. These discoveries lay an important foundation for the futuer function study of the methylarginined marks and TDRDs.
引文
[1]Holliday R., Epigenetics:a historical overview. Epigenetics,2006,1(2):76-80.
[2]Goldberg A.D., C.D. Allis, E. Bernstein, Epigenetics:a landscape takes shape. Cell,2007,128(4): 635-8.
[3]Egger G., G. Liang, A. Aparicio, et al., Epigenetics in human disease and prospects for epigenetic therapy. Nature,2004,429(6990):457-63.
[4]Kim T.Y., Y.J. Bang, K.D. Robertson, Histone deacetylase inhibitors for cancer therapy. Epigenetics,2006,1(1):14-23.
[5]Yoo C.B., P.A. Jones, Epigenetic therapy of cancer:past, present and future. Nature Reviews Drug Discovery,2006,5(1):37-50.
[6]Schroeder M., M.O. Krebs, S. Bleich, et al., Epigenetics and depression:current challenges and new therapeutic options. Current Opinion in Psychiatry,2010,23(6):588-92.
[7]Caffarelli E., P. Filetici, Epigenetic regulation in cancer development. Frontiers in Bioscience, 2011,17:2682-94.
[8]Portela A., M. Esteller, Epigenetic modifications and human disease. Nature Biotechnology,2010, 28(10):1057-68.
[9]Patra S.K., S. Bettuzzi, Epigenetic DNA-(cytosine-5-carbon) modifications:5-aza-2'-deoxy-cytidine and DNA-demethylation. Biochemistry (Mosc),2009,74(6):613-9.
[10]Gronbaek K., C. Hother, P.A. Jones, Epigenetic changes in cancer. Apmis,2007,115(10): 1039-59.
[11]Mai A., Small-molecule chromatin-modifying agents:therapeutic applications. Epigenomics, 2010,2(2):307-24.
[12]Schaefer A., S.C. Sampath, A. Intrator, et al., Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron,2009,64(5):678-91.
[13]Kubicek S., R.J. O'Sullivan, E.M. August, et al., Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase. Molecular Cell,2007,25(3):473-81.
[14]Greiner D., T. Bonaldi, R. Eskeland, et al., Identification of a specific inhibitor of the histone methyltransferase SU (VAR) 3-9. Nature Chemical Biology,2005,1(3):143-5.
[15]Ganesan A., L. Nolan, S. J. Crabb, et al., Epigenetic therapy:histone acetylation, DNA methy-lation and anti-cancer drug discovery. Current Cancer Drug Targets,2009,9(8):963-81.
[16]Ho L., G.R. Crabtree, Chromatin remodelling during development. Nature,2010,463(7280): 474-84.
[17]Taverna S.D., H. Li, A.J. Ruthenburg, et al., How chromatin-binding modules interpret histone modifications:lessons from professional pocket pickers. Nature Structural & Molecular Biology,2007,14(11):1025-40.
[18]Strahl B.D., C.D. Allis, The language of covalent histone modifications. Nature,2000,403(6765) 41-5.
[19]Jenuwein T., C.D. Allis, Translating the histone code. Science,2001,293(5532):1074-80.
[20]Kouzarides T., Chromatin modifications and their function. Cell,2007,128(4):693-705.
[21]Mai A., L. Altucci, Epi-drugs to fight cancer:from chemistry to cancer treatment, the road ahead. International Journal of Biochemistry & Cell Biology,2009,41(1):199-213.
[22]Chu C.Y., T.M. Rana, Small RNAs:regulators and guardians of the genome. Journal of Cellular Physiology,2007,213(2):412-9.
[23]Filipowicz W., S.N. Bhattacharyya, N. Sonenberg, Mechanisms of post-transcriptional regulation by microRNAs:are the answers in sight? Nature Reviews Genetics,2008,9(2):102-14.
[24]Brennecke J., A.A. Aravin, A. Stark, et al., Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell,2007,128(6):1089-103.
[25]Houwing S., L.M. Kamminga, E. Berezikov, et al., A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell,2007,129(1):69-82.
[26]Pak J., A. Fire, Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science,2007,315(5809):241-4.
[27]Vagin V.V., A. Sigova, C. Li, et al., A distinct small RNA pathway silences selfish genetic elements in the germline. Science,2006,313(5785):320-4.
[28]Sijen T., F.A. Steiner, K.L. Thijssen, et al., Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science,2007,315(5809):244-7.
[29]Czech B., G.J. Hannon, Small RNA sorting:matchmaking for Argonautes. Nature Reviews Genetics,2011,12(1):19-31.
[30]Martinez J., A. Patkaniowska, H. Urlaub, et al., Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell,2002,110(5):563-74.
[31]Okamura K., N. Liu, E.C. Lai, Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Molecular Cell,2009,36(3):431-44.
[32]Khvorova A., A. Reynolds, S.D. Jayasena, Functional siRNAs and miRNAs exhibit strand bias. Cell,2003,115(2):209-16.
[33]Schwarz D.S., G. Hutvagner, T. Du, et al., Asymmetry in the assembly of the RNAi enzyme complex. Cell,2003,115(2):199-208.
[34]Liu Y., X. Ye, F. Jiang, et al., C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science,2009,325(5941):750-753.
[35]Horwich M.D., C. Li, C. Matranga, et al., The Drosophila RNA methyltransferase, DmHenl, modifies germline piRNAs and single-stranded siRNAs in RISC. Current Biology,2007, 17(14):1265-1272.
[36]Li N., A. Nguyen, J. Diedrich, et al., Separation of miRNA and its methylation products by capillary electrophoresis. Journal of Chromatography A,2008,1202(2):220-223.
[37]Yu B., Z. Yang, J. Li, et al., Methylation as a crucial step in plant microRNA biogenesis. Science, 2005,307(5711):932-935.
[38]Ameres S.L., M.D. Horwich, J.H. Hung, et al., Target RNA-directed trimming and tailing of small silencing RNAs. Science,2010,328(5985):1534-1539.
[39]Fabian M.R., N. Sonenberg, W. Filipowicz, Regulation of mRNA translation and stability by microRNAs. Annual Review of Biochemistry,2010,79:351-379.
[40]Brodersen P. and O. Voinnet, Revisiting the principles of microRNA target recognition and mode of action. Nature Reviews Molecular Cell Biology,2009,10(2):141-148.
[41]Forstemann K., M.D. Horwich, L. Wee, et al., Drosophila microRNAs are sorted into func-tionally distinct argonaute complexes after production by dicer-1. Cell,2007,130(2): 287-297.
[42]Iwasaki S., T. Kawamata, Y. Tomari, Drosophila argonautel and argonaute2 employ distinct mechanisms for translational repression. Molecular Cell,2009,34(1):58-67.
[43]Yekta S., I.H. Shih, D.P. Bartel, MicroRNA-directed cleavage of HOXB8 mRNA. Science,2004, 304(5670):594-6.
[44]Ma J.B., Y.R. Yuan, G. Meister, et al., Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature,2005,434(7033):666-70.
[45]Song J.J., S.K. Smith, G.J. Hannon, et al., Crystal structure of Argonaute and its implications for RISC slicer activity. Science,2004,305(5689):1434-7.
[46]Parker J.S., S.M. Roe, D. Barford, Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO Journal,2004,23(24):4727-37.
[47]Yuan Y.R., Y. Pei, H.Y. Chen, et al., A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA. Structure,2006,14(10):1557-65.
[48]Yuan Y.R., Y. Pei, J.B. Ma, et al., Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Molecular Cell,2005,19(3):405-19.
[49]Wang Y., S. Juranek, H. Li, et al., Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature,2008,456(7224):921-6.
[50]Lapatto R., T. Blundell, A. Hemmings, et al., X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature,1989,342(6247): 299-302.
[51]Miller M., J. Schneider, B.K. Sathyanarayana, et al., Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science,1989,246(4934): 1149-52.
[52]Ali H.I., T. Nagamatsu, E. Akaho, Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors. Bioinformation,2011,5(9):368-74.
[53]Hetenyi C., U. Maran, A.T. Garcia-Sosa, et al., Structure-based calculation of drug efficiency indices. Bioinformatics,2007,23(20):2678-85.
[54]Kapoor N., T. Banerjee, P. Babu, et al., Design, development, synthesis, and docking analysis of 2'-substituted triclosan analogs as inhibitors for Plasmodium falciparum enoyl-ACP reductase. IUBMB Life,2009,61(11):1083-91.
[55]Anderson A.C., Winning the Arms Race by Improving Drug Discovery against Mutating Targets. ACS Chemical Biology,2012,7(2):278-88.
[56]Yun M., J. Wu, J.L. Workman, et al., Readers of histone modifications. Cell Research,2011, 21(4):564-578.
[57]Herold J.M., L.A. Ingerman, C. Gao, et al., Drug discovery toward antagonists of methyl-lysine binding proteins. Current Chemical Genomics,2011,5:51-61.
[58]Bao J., L. Wang, J. Lei, et al., STK31 (TDRD8) is dynamically regulated throughout mouse spermatogenesis and interacts with MIWI protein. Histochemistry and Cell Biology,2012, 137(3):377-89.
[59]Yabuta Y, H. Ohta, T. Abe, et al, TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. Journal of Cell Biology,2011,192(5):781-95.
[60]Kojima K., S. Kuramochi-Miyagawa, S. Chuma, et al., Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells. Genes to Cells,2009,14(10):1155-65.
[61]Vasileva A., D. Tiedau, A. Firooznia, et al., Tdrd6 is required for spermiogenesis, chromatoid body architecture, and regulation of miRNA expression. Current Biology,2009,19(8):630-9.
[62]Grivna S.T., B. Pyhtila, H. Lin, MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proceedings of the National Academy of Sciences of the United States of America,2006,103(36):13415-20.
[63]Aravin A., D. Gaidatzis, S. Pfeffer, et al., A novel class of small RNAs bind to MILI protein in mouse testes. Nature,2006,442(7099):203-7.
[64]Lallous N., P. Legrand, A.G McEwen, et al., The PHD finger of human UHRF1 reveals a new subgroup of unmethylated histone H3 tail readers. PLoS One,2011,6(11):e27599.
[65]Varier R.A., N.S. Outchkourov, P. de Graaf, et al., A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes. EMBO Journal,2010,29(23): 3967-78.
[66]Fischle W., B.S. Tseng, H.L. Dormann, et al., Regulation of HPl-chromatin binding by histone H3 methylation and phosphorylation. Nature,2005,438(7071):1116-22.
[67]Sun B., J. Hong, P. Zhang, et al., Molecular basis of the interaction of Saccharomyces cerevisiae Eaf3 chromo domain with methylated H3K36. Journal of Biological Chemistry,2008, 283(52):36504-12.
[68]Xu C., G Cui, M.V. Botuyan, et al., Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure,2008,16(11): 1740-50.
[69]Li B., M. Gogol, M. Carey, et al., Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science,2007,316(5827):1050-4.
[70]Turner B.M. and L.P. O'Neill, Histone acetylation in chromatin and chromosomes. Seminars in Cell Biology,1995,6(4):229-36.
[71]Nakajima H., A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Tanpakushitsu Kakusan Koso,2007,52(13 Suppl):1790-1.
[72]Brownell J.E., J. Zhou, T. Ranalli, et al, Tetrahymena histone acetyltransferase A:a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell,1996,84(6):843-51.
[73]Mujtaba S., L. Zeng, M.M. Zhou, Structure and acetyl-lysine recognition of the bromodomain. Oncogene,2007,26(37):5521-7.
[74]Zeng L., Q. Zhang, S. Li, et al., Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature,2010,466(7303):258-62.
[75]Hudson B.P., M.A. Martinez-Yamout, H.J. Dyson, et al., Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. Journal of Molecular Biology,2000,304(3): 355-70.
[76]Owen D.J., P. Ornaghi, J.C. Yang, et al., The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO Journal, 2000,19(22):6141-9.
[77]Mujtaba S., Y. He, L. Zeng, et al., Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Molecular Cell,2002,9(3):575-86.
[78]Nakamura Y., T. Umehara, K. Nakano, et al., Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. Journal of Biological Chemistry,2007,282(6):4193-201.
[79]Mujtaba S., Y. He, L. Zeng, et al., Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Molecular Cell,2004,13(2):251-63.
[80]Li H., S. Ilin, W. Wang, et al., Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature,2006,442(7098):91-5.
[81]Shen W., C. Xu, W. Huang, et al., Solution structure of human Brgl bromodomain and its specific binding to acetylated histone tails. Biochemistry,2007,46(8):2100-10.
[82]Dhalluin C., J.E. Carlson, L. Zeng, et al., Structure and ligand of a histone acetyltransferase bromodomain. Nature,1999,399(6735):491-6.
[83]Umehara T., Y. Nakamura, M.K. Jang, et al., Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain. Journal of Biological Chemistry,2010, 285(10):7610-8.
[84]Huang H., J. Zhang, W. Shen, et al., Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC Structural Biology,2007,7:57.
[85]Seet B.T., I. Dikic, M.M. Zhou, et al., Reading protein modifications with interaction domains. Nature Reviews Molecular Cell Biology,2006,7(7):473-83.
[86]Cheung P., C.D. Allis, P. Sassone-Corsi, Signaling to chromatin through histone modifications. Cell,2000,103(2):263-71.
[87]Cheung P., K.G. Tanner, W.L. Cheung, et al., Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Molecular Cell,2000, 5(6):905-15.
[88]Thomson S., A.L. Clayton, C.A. Hazzalin, et al., The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades:MSK1 as a potential histone H3/HMG-14 kinase. EMBO Journal,1999,18(17):4779-93.
[89]Macdonald N., J.P. Welburn, M.E. Noble, et al., Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. Molecular Cell,2005,20(2): 199-211.
[90]Stucki M., J.A. Clapperton, D. Mohammad, et al., MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell,2005,123(7): 1213-26.
[91]Jeyaprakash A.A., C. Basquin, U. Jayachandran, et al., Structural basis for the recognition of phosphorylated histone h3 by the survivin subunit of the chromosomal passenger complex. Structure,2011,19(11):1625-34.
[92]Bannister A.J., T. Kouzarides, Reversing histone methylation. Nature,2005,436(7054):1103-6.
[93]Martin C., Y. Zhang, The diverse functions of histone lysine methylation. Nature Reviews Molecular Cell Biology,2005,6(11):838-49.
[94]Jacobs S.A., S. Khorasanizadeh, Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science,2002,295(5562):2080-3.
[95]Nielsen P.R., D. Nietlispach, H.R. Mott, et al., Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature,2002,416(6876):103-7.
[96]Min J., Y. Zhang, R.M. Xu, Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes & Development,2003,17(15):1823-8.
[97]Li J., Z. Li, J. Ruan, et al., Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9. PLoS One,2011,6(10):e25104.
[98]Pray-Grant M.G., J.A. Daniel, D. Schieltz, et al., Chdl chromodomain links histone H3 methylation with SAGA-and SLIK-dependent acetylation. Nature,2005,433(7024):434-8.
[99]Flanagan J.F., L.Z. Mi, M. Chruszcz, et al., Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature,2005,438(7071):1181-5.
[100]Bertram M.J., O.M. Pereira-Smith, Conservation of the MORF4 related gene family: identification of a new chromo domain subfamily and novel protein motif. Gene,2001, 266(1-2):111-21.
[101]Zhang P., J. Du, B. Sun, et al, Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Research,2006,34(22):6621-8.
[102]Ruthenburg A.J., C.D. Allis, J. Wysocka, Methylation of lysine 4 on histone H3:intricacy of writing and reading a single epigenetic mark. Molecular Cell,2007,25(1):15-30.
[103]Stec I., S.B. Nagl, G.J. van Ommen, et al., The PWWP domain:a potential protein-protein interaction domain in nuclear proteins influencing differentiation? FEBS Lett,2000,473(1): 1-5.
[104]Qiu C., K. Sawada, X. Zhang, et al, The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature Structural & Molecular Biology, 2002,9(3):217-24.
[105]Maurer-Stroh S., N.J. Dickens, L. Hughes-Davies, et al, The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends in Biochemical Sciences, 2003,28(2):69-74.
[106]Wang Y., B. Reddy, J. Thompson, et al., Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein. Molecular Cell,2009,33(4):428-37.
[107]Dhayalan A., A. Rajavelu, P. Rathert, et al., The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. Journal of Biological Chemistry,2010, 285(34):26114-20.
[108]Vezzoli A., N. Bonadies, M.D. Allen, et al., Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpfl. Nature Structural & Molecular Biology,2010,17(5):617-9.
[109]Vermeulen M., H.C. Eberl, F. Matarese, et al., Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell,2010,142(6): 967-80.
[110]Wu H., H. Zeng, R. Lam, et al., Structural and histone binding ability characterizations of human PWWP domains. PLoS One,2011,6(6):e18919.
[111]Bienz M., The PHD finger, a nuclear protein-interaction domain. Trends in Biochemical Sciences,2006,31(1):35-40.
[112]Pena P.V., F. Davrazou, X. Shi, et al., Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature,2006,442(7098):100-3.
[113]Lan F., R.E. Collins, R. De Cegli, et al., Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSDl-mediated gene repression. Nature,2007,448(7154):718-22.
[114]Ooi S.K., C. Qiu, E. Bernstein, et al., DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature,2007,448(7154):714-7.
[115]Adams-Cioaba M.A., J. Min, Structure and function of histone methylation binding proteins. International Journal of Biochemistry & Cell Biology,2009,87(1):93-105.
[116]Botuyan M.V., J. Lee, I.M. Ward, et al., Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell,2006,127(7): 1361-73.
[117]Lee J., J.R. Thompson, M.V. Botuyan, et al., Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor. Nature Structural & Molecular Biology,2008,15(1):109-11.
[118]Bian C., C. Xu, J. Ruan, et al., Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. EMBO Journal,2011,30(14):2829-42.
[119]Huang Y., J. Fang, M.T. Bedford, et al., Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science,2006,312(5774):748-51.
[120]Wang W., Z. Chen, Z. Mao, et al., Nucleolar protein Spindlinl recognizes H3K4 methylation and stimulates the expression of rRNA genes. EMBO reports,2011,12(11):1160-6.
[121]Kalakonda N., W. Fischle, P. Boccuni, et al., Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1. Oncogene,2008,27(31):4293-304.
[122]Li H., W. Fischle, W. Wang, et al., Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Molecular Cell,2007, 28(4):677-91.
[123]Guo Y., N. Nady, C. Qi, et al., Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Research,2009,37(7):2204-10.
[124]Xu C., C. Bian, W. Yang, et al., Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proceedings of the National Academy of Sciences of the United States of America,2010,107(45):19266-71.
[125]Margueron R., N. Justin, K. Ohno, et al., Role of the polycomb protein EED in the propagation of repressive histone marks. Nature,2009,461(7265):762-7.
[126]Han Z., L. Guo, H. Wang, et al., Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Molecular Cell,2006,22(1):137-44.
[127]Ruthenburg A.J., W. Wang, D.M. Graybosch, et al, Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nature Structural & Molecular Biology,2006, 13(8):704-12.
[128]Schuetz A., A. Allali-Hassani, F. Martin, et al., Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO Journal,2006,25(18):4245-52.
[129]Aravin A.A., N.M. Naumova, A.V. Tulin, et al., Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Current Biology,2001,11(13):1017-27.
[130]Aravin A.A., M. Lagos-Quintana, A. Yalcin, et al., The small RNA profile during Drosophila melanogaster development. Developmental Cell,2003,5(2):337-50.
[131]Girard A., R. Sachidanandam, GJ. Hannon, et al., A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature,2006,442(7099):199-202.
[132]Aravin A.A., R. Sachidanandam, A. Girard, et al., Developmentally regulated piRNA clusters implicate MILI in transposon control. Science,2007,316(5825):744-7.
[133]Aravin A.A., GJ. Hannon, J. Brennecke, The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science,2007,318(5851):761-4.
[134]Siomi M.C., S. Kuramochi-Miyagawa, RNA silencing in germlines-exquisite collaboration of Argonaute proteins with small RNAs for germline survival. Current Opinion in Cell Biology, 2009,21(3):426-34.
[135]Siomi H., M.C. Siomi, RISC hitches onto endosome trafficking. Nature cell biology,2009, 11(9):1049-51.
[136]Siomi M.C., Journal club. A biologist praises a mouse model of autism inheritance. Nature, 2009,461(7263):451.
[137]Cox D.N., A. Chao, J. Baker, et al., A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes & Development,1998,12(23):3715-27.
[138]Harris A.N., P.M. Macdonald, Aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C. Development,2001,128(14):2823-32.
[139]Kuramochi-Miyagawa S., T. Kimura, T.W. Ijiri, et al., Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development,2004,131(4):839-49.
[140]Deng W., H. Lin, miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Developmental Cell,2002,2(6):819-30.
[141]Carmell M.A., A. Girard, H.J. van de Kant, et al., MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Developmental Cell,2007,12(4): 503-14.
[142]Wilczynska A., N. Minshall, J. Armisen, et al., Two Piwi proteins, Xiwi and Xili, are expressed in the Xenopus female germline. RNA,2009,15(2):337-45.
[143]Kirino Y., A. Vourekas, N. Sayed, et al., Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA,2010,16(1):70-8.
[144]Vagin V.V., J. Wohlschlegel, J. Qu, et al., Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes & Development,2009,23(15):1749-62.
[145]Kirino Y., N. Kim, M. de Planell-Saguer, et al., Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nature cell biology,2009,11(5):652-8.
[146]Siomi M.C., T. Mannen, H. Siomi, How does the royal family of Tudor rule the PIWI-interacting RNA pathway? Genes & Development,2010,24(7):636-46.
[147]Girard A., GJ. Hannon, Conserved themes in small-RNA-mediated transposon control. Trends in Cell Biology,2008,18(3):136-48.
[148]Pal-Bhadra M., B.A. Leibovitch, S.G Gandhi, et al., Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science,2004,303(5658): 669-72.
[149]Lin H., H. Yin, A novel epigenetic mechanism in Drosophila somatic cells mediated by Piwi and piRNAs. Cold Spring Harbor Symposia on Quantitative Biology,2008,73:273-81.
[150]Bedford M.T., S.G. Clarke, Protein arginine methylation in mammals:who, what, and why. Molecular Cell,2009,33(1):1-13.
[151]Bedford M.T., S. Richard, Arginine methylation an emerging regulator of protein function. Molecular Cell,2005,18(3):263-72.
[152]Cook J.R., J.H. Lee, Z.H. Yang, et al., FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues. Biochemical and Bioph-ysical Research Communications,2006,342(2):472-81.
[153]Friesen W.J., S. Massenet, S. Paushkin, et al., SMN, the product of the spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein targets. Molecular Cell, 2001,7(5):1111-7.
[154]Zhao Q., G Rank, Y.T. Tan, et al., PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing.Nature Structural & Molecular Biology,2009,16(3):304-11.
[155]Guccione E., C. Bassi, F. Casadio, et al., Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature,2007,449(7164):933-7.
[156]Lin W.J., J.D. Gary, M.C. Yang, et al., The mammalian immediate-early TIS21 protein and the leukemia-associated BTG1 protein interact with a protein-arginine N-methyl-transferase. Journal of Biological Chemistry,1996,271(25):15034-44.
[157]Pal S., S.N. Vishwanath, H. Erdjument-Bromage, et al., Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Molecular and Cellular Biology,2004,24(21):9630-45.
[158]Lacroix M., S. El Messaoudi, G Rodier, et al., The histone-binding protein COPR5 is required for nuclear functions of the protein arginine methyltransferase PRMT5. EMBO reports,2008, 9(5):452-8.
[159]Iberg A.N., A. Espejo, D. Cheng, et al., Arginine methylation of the histone H3 tail impedes effector binding. Journal of Biological Chemistry,2008,283(6):3006-10.
[160](?) Drosophila melanogaster. Cell,1985,43(1):97-104.
[161]Chen C., J. Jiri, D.A. James, et al., Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proceedings of the National Academy of Sciences of the United States of America,2009,106(48):20336-41.
[162]Reuter M., S. Chuma, T. Tanaka, et al., Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nature Structural & Molecular Biology,2009,16(6):639-46.
[163]Wang J., J.P. Saxe, T. Tanaka, et al., Mili interacts with tudor domain-containing protein 1 in regulating spermatogenesis. Current Biology,2009,19(8):640-4.
[164]Lachke S.A., F.S. Alkuraya, S.C. Kneeland, et al., Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science,2011,331(6024):1571-6.
[165]Tanaka T., M. Hosokawa, V.V. Vagin, et al., Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. Proceedings of the National Academy of Sciences of the United States of America,2011, 108(26):10579-84.
[166]Shoji M., T. Tanaka, M. Hosokawa, et al., The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Developmental Cell, 2009,17(6):775-87.
[167]Kim J., J. Daniel, A. Espejo, et al., Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Reports,2006,7(4):397-403.
[168]Jin J., X. Xie, C. Chen, et al., Eukaryotic protein domains as functional units of cellular evolution. Science signaling,2009,2(98):ra76.
[169]Boisvert F.M., J. Cote, M.C. Boulanger, et al., A proteomic analysis of arginine-methylated protein complexes. Molecular & Cellular Proteomics,2003,2(12):1319-30.
[170]Boisvert F.M., M.J. Hendzel, J.Y. Masson, et al., Methylation of MRE11 regulates its nuclear compartmentalization. Cell Cycle,2005,4(7):981-9.
[171]El-Andaloussi N., T. Valovka, M. Toueille, et al., Methylation of DNA polymerase beta by protein arginine methyltransferase 1 regulates its binding to proliferating cell nuclear antigen. FASEB Journal,2007,21(1):26-34.
[172]El-Andaloussi N., T. Valovka, M. Toueille, et al., Arginine methylation regulates DNA polymerase beta. Molecular Cell,2006,22(1):51-62.
[173]Mowen K.A., B.T. Schurter, J.W. Fathman, et al., Arginine methylation of NIP45 modulates cytokine gene expression in effector T lymphocytes. Molecular Cell,2004,15(4):559-71.
[174]Gonsalvez G.B., L. Tian, J.K. Ospina, et al., Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. Journal of Cell Biology,2007,178(5): 733-40.
[175]Friesen W.J., S. Paushkin, A. Wyce, et al., The methylosome, a 20S complex containing JBP1 and pICln, produces dimethylarginine-modified Sm proteins. Molecular and Cellular Biology, 2001,21(24):8289-300.
[176]Khusial P.R., K. Vaidya, G.W. Zieve, The symmetrical dimethylarginine post-translational modification of the SmD3 protein is not required for snRNP assembly and nuclear transport. Biochemical and Biophysical Research Communications,2005,337(4):1119-24.
[177]Tong X., R. Drapkin, R. Yalamanchili, et al., The Epstein-Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interact with TFIIE. Molecular and Cellular Biology,1995,15(9):4735-44.
[178]Paukku K., J. Yang, O. Silvennoinen, Tudor and nuclease-like domains containing protein p100 function as coactivators for signal transducer and activator of transcription 5. Molecular Endocrinology,2003,17(9):1805-14.
[179]Yang J., S. Aittomaki, M. Pesu, et al., Identification of p100 as a coactivator for STAT6 that bridges STAT6 with RNA polymerase II. EMBO Journal,2002,21(18):4950-8.
[180]Li C.L., W.Z. Yang, Y.P. Chen, et al., Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing. Nucleic Acids Research,2008,36(11): 3579-89.
[181]Scadden A.D., The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nature Structural & Molecular Biology,2005,12(6):489-96.
[182]Leverson J.D., P.J. Koskinen, F.C. Orrico, et al., Pim-1 kinase and p100 cooperate to enhance c-Myb activity. Molecular Cell,1998,2(4):417-25.
[183]Yang J., T. Valineva, J. Hong, et al., Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Research, 2007,35(13):4485-94.
[184]Callebaut I., J.P. Mornon, The human EBNA-2 coactivator p100:multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. Biochemical Journal,1997,321 (Pt 1):125-32.
[185]Ponting C.P., P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease. Protein Science,1997,6(2):459-63.
[186]Shaw N., M. Zhao, C. Cheng, et al., The multifunctional human p100 protein'hooks' methylated ligands. Nature Structural & Molecular Biology,2007,14(8):779-84.
[187]Otwinowski Z M., Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol,1997,276:307-326.
[188]Emsley P., K. Cowtan, Coot:model-building tools for molecular graphics. Acta Crystallographica Section D. Biological Crystallography,2004,60(Pt 12 Pt 1):2126-32.
[189]Winn M.D., G.N. Murshudov, M.Z. Papiz, Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol,2003,374:300-21.
[190]Winn M.D., M.N. Isupov, G.N. Murshudov, Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallographica Section D. Biological Crystallography,2001,57(Pt 1):122-33.
[191]Liu H., J.Y. Wang, Y. Huang, et al., Structural basis for methylarginine-dependent recognition of Aubergine by Tudor. Genes & Development,2010,24(17):1876-81.
[192]Lim W.A., R.O. Fox, F.M. Richards, Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5. Protein Science,1994,3(8): 1261-6.
[193]Alexandropoulos K., G Cheng, D. Baltimore, Proline-rich sequences that bind to Src homology 3 domains with individual specificities. Proceedings of the National Academy of Sciences of the United States of America,1995,92(8):3110-4.
[194]Min J., A. Allali-Hassani, N. Nady, et al, L3MBTL1 recognition of mono-and dimethylated histones. Nature Structural & Molecular Biology,2007,14(12):1229-30.
[195]Jozic D., N. Cardenes, Y.L. Deribe, et al., Cbl promotes clustering of endocytic adaptor proteins. Nature Structural & Molecular Biology,2005,12(11):972-9.
[196]Yin J., A. Sobeck, C. Xu, et al., BLAP75, an essential component of Bloom's syndrome protein complexes that maintain genome integrity. EMBO Journal,2005,24(7):1465-76.
[197]Linder B., O. Plottner, M. Kroiss, et al., Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP. Human Molecular Genetics,2008, 17(20):3236-46.
[198]Hurley J.H., S. Lee, G Prag, Ubiquitin-binding domains. Biochemical Journal,2006,399(3): 361-72.
[199]Yang Y., Y. Lu, A. Espejo, et al., TDRD3 is an effector molecule for arginine-methylated histone marks. Molecular Cell,2010,40(6):1016-23.
[200]Goulet I., S. Boisvenue, S. Mokas, et al., TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. Human Molecular Genetics,2008,17(19): 3055-74.
[201]Pellizzoni L., N. Kataoka, B. Charroux, et al., A novel function for SMN, the spinal muscular atrophy disease gene product, in pre-mRNA splicing. Cell,1998,95(5):615-24.
[202]Meister G, C. Eggert, D. Buhler, et al., Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln. Current Biology,2001,11(24): 1990-4.
[203]Brahms H., L. Meheus, V. de Brabandere, et al., Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B'and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA,2001,7(11):1531-42.
[204]Whitehead S.E., K.W. Jones, X. Zhang, et al., Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1. Journal of Biological Chemistry,2002,277(50): 48087-93.
[205]Young P.J., J.W. Francis, D. Lince, et al., The Ewing's sarcoma protein interacts with the Tudor domain of the survival motor neuron protein. Brain Research Molecular Brain Research, 2003,119(1):37-49.
[206]Cheng D., J. Cote, S. Shaaban, et al., The arginine methyltransferase CARM1 regulates the coupling of transcription and mRNA processing. Molecular Cell,2007,25(1):71-83.
[207]Cote J., S. Richard, Tudor domains bind symmetrical dimethylated arginines. Journal of Biological Chemistry,2005,280(31):28476-83.
[208]Dauter Z., M. Dauter, E. Dodson, Jolly SAD. Acta Crystallographica Section D. Biological Crystallography,2002,58(Pt 3):494-506.
[209]Dodson E., Is it jolly SAD? Acta Crystallographica Section D. Biological Crystallography,2003, 59(Pt 11):1958-65.
[210]Schneider T.R., G.M. Sheldrick, Substructure solution with SHELXD. Acta Crystallo-graphica Section D. Biological Crystallography,2002,58(Pt 10 Pt 2):1772-9.
[211]Bricogrie G, C. Vonrhein, C. Flensburg, et al., Generation, representation and flow of phase information in structure determination:recent developments in and around SHARP 2.0. Acta Crystallographica Section D. Biological Crystallography,2003,59(Pt 11):2023-30.
[212]Perrakis A., M. Harkiolaki, K.S. Wilson, et al, ARP/wARP and molecular replacement. Acta Crystallographica Section D. Biological Crystallography,2001,57(Pt 10):1445-50.
[213]Perrakis A., R. Morris, V.S. Lamzin, Automated protein model building combined with iterative structure refinement. Nature Structural Biology,1999,6(5):458-63.
[214]Murshudov GN., A.A. Vagin, E.J. Dodson, Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica Section D. Biological Crystall-ography, 1997,53(Pt 3):240-55.
[215]Liu K., C. Chen, Y. Guo, et al., Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proceedings of the National Academy of Sciences of the United States of America,2010,107 (43):18398-403.
[216]Tripsianes K., T. Madl, M. Machyna, et al., Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nature Structural & Molecular Biology,2011,18(12):1414-20.
[217]Sprangers R., M.R. Groves, I. Sinning, et al., High-resolution X-ray and NMR structures of the SMN Tudor domain:conformational variation in the binding site for symmetrically dimethylated arginine residues. Journal of Molecular Biology,2003,327(2):507-20.
[218]Eryilmaz J., P. Pan, M.F. Amaya, et al, Structural studies of a four-MBT repeat protein MBTD1. PLoS One,2009,4(10):e7274.
[219]Adams-Cioaba M.A., Y. Guo, C. Bian, et al, Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2. PLoS One,5(11):e13559.
[2]Goldberg A.D., C.D. Allis, E. Bernstein, Epigenetics:a landscape takes shape. Cell,2007,128(4): 635-8.
[3]Egger G., G. Liang, A. Aparicio, et al., Epigenetics in human disease and prospects for epigenetic therapy. Nature,2004,429(6990):457-63.
[4]Kim T.Y., Y.J. Bang, K.D. Robertson, Histone deacetylase inhibitors for cancer therapy. Epigenetics,2006,1(1):14-23.
[5]Yoo C.B., P.A. Jones, Epigenetic therapy of cancer:past, present and future. Nature Reviews Drug Discovery,2006,5(1):37-50.
[6]Schroeder M., M.O. Krebs, S. Bleich, et al., Epigenetics and depression:current challenges and new therapeutic options. Current Opinion in Psychiatry,2010,23(6):588-92.
[7]Caffarelli E., P. Filetici, Epigenetic regulation in cancer development. Frontiers in Bioscience, 2011,17:2682-94.
[8]Portela A., M. Esteller, Epigenetic modifications and human disease. Nature Biotechnology,2010, 28(10):1057-68.
[9]Patra S.K., S. Bettuzzi, Epigenetic DNA-(cytosine-5-carbon) modifications:5-aza-2'-deoxy-cytidine and DNA-demethylation. Biochemistry (Mosc),2009,74(6):613-9.
[10]Gronbaek K., C. Hother, P.A. Jones, Epigenetic changes in cancer. Apmis,2007,115(10): 1039-59.
[11]Mai A., Small-molecule chromatin-modifying agents:therapeutic applications. Epigenomics, 2010,2(2):307-24.
[12]Schaefer A., S.C. Sampath, A. Intrator, et al., Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron,2009,64(5):678-91.
[13]Kubicek S., R.J. O'Sullivan, E.M. August, et al., Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase. Molecular Cell,2007,25(3):473-81.
[14]Greiner D., T. Bonaldi, R. Eskeland, et al., Identification of a specific inhibitor of the histone methyltransferase SU (VAR) 3-9. Nature Chemical Biology,2005,1(3):143-5.
[15]Ganesan A., L. Nolan, S. J. Crabb, et al., Epigenetic therapy:histone acetylation, DNA methy-lation and anti-cancer drug discovery. Current Cancer Drug Targets,2009,9(8):963-81.
[16]Ho L., G.R. Crabtree, Chromatin remodelling during development. Nature,2010,463(7280): 474-84.
[17]Taverna S.D., H. Li, A.J. Ruthenburg, et al., How chromatin-binding modules interpret histone modifications:lessons from professional pocket pickers. Nature Structural & Molecular Biology,2007,14(11):1025-40.
[18]Strahl B.D., C.D. Allis, The language of covalent histone modifications. Nature,2000,403(6765) 41-5.
[19]Jenuwein T., C.D. Allis, Translating the histone code. Science,2001,293(5532):1074-80.
[20]Kouzarides T., Chromatin modifications and their function. Cell,2007,128(4):693-705.
[21]Mai A., L. Altucci, Epi-drugs to fight cancer:from chemistry to cancer treatment, the road ahead. International Journal of Biochemistry & Cell Biology,2009,41(1):199-213.
[22]Chu C.Y., T.M. Rana, Small RNAs:regulators and guardians of the genome. Journal of Cellular Physiology,2007,213(2):412-9.
[23]Filipowicz W., S.N. Bhattacharyya, N. Sonenberg, Mechanisms of post-transcriptional regulation by microRNAs:are the answers in sight? Nature Reviews Genetics,2008,9(2):102-14.
[24]Brennecke J., A.A. Aravin, A. Stark, et al., Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell,2007,128(6):1089-103.
[25]Houwing S., L.M. Kamminga, E. Berezikov, et al., A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell,2007,129(1):69-82.
[26]Pak J., A. Fire, Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science,2007,315(5809):241-4.
[27]Vagin V.V., A. Sigova, C. Li, et al., A distinct small RNA pathway silences selfish genetic elements in the germline. Science,2006,313(5785):320-4.
[28]Sijen T., F.A. Steiner, K.L. Thijssen, et al., Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science,2007,315(5809):244-7.
[29]Czech B., G.J. Hannon, Small RNA sorting:matchmaking for Argonautes. Nature Reviews Genetics,2011,12(1):19-31.
[30]Martinez J., A. Patkaniowska, H. Urlaub, et al., Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell,2002,110(5):563-74.
[31]Okamura K., N. Liu, E.C. Lai, Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Molecular Cell,2009,36(3):431-44.
[32]Khvorova A., A. Reynolds, S.D. Jayasena, Functional siRNAs and miRNAs exhibit strand bias. Cell,2003,115(2):209-16.
[33]Schwarz D.S., G. Hutvagner, T. Du, et al., Asymmetry in the assembly of the RNAi enzyme complex. Cell,2003,115(2):199-208.
[34]Liu Y., X. Ye, F. Jiang, et al., C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science,2009,325(5941):750-753.
[35]Horwich M.D., C. Li, C. Matranga, et al., The Drosophila RNA methyltransferase, DmHenl, modifies germline piRNAs and single-stranded siRNAs in RISC. Current Biology,2007, 17(14):1265-1272.
[36]Li N., A. Nguyen, J. Diedrich, et al., Separation of miRNA and its methylation products by capillary electrophoresis. Journal of Chromatography A,2008,1202(2):220-223.
[37]Yu B., Z. Yang, J. Li, et al., Methylation as a crucial step in plant microRNA biogenesis. Science, 2005,307(5711):932-935.
[38]Ameres S.L., M.D. Horwich, J.H. Hung, et al., Target RNA-directed trimming and tailing of small silencing RNAs. Science,2010,328(5985):1534-1539.
[39]Fabian M.R., N. Sonenberg, W. Filipowicz, Regulation of mRNA translation and stability by microRNAs. Annual Review of Biochemistry,2010,79:351-379.
[40]Brodersen P. and O. Voinnet, Revisiting the principles of microRNA target recognition and mode of action. Nature Reviews Molecular Cell Biology,2009,10(2):141-148.
[41]Forstemann K., M.D. Horwich, L. Wee, et al., Drosophila microRNAs are sorted into func-tionally distinct argonaute complexes after production by dicer-1. Cell,2007,130(2): 287-297.
[42]Iwasaki S., T. Kawamata, Y. Tomari, Drosophila argonautel and argonaute2 employ distinct mechanisms for translational repression. Molecular Cell,2009,34(1):58-67.
[43]Yekta S., I.H. Shih, D.P. Bartel, MicroRNA-directed cleavage of HOXB8 mRNA. Science,2004, 304(5670):594-6.
[44]Ma J.B., Y.R. Yuan, G. Meister, et al., Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature,2005,434(7033):666-70.
[45]Song J.J., S.K. Smith, G.J. Hannon, et al., Crystal structure of Argonaute and its implications for RISC slicer activity. Science,2004,305(5689):1434-7.
[46]Parker J.S., S.M. Roe, D. Barford, Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO Journal,2004,23(24):4727-37.
[47]Yuan Y.R., Y. Pei, H.Y. Chen, et al., A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA. Structure,2006,14(10):1557-65.
[48]Yuan Y.R., Y. Pei, J.B. Ma, et al., Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Molecular Cell,2005,19(3):405-19.
[49]Wang Y., S. Juranek, H. Li, et al., Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature,2008,456(7224):921-6.
[50]Lapatto R., T. Blundell, A. Hemmings, et al., X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature,1989,342(6247): 299-302.
[51]Miller M., J. Schneider, B.K. Sathyanarayana, et al., Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science,1989,246(4934): 1149-52.
[52]Ali H.I., T. Nagamatsu, E. Akaho, Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors. Bioinformation,2011,5(9):368-74.
[53]Hetenyi C., U. Maran, A.T. Garcia-Sosa, et al., Structure-based calculation of drug efficiency indices. Bioinformatics,2007,23(20):2678-85.
[54]Kapoor N., T. Banerjee, P. Babu, et al., Design, development, synthesis, and docking analysis of 2'-substituted triclosan analogs as inhibitors for Plasmodium falciparum enoyl-ACP reductase. IUBMB Life,2009,61(11):1083-91.
[55]Anderson A.C., Winning the Arms Race by Improving Drug Discovery against Mutating Targets. ACS Chemical Biology,2012,7(2):278-88.
[56]Yun M., J. Wu, J.L. Workman, et al., Readers of histone modifications. Cell Research,2011, 21(4):564-578.
[57]Herold J.M., L.A. Ingerman, C. Gao, et al., Drug discovery toward antagonists of methyl-lysine binding proteins. Current Chemical Genomics,2011,5:51-61.
[58]Bao J., L. Wang, J. Lei, et al., STK31 (TDRD8) is dynamically regulated throughout mouse spermatogenesis and interacts with MIWI protein. Histochemistry and Cell Biology,2012, 137(3):377-89.
[59]Yabuta Y, H. Ohta, T. Abe, et al, TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. Journal of Cell Biology,2011,192(5):781-95.
[60]Kojima K., S. Kuramochi-Miyagawa, S. Chuma, et al., Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells. Genes to Cells,2009,14(10):1155-65.
[61]Vasileva A., D. Tiedau, A. Firooznia, et al., Tdrd6 is required for spermiogenesis, chromatoid body architecture, and regulation of miRNA expression. Current Biology,2009,19(8):630-9.
[62]Grivna S.T., B. Pyhtila, H. Lin, MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proceedings of the National Academy of Sciences of the United States of America,2006,103(36):13415-20.
[63]Aravin A., D. Gaidatzis, S. Pfeffer, et al., A novel class of small RNAs bind to MILI protein in mouse testes. Nature,2006,442(7099):203-7.
[64]Lallous N., P. Legrand, A.G McEwen, et al., The PHD finger of human UHRF1 reveals a new subgroup of unmethylated histone H3 tail readers. PLoS One,2011,6(11):e27599.
[65]Varier R.A., N.S. Outchkourov, P. de Graaf, et al., A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes. EMBO Journal,2010,29(23): 3967-78.
[66]Fischle W., B.S. Tseng, H.L. Dormann, et al., Regulation of HPl-chromatin binding by histone H3 methylation and phosphorylation. Nature,2005,438(7071):1116-22.
[67]Sun B., J. Hong, P. Zhang, et al., Molecular basis of the interaction of Saccharomyces cerevisiae Eaf3 chromo domain with methylated H3K36. Journal of Biological Chemistry,2008, 283(52):36504-12.
[68]Xu C., G Cui, M.V. Botuyan, et al., Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure,2008,16(11): 1740-50.
[69]Li B., M. Gogol, M. Carey, et al., Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science,2007,316(5827):1050-4.
[70]Turner B.M. and L.P. O'Neill, Histone acetylation in chromatin and chromosomes. Seminars in Cell Biology,1995,6(4):229-36.
[71]Nakajima H., A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Tanpakushitsu Kakusan Koso,2007,52(13 Suppl):1790-1.
[72]Brownell J.E., J. Zhou, T. Ranalli, et al, Tetrahymena histone acetyltransferase A:a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell,1996,84(6):843-51.
[73]Mujtaba S., L. Zeng, M.M. Zhou, Structure and acetyl-lysine recognition of the bromodomain. Oncogene,2007,26(37):5521-7.
[74]Zeng L., Q. Zhang, S. Li, et al., Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature,2010,466(7303):258-62.
[75]Hudson B.P., M.A. Martinez-Yamout, H.J. Dyson, et al., Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. Journal of Molecular Biology,2000,304(3): 355-70.
[76]Owen D.J., P. Ornaghi, J.C. Yang, et al., The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO Journal, 2000,19(22):6141-9.
[77]Mujtaba S., Y. He, L. Zeng, et al., Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Molecular Cell,2002,9(3):575-86.
[78]Nakamura Y., T. Umehara, K. Nakano, et al., Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. Journal of Biological Chemistry,2007,282(6):4193-201.
[79]Mujtaba S., Y. He, L. Zeng, et al., Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Molecular Cell,2004,13(2):251-63.
[80]Li H., S. Ilin, W. Wang, et al., Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature,2006,442(7098):91-5.
[81]Shen W., C. Xu, W. Huang, et al., Solution structure of human Brgl bromodomain and its specific binding to acetylated histone tails. Biochemistry,2007,46(8):2100-10.
[82]Dhalluin C., J.E. Carlson, L. Zeng, et al., Structure and ligand of a histone acetyltransferase bromodomain. Nature,1999,399(6735):491-6.
[83]Umehara T., Y. Nakamura, M.K. Jang, et al., Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain. Journal of Biological Chemistry,2010, 285(10):7610-8.
[84]Huang H., J. Zhang, W. Shen, et al., Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC Structural Biology,2007,7:57.
[85]Seet B.T., I. Dikic, M.M. Zhou, et al., Reading protein modifications with interaction domains. Nature Reviews Molecular Cell Biology,2006,7(7):473-83.
[86]Cheung P., C.D. Allis, P. Sassone-Corsi, Signaling to chromatin through histone modifications. Cell,2000,103(2):263-71.
[87]Cheung P., K.G. Tanner, W.L. Cheung, et al., Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Molecular Cell,2000, 5(6):905-15.
[88]Thomson S., A.L. Clayton, C.A. Hazzalin, et al., The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades:MSK1 as a potential histone H3/HMG-14 kinase. EMBO Journal,1999,18(17):4779-93.
[89]Macdonald N., J.P. Welburn, M.E. Noble, et al., Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. Molecular Cell,2005,20(2): 199-211.
[90]Stucki M., J.A. Clapperton, D. Mohammad, et al., MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell,2005,123(7): 1213-26.
[91]Jeyaprakash A.A., C. Basquin, U. Jayachandran, et al., Structural basis for the recognition of phosphorylated histone h3 by the survivin subunit of the chromosomal passenger complex. Structure,2011,19(11):1625-34.
[92]Bannister A.J., T. Kouzarides, Reversing histone methylation. Nature,2005,436(7054):1103-6.
[93]Martin C., Y. Zhang, The diverse functions of histone lysine methylation. Nature Reviews Molecular Cell Biology,2005,6(11):838-49.
[94]Jacobs S.A., S. Khorasanizadeh, Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science,2002,295(5562):2080-3.
[95]Nielsen P.R., D. Nietlispach, H.R. Mott, et al., Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature,2002,416(6876):103-7.
[96]Min J., Y. Zhang, R.M. Xu, Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes & Development,2003,17(15):1823-8.
[97]Li J., Z. Li, J. Ruan, et al., Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9. PLoS One,2011,6(10):e25104.
[98]Pray-Grant M.G., J.A. Daniel, D. Schieltz, et al., Chdl chromodomain links histone H3 methylation with SAGA-and SLIK-dependent acetylation. Nature,2005,433(7024):434-8.
[99]Flanagan J.F., L.Z. Mi, M. Chruszcz, et al., Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature,2005,438(7071):1181-5.
[100]Bertram M.J., O.M. Pereira-Smith, Conservation of the MORF4 related gene family: identification of a new chromo domain subfamily and novel protein motif. Gene,2001, 266(1-2):111-21.
[101]Zhang P., J. Du, B. Sun, et al, Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Research,2006,34(22):6621-8.
[102]Ruthenburg A.J., C.D. Allis, J. Wysocka, Methylation of lysine 4 on histone H3:intricacy of writing and reading a single epigenetic mark. Molecular Cell,2007,25(1):15-30.
[103]Stec I., S.B. Nagl, G.J. van Ommen, et al., The PWWP domain:a potential protein-protein interaction domain in nuclear proteins influencing differentiation? FEBS Lett,2000,473(1): 1-5.
[104]Qiu C., K. Sawada, X. Zhang, et al, The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nature Structural & Molecular Biology, 2002,9(3):217-24.
[105]Maurer-Stroh S., N.J. Dickens, L. Hughes-Davies, et al, The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends in Biochemical Sciences, 2003,28(2):69-74.
[106]Wang Y., B. Reddy, J. Thompson, et al., Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein. Molecular Cell,2009,33(4):428-37.
[107]Dhayalan A., A. Rajavelu, P. Rathert, et al., The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. Journal of Biological Chemistry,2010, 285(34):26114-20.
[108]Vezzoli A., N. Bonadies, M.D. Allen, et al., Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpfl. Nature Structural & Molecular Biology,2010,17(5):617-9.
[109]Vermeulen M., H.C. Eberl, F. Matarese, et al., Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell,2010,142(6): 967-80.
[110]Wu H., H. Zeng, R. Lam, et al., Structural and histone binding ability characterizations of human PWWP domains. PLoS One,2011,6(6):e18919.
[111]Bienz M., The PHD finger, a nuclear protein-interaction domain. Trends in Biochemical Sciences,2006,31(1):35-40.
[112]Pena P.V., F. Davrazou, X. Shi, et al., Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature,2006,442(7098):100-3.
[113]Lan F., R.E. Collins, R. De Cegli, et al., Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSDl-mediated gene repression. Nature,2007,448(7154):718-22.
[114]Ooi S.K., C. Qiu, E. Bernstein, et al., DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature,2007,448(7154):714-7.
[115]Adams-Cioaba M.A., J. Min, Structure and function of histone methylation binding proteins. International Journal of Biochemistry & Cell Biology,2009,87(1):93-105.
[116]Botuyan M.V., J. Lee, I.M. Ward, et al., Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell,2006,127(7): 1361-73.
[117]Lee J., J.R. Thompson, M.V. Botuyan, et al., Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor. Nature Structural & Molecular Biology,2008,15(1):109-11.
[118]Bian C., C. Xu, J. Ruan, et al., Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. EMBO Journal,2011,30(14):2829-42.
[119]Huang Y., J. Fang, M.T. Bedford, et al., Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science,2006,312(5774):748-51.
[120]Wang W., Z. Chen, Z. Mao, et al., Nucleolar protein Spindlinl recognizes H3K4 methylation and stimulates the expression of rRNA genes. EMBO reports,2011,12(11):1160-6.
[121]Kalakonda N., W. Fischle, P. Boccuni, et al., Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1. Oncogene,2008,27(31):4293-304.
[122]Li H., W. Fischle, W. Wang, et al., Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Molecular Cell,2007, 28(4):677-91.
[123]Guo Y., N. Nady, C. Qi, et al., Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Research,2009,37(7):2204-10.
[124]Xu C., C. Bian, W. Yang, et al., Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proceedings of the National Academy of Sciences of the United States of America,2010,107(45):19266-71.
[125]Margueron R., N. Justin, K. Ohno, et al., Role of the polycomb protein EED in the propagation of repressive histone marks. Nature,2009,461(7265):762-7.
[126]Han Z., L. Guo, H. Wang, et al., Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Molecular Cell,2006,22(1):137-44.
[127]Ruthenburg A.J., W. Wang, D.M. Graybosch, et al, Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nature Structural & Molecular Biology,2006, 13(8):704-12.
[128]Schuetz A., A. Allali-Hassani, F. Martin, et al., Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO Journal,2006,25(18):4245-52.
[129]Aravin A.A., N.M. Naumova, A.V. Tulin, et al., Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Current Biology,2001,11(13):1017-27.
[130]Aravin A.A., M. Lagos-Quintana, A. Yalcin, et al., The small RNA profile during Drosophila melanogaster development. Developmental Cell,2003,5(2):337-50.
[131]Girard A., R. Sachidanandam, GJ. Hannon, et al., A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature,2006,442(7099):199-202.
[132]Aravin A.A., R. Sachidanandam, A. Girard, et al., Developmentally regulated piRNA clusters implicate MILI in transposon control. Science,2007,316(5825):744-7.
[133]Aravin A.A., GJ. Hannon, J. Brennecke, The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science,2007,318(5851):761-4.
[134]Siomi M.C., S. Kuramochi-Miyagawa, RNA silencing in germlines-exquisite collaboration of Argonaute proteins with small RNAs for germline survival. Current Opinion in Cell Biology, 2009,21(3):426-34.
[135]Siomi H., M.C. Siomi, RISC hitches onto endosome trafficking. Nature cell biology,2009, 11(9):1049-51.
[136]Siomi M.C., Journal club. A biologist praises a mouse model of autism inheritance. Nature, 2009,461(7263):451.
[137]Cox D.N., A. Chao, J. Baker, et al., A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes & Development,1998,12(23):3715-27.
[138]Harris A.N., P.M. Macdonald, Aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C. Development,2001,128(14):2823-32.
[139]Kuramochi-Miyagawa S., T. Kimura, T.W. Ijiri, et al., Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development,2004,131(4):839-49.
[140]Deng W., H. Lin, miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Developmental Cell,2002,2(6):819-30.
[141]Carmell M.A., A. Girard, H.J. van de Kant, et al., MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Developmental Cell,2007,12(4): 503-14.
[142]Wilczynska A., N. Minshall, J. Armisen, et al., Two Piwi proteins, Xiwi and Xili, are expressed in the Xenopus female germline. RNA,2009,15(2):337-45.
[143]Kirino Y., A. Vourekas, N. Sayed, et al., Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA,2010,16(1):70-8.
[144]Vagin V.V., J. Wohlschlegel, J. Qu, et al., Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes & Development,2009,23(15):1749-62.
[145]Kirino Y., N. Kim, M. de Planell-Saguer, et al., Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nature cell biology,2009,11(5):652-8.
[146]Siomi M.C., T. Mannen, H. Siomi, How does the royal family of Tudor rule the PIWI-interacting RNA pathway? Genes & Development,2010,24(7):636-46.
[147]Girard A., GJ. Hannon, Conserved themes in small-RNA-mediated transposon control. Trends in Cell Biology,2008,18(3):136-48.
[148]Pal-Bhadra M., B.A. Leibovitch, S.G Gandhi, et al., Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science,2004,303(5658): 669-72.
[149]Lin H., H. Yin, A novel epigenetic mechanism in Drosophila somatic cells mediated by Piwi and piRNAs. Cold Spring Harbor Symposia on Quantitative Biology,2008,73:273-81.
[150]Bedford M.T., S.G. Clarke, Protein arginine methylation in mammals:who, what, and why. Molecular Cell,2009,33(1):1-13.
[151]Bedford M.T., S. Richard, Arginine methylation an emerging regulator of protein function. Molecular Cell,2005,18(3):263-72.
[152]Cook J.R., J.H. Lee, Z.H. Yang, et al., FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues. Biochemical and Bioph-ysical Research Communications,2006,342(2):472-81.
[153]Friesen W.J., S. Massenet, S. Paushkin, et al., SMN, the product of the spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein targets. Molecular Cell, 2001,7(5):1111-7.
[154]Zhao Q., G Rank, Y.T. Tan, et al., PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing.Nature Structural & Molecular Biology,2009,16(3):304-11.
[155]Guccione E., C. Bassi, F. Casadio, et al., Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature,2007,449(7164):933-7.
[156]Lin W.J., J.D. Gary, M.C. Yang, et al., The mammalian immediate-early TIS21 protein and the leukemia-associated BTG1 protein interact with a protein-arginine N-methyl-transferase. Journal of Biological Chemistry,1996,271(25):15034-44.
[157]Pal S., S.N. Vishwanath, H. Erdjument-Bromage, et al., Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Molecular and Cellular Biology,2004,24(21):9630-45.
[158]Lacroix M., S. El Messaoudi, G Rodier, et al., The histone-binding protein COPR5 is required for nuclear functions of the protein arginine methyltransferase PRMT5. EMBO reports,2008, 9(5):452-8.
[159]Iberg A.N., A. Espejo, D. Cheng, et al., Arginine methylation of the histone H3 tail impedes effector binding. Journal of Biological Chemistry,2008,283(6):3006-10.
[160](?) Drosophila melanogaster. Cell,1985,43(1):97-104.
[161]Chen C., J. Jiri, D.A. James, et al., Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proceedings of the National Academy of Sciences of the United States of America,2009,106(48):20336-41.
[162]Reuter M., S. Chuma, T. Tanaka, et al., Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nature Structural & Molecular Biology,2009,16(6):639-46.
[163]Wang J., J.P. Saxe, T. Tanaka, et al., Mili interacts with tudor domain-containing protein 1 in regulating spermatogenesis. Current Biology,2009,19(8):640-4.
[164]Lachke S.A., F.S. Alkuraya, S.C. Kneeland, et al., Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science,2011,331(6024):1571-6.
[165]Tanaka T., M. Hosokawa, V.V. Vagin, et al., Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. Proceedings of the National Academy of Sciences of the United States of America,2011, 108(26):10579-84.
[166]Shoji M., T. Tanaka, M. Hosokawa, et al., The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Developmental Cell, 2009,17(6):775-87.
[167]Kim J., J. Daniel, A. Espejo, et al., Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Reports,2006,7(4):397-403.
[168]Jin J., X. Xie, C. Chen, et al., Eukaryotic protein domains as functional units of cellular evolution. Science signaling,2009,2(98):ra76.
[169]Boisvert F.M., J. Cote, M.C. Boulanger, et al., A proteomic analysis of arginine-methylated protein complexes. Molecular & Cellular Proteomics,2003,2(12):1319-30.
[170]Boisvert F.M., M.J. Hendzel, J.Y. Masson, et al., Methylation of MRE11 regulates its nuclear compartmentalization. Cell Cycle,2005,4(7):981-9.
[171]El-Andaloussi N., T. Valovka, M. Toueille, et al., Methylation of DNA polymerase beta by protein arginine methyltransferase 1 regulates its binding to proliferating cell nuclear antigen. FASEB Journal,2007,21(1):26-34.
[172]El-Andaloussi N., T. Valovka, M. Toueille, et al., Arginine methylation regulates DNA polymerase beta. Molecular Cell,2006,22(1):51-62.
[173]Mowen K.A., B.T. Schurter, J.W. Fathman, et al., Arginine methylation of NIP45 modulates cytokine gene expression in effector T lymphocytes. Molecular Cell,2004,15(4):559-71.
[174]Gonsalvez G.B., L. Tian, J.K. Ospina, et al., Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. Journal of Cell Biology,2007,178(5): 733-40.
[175]Friesen W.J., S. Paushkin, A. Wyce, et al., The methylosome, a 20S complex containing JBP1 and pICln, produces dimethylarginine-modified Sm proteins. Molecular and Cellular Biology, 2001,21(24):8289-300.
[176]Khusial P.R., K. Vaidya, G.W. Zieve, The symmetrical dimethylarginine post-translational modification of the SmD3 protein is not required for snRNP assembly and nuclear transport. Biochemical and Biophysical Research Communications,2005,337(4):1119-24.
[177]Tong X., R. Drapkin, R. Yalamanchili, et al., The Epstein-Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interact with TFIIE. Molecular and Cellular Biology,1995,15(9):4735-44.
[178]Paukku K., J. Yang, O. Silvennoinen, Tudor and nuclease-like domains containing protein p100 function as coactivators for signal transducer and activator of transcription 5. Molecular Endocrinology,2003,17(9):1805-14.
[179]Yang J., S. Aittomaki, M. Pesu, et al., Identification of p100 as a coactivator for STAT6 that bridges STAT6 with RNA polymerase II. EMBO Journal,2002,21(18):4950-8.
[180]Li C.L., W.Z. Yang, Y.P. Chen, et al., Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing. Nucleic Acids Research,2008,36(11): 3579-89.
[181]Scadden A.D., The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nature Structural & Molecular Biology,2005,12(6):489-96.
[182]Leverson J.D., P.J. Koskinen, F.C. Orrico, et al., Pim-1 kinase and p100 cooperate to enhance c-Myb activity. Molecular Cell,1998,2(4):417-25.
[183]Yang J., T. Valineva, J. Hong, et al., Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Research, 2007,35(13):4485-94.
[184]Callebaut I., J.P. Mornon, The human EBNA-2 coactivator p100:multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. Biochemical Journal,1997,321 (Pt 1):125-32.
[185]Ponting C.P., P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease. Protein Science,1997,6(2):459-63.
[186]Shaw N., M. Zhao, C. Cheng, et al., The multifunctional human p100 protein'hooks' methylated ligands. Nature Structural & Molecular Biology,2007,14(8):779-84.
[187]Otwinowski Z M., Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol,1997,276:307-326.
[188]Emsley P., K. Cowtan, Coot:model-building tools for molecular graphics. Acta Crystallographica Section D. Biological Crystallography,2004,60(Pt 12 Pt 1):2126-32.
[189]Winn M.D., G.N. Murshudov, M.Z. Papiz, Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol,2003,374:300-21.
[190]Winn M.D., M.N. Isupov, G.N. Murshudov, Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallographica Section D. Biological Crystallography,2001,57(Pt 1):122-33.
[191]Liu H., J.Y. Wang, Y. Huang, et al., Structural basis for methylarginine-dependent recognition of Aubergine by Tudor. Genes & Development,2010,24(17):1876-81.
[192]Lim W.A., R.O. Fox, F.M. Richards, Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5. Protein Science,1994,3(8): 1261-6.
[193]Alexandropoulos K., G Cheng, D. Baltimore, Proline-rich sequences that bind to Src homology 3 domains with individual specificities. Proceedings of the National Academy of Sciences of the United States of America,1995,92(8):3110-4.
[194]Min J., A. Allali-Hassani, N. Nady, et al, L3MBTL1 recognition of mono-and dimethylated histones. Nature Structural & Molecular Biology,2007,14(12):1229-30.
[195]Jozic D., N. Cardenes, Y.L. Deribe, et al., Cbl promotes clustering of endocytic adaptor proteins. Nature Structural & Molecular Biology,2005,12(11):972-9.
[196]Yin J., A. Sobeck, C. Xu, et al., BLAP75, an essential component of Bloom's syndrome protein complexes that maintain genome integrity. EMBO Journal,2005,24(7):1465-76.
[197]Linder B., O. Plottner, M. Kroiss, et al., Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP. Human Molecular Genetics,2008, 17(20):3236-46.
[198]Hurley J.H., S. Lee, G Prag, Ubiquitin-binding domains. Biochemical Journal,2006,399(3): 361-72.
[199]Yang Y., Y. Lu, A. Espejo, et al., TDRD3 is an effector molecule for arginine-methylated histone marks. Molecular Cell,2010,40(6):1016-23.
[200]Goulet I., S. Boisvenue, S. Mokas, et al., TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. Human Molecular Genetics,2008,17(19): 3055-74.
[201]Pellizzoni L., N. Kataoka, B. Charroux, et al., A novel function for SMN, the spinal muscular atrophy disease gene product, in pre-mRNA splicing. Cell,1998,95(5):615-24.
[202]Meister G, C. Eggert, D. Buhler, et al., Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln. Current Biology,2001,11(24): 1990-4.
[203]Brahms H., L. Meheus, V. de Brabandere, et al., Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B'and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA,2001,7(11):1531-42.
[204]Whitehead S.E., K.W. Jones, X. Zhang, et al., Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1. Journal of Biological Chemistry,2002,277(50): 48087-93.
[205]Young P.J., J.W. Francis, D. Lince, et al., The Ewing's sarcoma protein interacts with the Tudor domain of the survival motor neuron protein. Brain Research Molecular Brain Research, 2003,119(1):37-49.
[206]Cheng D., J. Cote, S. Shaaban, et al., The arginine methyltransferase CARM1 regulates the coupling of transcription and mRNA processing. Molecular Cell,2007,25(1):71-83.
[207]Cote J., S. Richard, Tudor domains bind symmetrical dimethylated arginines. Journal of Biological Chemistry,2005,280(31):28476-83.
[208]Dauter Z., M. Dauter, E. Dodson, Jolly SAD. Acta Crystallographica Section D. Biological Crystallography,2002,58(Pt 3):494-506.
[209]Dodson E., Is it jolly SAD? Acta Crystallographica Section D. Biological Crystallography,2003, 59(Pt 11):1958-65.
[210]Schneider T.R., G.M. Sheldrick, Substructure solution with SHELXD. Acta Crystallo-graphica Section D. Biological Crystallography,2002,58(Pt 10 Pt 2):1772-9.
[211]Bricogrie G, C. Vonrhein, C. Flensburg, et al., Generation, representation and flow of phase information in structure determination:recent developments in and around SHARP 2.0. Acta Crystallographica Section D. Biological Crystallography,2003,59(Pt 11):2023-30.
[212]Perrakis A., M. Harkiolaki, K.S. Wilson, et al, ARP/wARP and molecular replacement. Acta Crystallographica Section D. Biological Crystallography,2001,57(Pt 10):1445-50.
[213]Perrakis A., R. Morris, V.S. Lamzin, Automated protein model building combined with iterative structure refinement. Nature Structural Biology,1999,6(5):458-63.
[214]Murshudov GN., A.A. Vagin, E.J. Dodson, Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica Section D. Biological Crystall-ography, 1997,53(Pt 3):240-55.
[215]Liu K., C. Chen, Y. Guo, et al., Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proceedings of the National Academy of Sciences of the United States of America,2010,107 (43):18398-403.
[216]Tripsianes K., T. Madl, M. Machyna, et al., Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nature Structural & Molecular Biology,2011,18(12):1414-20.
[217]Sprangers R., M.R. Groves, I. Sinning, et al., High-resolution X-ray and NMR structures of the SMN Tudor domain:conformational variation in the binding site for symmetrically dimethylated arginine residues. Journal of Molecular Biology,2003,327(2):507-20.
[218]Eryilmaz J., P. Pan, M.F. Amaya, et al, Structural studies of a four-MBT repeat protein MBTD1. PLoS One,2009,4(10):e7274.
[219]Adams-Cioaba M.A., Y. Guo, C. Bian, et al, Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2. PLoS One,5(11):e13559.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |