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Review Article

Keeping it in the family: diverse histone recognition by conserved structural folds

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Pages 488-505 | Received 12 May 2010, Accepted 27 Jul 2010, Published online: 06 Oct 2010

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L. Aravind, Vivek Anantharaman, Saraswathi Abhiman & Lakshminarayan M. Iyer. 2013. Protein Families. Protein Families 421 502 .
Chris M. Egan, Ulrika Nyman, Julie Skotte, Gundula Streubel, Siobhán Turner, David J. O’Connell, Vilma Rraklli, Michael J. Dolan, Naomi Chadderton, Klaus Hansen, Gwyneth Jane Farrar, Kristian Helin, Johan Holmberg & Adrian P. Bracken. (2013) CHD5 Is Required for Neurogenesis and Has a Dual Role in Facilitating Gene Expression and Polycomb Gene Repression. Developmental Cell 26:3, pages 223-236.
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Dinshaw J. PatelZhanxin Wang. (2013) Readout of Epigenetic Modifications. Annual Review of Biochemistry 82:1, pages 81-118.
Crossref
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Vincent Zecchini & David E. Neal. (2013) Targeting the pro‐survival side‐effects of androgen‐deprivation therapy in prostate cancer. BJU International 111:4, pages 532-533.
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Ulrich Braunschweig, Serge Gueroussov, Alex M. Plocik, Brenton R. Graveley & Benjamin J. Blencowe. (2013) Dynamic Integration of Splicing within Gene Regulatory Pathways. Cell 152:6, pages 1252-1269.
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Crossref
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Crossref
Miroslav Nikolov & Wolfgang Fischle. (2013) Systematic analysis of histone modification readout. Mol. BioSyst. 9:2, pages 182-194.
Crossref
Michaela Smolle & Jerry L. Workman. (2013) Transcription-associated histone modifications and cryptic transcription. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1829:1, pages 84-97.
Crossref
Yong Ding, Ivan Ndamukong, Zaoshi Xu, Hanna Lapko, Michael Fromm & Zoya Avramova. (2012) ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes. PLoS Genetics 8:12, pages e1003111.
Crossref
Wolfgang Fischle. (2012) One, two, three: how histone methylation is read. Epigenomics 4:6, pages 641-653.
Crossref
WILLIAM L. BERRY, SOOK SHIN, STAN A. LIGHTFOOT & RALF JANKNECHT. (2012) Oncogenic features of the JMJD2A histone demethylase in breast cancer. International Journal of Oncology 41:5, pages 1701-1706.
Crossref
Jingjing Li, Fan Zhou, Deguo Zhan, Qinqin Gao, Nan Cui, Jiwen Li, Elena Iakhiaeva, Christian Zwieb, Biaoyang Lin & Jiemin Wong. (2012) A Novel Histone H4 Arginine 3 Methylation-sensitive Histone H4 Binding Activity and Transcriptional Regulatory Function for Signal Recognition Particle Subunits SRP68 and SRP72. Journal of Biological Chemistry 287:48, pages 40641-40651.
Crossref
Lei Liu, Su Qin, Jiahai Zhang, Peng Ji, Yunyu Shi & Jihui Wu. (2012) Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA. Journal of Structural Biology 180:1, pages 165-173.
Crossref
Joan Massagué & Qiaoran Xi. (2012) TGF-β control of stem cell differentiation genes. FEBS Letters 586:14, pages 1953-1958.
Crossref
Jing Wu, Nan Cui, Rui Wang, Jiwen Li & Jiemin Wong. (2012) A Role for CARM1-Mediated Histone H3 Arginine Methylation in Protecting Histone Acetylation by Releasing Corepressors from Chromatin. PLoS ONE 7:6, pages e34692.
Crossref
Anke Samel, Alessandro Cuomo, Tiziana Bonaldi & Ann E. Ehrenhofer-Murray. (2012) Methylation of CenH3 arginine 37 regulates kinetochore integrity and chromosome segregation. Proceedings of the National Academy of Sciences 109:23, pages 9029-9034.
Crossref
Chhavi ChauhanClaudia B. ZralyMegan ParillaManuel O. DiazAndrew K. Dingwall. (2012) Histone recognition and nuclear receptor co-activator functions of Drosophila Cara Mitad, a homolog of the N-terminal portion of mammalian MLL2 and MLL3 . Development 139:11, pages 1997-2008.
Crossref
Simon M. CarrShonagh MunroNicholas B. La Thangue. (2012) Lysine methylation and the regulation of p53. Essays in Biochemistry 52, pages 79-92.
Crossref
Susanne Marije Kooistra & Kristian Helin. (2012) Molecular mechanisms and potential functions of histone demethylases. Nature Reviews Molecular Cell Biology 13:5, pages 297-311.
Crossref
Tae-Dong Kim, Sangphil Oh, Sook Shin & Ralf Janknecht. (2012) Regulation of Tumor Suppressor p53 and HCT116 Cell Physiology by Histone Demethylase JMJD2D/KDM4D. PLoS ONE 7:4, pages e34618.
Crossref
Joel C. Eissenberg. (2012) Structural biology of the chromodomain: Form and function. Gene 496:2, pages 69-78.
Crossref
Melanie A. Adams-Cioaba, Zhihong Li, Wolfram Tempel, Yahong Guo, Chuanbing Bian, Yanjun Li, Robert Lam & Jinrong Min. (2012) Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins. FEBS Letters 586:6, pages 859-865.
Crossref
Weibin Gong, Tao Zhou, Jinjin Mo, Sarah Perrett, Jinfeng Wang & Yingang Feng. (2012) Structural Insight into Recognition of Methylated Histone Tails by Retinoblastoma-binding Protein 1. Journal of Biological Chemistry 287:11, pages 8531-8540.
Crossref
Ke Liu, Yahong Guo, Haiping Liu, Chuanbing Bian, Robert Lam, Yongsong Liu, Farrell Mackenzie, Luis Alejandro Rojas, Danny Reinberg, Mark T. Bedford, Rui-Ming Xu & Jinrong Min. (2012) Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30. PLoS ONE 7:2, pages e30375.
Crossref
Sagar Darvekar, Sylvia Sagen Johnsen, Agnete Bratsberg Eriksen, Terje Johansen & Eva Sjøttem. (2012) Identification of two independent nucleosome-binding domains in the transcriptional co-activator SPBP. Biochemical Journal 442:1, pages 65-75.
Crossref
C. Santiago, K. Nguyen & M. Schapira. (2011) Druggability of methyl-lysine binding sites. Journal of Computer-Aided Molecular Design 25:12, pages 1171-1178.
Crossref
Chen Chen, Timothy J. Nott, Jing Jin & Tony Pawson. (2011) Deciphering arginine methylation: Tudor tells the tale. Nature Reviews Molecular Cell Biology 12:10, pages 629-642.
Crossref
Steven Henikoff & Ali Shilatifard. (2011) Histone modification: cause or cog?. Trends in Genetics 27:10, pages 389-396.
Crossref
Simon Messner & Michael O. Hottiger. (2011) Histone ADP-ribosylation in DNA repair, replication and transcription. Trends in Cell Biology 21:9, pages 534-542.
Crossref
Edwin Smith, Chengqi Lin & Ali Shilatifard. (2011) The super elongation complex (SEC) and MLL in development and disease. Genes & Development 25:7, pages 661-672.
Crossref
Roberto Sanchez & Ming-Ming Zhou. (2011) The PHD finger: a versatile epigenome reader. Trends in Biochemical Sciences.
Crossref
Kyoko L. Yap & Ming-Ming Zhou. (2011) Structure and Mechanisms of Lysine Methylation Recognition by the Chromodomain in Gene Transcription. Biochemistry 50:12, pages 1966-1980.
Crossref
Lakshminarayan M. Iyer, Saraswathi Abhiman & L. Aravind. 2011. Modifications of Nuclear DNA and its Regulatory Proteins. Modifications of Nuclear DNA and its Regulatory Proteins 25 104 .

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