View Item 

Show simple item record

The functional interactome landscape of the human histone deacetylase family

dc.contributor.authorJoshi, Preetien_US
dc.contributor.authorGreco, Todd Men_US
dc.contributor.authorGuise, Amanda Jen_US
dc.contributor.authorLuo, Yangen_US
dc.contributor.authorYu, Fangen_US
dc.contributor.authorNesvizhskii, Alexey Ien_US
dc.contributor.authorCristea, Ileana Men_US
dc.date.accessioned2014-01-08T20:34:57Z
dc.date.available2014-09-02T14:12:52Zen_US
dc.date.issued2013-07-16en_US
dc.identifier.citationJoshi, Preeti; Greco, Todd M; Guise, Amanda J; Luo, Yang; Yu, Fang; Nesvizhskii, Alexey I; Cristea, Ileana M (2013). "The functional interactome landscape of the human histone deacetylase family." Molecular Systems Biology 9(1): n/a-n/a. <http://hdl.handle.net/2027.42/102187>en_US
dc.identifier.issn1744-4292en_US
dc.identifier.issn1744-4292en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/102187
dc.publisherJohn Wiley & Sons, Ltden_US
dc.subject.otherHDACen_US
dc.subject.otherInteractionsen_US
dc.subject.otherProteomicsen_US
dc.subject.otherSAINTen_US
dc.subject.otherI‐DIRTen_US
dc.titleThe functional interactome landscape of the human histone deacetylase familyen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biologyen_US
dc.subject.hlbtoplevelHealth Sciencesen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102187/1/msb201326-sup-0001.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102187/2/msb201326.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102187/3/msb201326.reviewer_comments.pdf
dc.identifier.doi10.1038/msb.2013.26en_US
dc.identifier.sourceMolecular Systems Biologyen_US
dc.identifier.citedreferenceSzklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C ( 2011 ) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561 – D568en_US
dc.identifier.citedreferenceTong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL ( 1998 ) Chromatin deacetylation by an ATP‐dependent nucleosome remodelling complex. Nature 395: 917 – 921en_US
dc.identifier.citedreferenceTsai YC, Greco TM, Boonmee A, Miteva Y, Cristea IM ( 2012 ) Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics 11: M111 015156en_US
dc.identifier.citedreferenceTurner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ ( 2010 ) iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. J Biol Datab Curation 2010: baq023en_US
dc.identifier.citedreferenceVerdin E, Dequiedt F, Kasler HG ( 2003 ) Class II histone deacetylases: versatile regulators. Trends Genet 19: 286 – 293en_US
dc.identifier.citedreferenceVermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M ( 2010 ) Quantitative interaction proteomics and genome‐wide profiling of epigenetic histone marks and their readers. Cell 142: 967 – 980en_US
dc.identifier.citedreferenceVizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Perez‐Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H ( 2013 ) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41: D1063 – D1069en_US
dc.identifier.citedreferenceWade PA, Jones PL, Vermaak D, Wolffe AP ( 1998 ) A multiple subunit Mi‐2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr Biol 8: 843 – 846en_US
dc.identifier.citedreferenceWang AH, Kruhlak MJ, Wu J, Bertos NR, Vezmar M, Posner BI, Bazett‐Jones DP, Yang XJ ( 2000 ) Regulation of histone deacetylase 4 by binding of 14‐3‐3 proteins. Mol Cell Biol 20: 6904 – 6912en_US
dc.identifier.citedreferenceWang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C ( 2012 ) PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life. Mol Cell Proteomics: MCP 11: 492 – 500en_US
dc.identifier.citedreferenceWang Y, Zhang H, Chen Y, Sun Y, Yang F, Yu W, Liang J, Sun L, Yang X, Shi L, Li R, Li Y, Zhang Y, Li Q, Yi X, Shang Y ( 2009 ) LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell 138: 660 – 672en_US
dc.identifier.citedreferenceWisniewski JR, Zougman A, Mann M ( 2009 ) Combination of FASP and StageTip‐based fractionation allows in‐depth analysis of the hippocampal membrane proteome. J Proteome Res 8: 5674 – 5678en_US
dc.identifier.citedreferenceWu XY, Li H, Park EJ, Chen JD ( 2001 ) SMRTe inhibits MEF2C transcriptional activation by targeting HDAC4 and 5 to nuclear domains. J Biol Chem 276: 24177 – 24185en_US
dc.identifier.citedreferenceXiong B, Lu S, Gerton JL ( 2010 ) Hos1 is a lysine deacetylase for the Smc3 subunit of cohesin. Curr Biol 20: 1660 – 1665en_US
dc.identifier.citedreferenceXue YT, Wong JM, Moreno GT, Young MK, Cote J, Wang WD ( 1998 ) NURD, a novel complex with both ATP‐dependent chromatin‐remodeling and histone deacetylase activities. Mol Cell 2: 851 – 861en_US
dc.identifier.citedreferenceYang XJ, Gregoire S ( 2005 ) Class II histone deacetylases: from sequence to function, regulation, and clinical implication. Mol Cell Biol 25: 2873 – 2884en_US
dc.identifier.citedreferenceYang XJ, Seto E ( 2008 ) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Revi Mol Cell Biol 9: 206 – 218en_US
dc.identifier.citedreferenceYou A, Tong JK, Grozinger CM, Schreiber SL ( 2001 ) CoREST is an integral component of the CoREST‐human histone deacetylase complex. Proc Nat Acad Sci USA 98: 1454 – 1458en_US
dc.identifier.citedreferenceZhang L, Zhao J, Edenberg HJ ( 1999 ) A human Raf‐responsive zinc‐finger protein that binds to divergent sequences. Nucleic Acids Res 27: 2947 – 2956en_US
dc.identifier.citedreferenceZhang Y, LeRoy G, Seelig HP, Lane WS, Reinberg D ( 1998 ) The dermatomyositis‐specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 95: 279 – 289en_US
dc.identifier.citedreferenceZhang Z, Lotti F, Dittmar K, Younis I, Wan L, Kasim M, Dreyfuss G ( 2008 ) SMN deficiency causes tissue‐specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell 133: 585 – 600en_US
dc.identifier.citedreferenceZhao W, Kruse JP, Tang Y, Jung SY, Qin J, Gu W ( 2008 ) Negative regulation of the deacetylase SIRT1 by DBC1. Nature 451: 587 – 590en_US
dc.identifier.citedreferenceZhao X, Ito A, Kane CD, Liao TS, Bolger TA, Lemrow SM, Means AR, Yao TP ( 2001 ) The modular nature of histone deacetylase HDAC4 confers phosphorylation‐dependent intracellular trafficking. J Biol Chem 276: 35042 – 35048en_US
dc.identifier.citedreferenceZybailov BL, Florens L, Washburn MP ( 2007 ) Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol Biosyst 3: 354 – 360en_US
dc.identifier.citedreferenceKäll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ ( 2007 ) Semi‐supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4: 923 – 925en_US
dc.identifier.citedreferenceRobertson HM, Zumpano KL ( 1997 ) Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome. Gene 205: 203 – 217en_US
dc.identifier.citedreferenceAkimova T, Beier UH, Liu Y, Wang L, Hancock WW ( 2012 ) Histone/protein deacetylases and T‐cell immune responses. Blood 119: 2443 – 2451en_US
dc.identifier.citedreferenceAndo Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, Kimura R, Tagata M, Ino Y, Hirano H, Chiba J, Suzuki H, Carninci P, Hayashizaki Y ( 2011 ) Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells. PloS one 6: e23385en_US
dc.identifier.citedreferenceAranda B, Achuthan P, Alam‐Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi‐Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K et al ( 2010 ) The IntAct molecular interaction database in 2010. Nucleic Acids Research 38: D525 – D531en_US
dc.identifier.citedreferenceBaba A, Ohtake F, Okuno Y, Yokota K, Okada M, Imai Y, Ni M, Meyer CA, Igarashi K, Kanno J, Brown M, Kato S ( 2011 ) PKA‐dependent regulation of the histone lysine demethylase complex PHF2‐ARID5B. Nature Cell Biol 13: 668 – 675en_US
dc.identifier.citedreferenceBanach‐Orlowska M, Pilecka I, Torun A, Pyrzynska B, Miaczynska M ( 2009 ) Functional characterization of the interactions between endosomal adaptor protein APPL1 and the NuRD co‐repressor complex. Biochem J 423: 389 – 400en_US
dc.identifier.citedreferenceBantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dumpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G et al ( 2011 ) Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat Biotechnol 29: 255 – 265en_US
dc.identifier.citedreferenceBarbero JL ( 2009 ) Cohesins: chromatin architects in chromosome segregation, control of gene expression and much more. Cellular and molecular life sciences: CMLS 66: 2025 – 2035en_US
dc.identifier.citedreferenceBeckouet F, Hu B, Roig MB, Sutani T, Komata M, Uluocak P, Katis VL, Shirahige K, Nasmyth K ( 2010 ) An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion. Mol Cell 39: 689 – 699en_US
dc.identifier.citedreferenceBerger SL ( 2007 ) The complex language of chromatin regulation during transcription. Nature 447: 407 – 412en_US
dc.identifier.citedreferenceBindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J ( 2009 ) ClueGO: a Cytoscape plug‐in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091 – 1093en_US
dc.identifier.citedreferenceBorges V, Lehane C, Lopez‐Serra L, Flynn H, Skehel M, Rolef Ben‐Shahar T, Uhlmann F ( 2010 ) Hos1 deacetylates Smc3 to close the cohesin acetylation cycle. Mol Cell 39: 677 – 688en_US
dc.identifier.citedreferenceBossuyt J, Helmstadter K, Wu X, Clements‐Jewery H, Haworth RS, Avkiran M, Martin JL, Pogwizd SM, Bers DM ( 2008 ) Ca2+/Calmodulin‐dependent protein kinase II delta and protein kinase D overexpression reinforce the histone deacetylase 5 redistribution in heart failure. Circ Res 102: 695 – 702en_US
dc.identifier.citedreferenceBoulisfane N, Choleza M, Rage F, Neel H, Soret J, Bordonne R ( 2011 ) Impaired minor tri‐snRNP assembly generates differential splicing defects of U12‐type introns in lymphoblasts derived from a type I SMA patient. Hum Mol Genet 20: 641 – 648en_US
dc.identifier.citedreferenceCalalb MB, McKinsey TA, Newkirk S, Huynh K, Sucharov CC, Bristow MR ( 2009 ) Increased phosphorylation‐dependent nuclear export of class II histone deacetylases in failing human heart. Clin Transl Sci 2: 325 – 332en_US
dc.identifier.citedreferenceCampion Y, Neel H, Gostan T, Soret J, Bordonne R ( 2010 ) Specific splicing defects in S. pombe carrying a degron allele of the Survival of Motor Neuron gene. EMBO J 29: 1817 – 1829en_US
dc.identifier.citedreferenceCharroux B, Pellizzoni L, Perkinson RA, Shevchenko A, Mann M, Dreyfuss G ( 1999 ) Gemin3: a novel DEAD box protein that interacts with SMN, the spinal muscular atrophy gene product, and is a component of gems. J Cell Biol 147: 1181 – 1194en_US
dc.identifier.citedreferenceCharroux B, Pellizzoni L, Perkinson RA, Yong J, Shevchenko A, Mann M, Dreyfuss G ( 2000 ) Gemin4. a novel component of the SMN complex that is found in both gems and nucleoli. J Cell Biol 148: 1177 – 1186en_US
dc.identifier.citedreferenceChini CC, Escande C, Nin V, Chini EN ( 2010 ) HDAC3 is negatively regulated by the nuclear protein DBC1. J Biol Chem 285: 40830 – 40837en_US
dc.identifier.citedreferenceChoi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI ( 2011 ) SAINT: probabilistic scoring of affinity purification‐mass spectrometry data. Nat Meth 8: 70 – 73en_US
dc.identifier.citedreferenceChoi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI ( 2012 ) Analyzing protein‐protein interactions from affinity purification‐mass spectrometry data with SAINT. Curr Protoc Bioinformatics 39: 8.15.1 – 8.15.23en_US
dc.identifier.citedreferenceCress WD, Seto E ( 2000 ) Histone deacetylases, transcriptional control, and cancer. J Cell Physiol 184: 1 – 16en_US
dc.identifier.citedreferenceCristea IM, Williams R, Chait BT, Rout MP ( 2005 ) Fluorescent proteins as proteomic probes. Mol Cell Proteomics 4: 1933 – 1941en_US
dc.identifier.citedreferenceDeardorff MA, Bando M, Nakato R, Watrin E, Itoh T, Minamino M, Saitoh K, Komata M, Katou Y, Clark D, Cole KE, De Baere E, Decroos C, Di Donato N, Ernst S, Francey LJ, Gyftodimou Y, Hirashima K, Hullings M, Ishikawa Y et al ( 2012 ) HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature 489: 313 – 317en_US
dc.identifier.citedreferenceDorsett D, Strom L ( 2012 ) The ancient and evolving roles of cohesin in gene expression and DNA repair. Curr Biol 22: R240 – R250en_US
dc.identifier.citedreferenceDovey OM, Foster CT, Conte N, Edwards SA, Edwards JM, Singh R, Vassiliou G, Bradley A, Cowley SM ( 2013 ) Histone deacetylase (HDAC) 1 and 2 are essential for normal T cell development and genomic stability in mice. Blood 121: 1335 – 1344en_US
dc.identifier.citedreferenceDoye V, Hurt E ( 1997 ) From nucleoporins to nuclear pore complexes. Curr Opin Cell Biol 9: 401 – 411en_US
dc.identifier.citedreferenceDoyon Y, Cote J ( 2004 ) The highly conserved and multifunctional NuA4 HAT complex. Curr Opin Genet Dev 14: 147 – 154en_US
dc.identifier.citedreferenceFeng W, Gubitz AK, Wan L, Battle DJ, Dostie J, Golembe TJ, Dreyfuss G ( 2005 ) Gemins modulate the expression and activity of the SMN complex. Hum Mol Genet 14: 1605 – 1611en_US
dc.identifier.citedreferenceFeng W, Lu Z, Luo RZ, Zhang X, Seto E, Liao WS, Yu Y ( 2007 ) Multiple histone deacetylases repress tumor suppressor gene ARHI in breast cancer. Int J Cancer 120: 1664 – 1668en_US
dc.identifier.citedreferenceFischer U, Liu Q, Dreyfuss G ( 1997 ) The SMN‐SIP1 complex has an essential role in spliceosomal snRNP biogenesis. Cell 90: 1023 – 1029en_US
dc.identifier.citedreferenceFischle W, Dequiedt F, Hendzel MJ, Guenther MG, Lazar MA, Voelter W, Verdin E ( 2002 ) Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N‐CoR. Mol Cell 9: 45 – 57en_US
dc.identifier.citedreferenceFranco PJ, Farooqui M, Seto E, Wei LN ( 2001 ) The orphan nuclear receptor TR2 interacts directly with both class I and class II histone deacetylases. Mol Endocrinol 15: 1318 – 1328en_US
dc.identifier.citedreferenceFu QS, Zhou CJ, Gao HC, Jiang YJ, Zhou ZR, Hong J, Yao WM, Song AX, Lin DH, Hu HY ( 2009 ) Structural basis for ubiquitin recognition by a novel domain from human phospholipase A2‐activating protein. J Biol Chem 284: 19043 – 19052en_US
dc.identifier.citedreferenceFujimoto R, Ozawa T, Itoyama T, Sadamori N, Kurosawa N, Isobe M ( 2012 ) HELIOS‐BCL11B fusion gene involvement in a t(2;14)(q34;q32) in an adult T‐cell leukemia patient. Cancer Genet 205: 356 – 364en_US
dc.identifier.citedreferenceGao L, Cueto MA, Asselbergs F, Atadja P ( 2002 ) Cloning and functional characterization of HDAC11, a novel member of the human histone deacetylase family. J Biol Chem 277: 25748 – 25755en_US
dc.identifier.citedreferenceGreco TM, Yu F, Guise AJ, Cristea IM ( 2011 ) Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics 10: M110 004317en_US
dc.identifier.citedreferenceGregoretti IV, Lee YM, Goodson HV ( 2004 ) Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. J Mol Biol 338: 17en_US
dc.identifier.citedreferenceGrozinger CM, Hassig CA, Schreiber SL ( 1999 ) Three proteins define a class of human histone deacetylases related to yeast Hda1p. Proc Natl Acad Sci USA 96: 4868 – 4873en_US
dc.identifier.citedreferenceGrozinger CM, Schreiber SL ( 2000 ) Regulation of histone deacetylase 4 and 5 and transcriptional activity by 14‐3‐3‐dependent cellular localization. Proc Natl Acad Sci USA 97: 7835 – 7840en_US
dc.identifier.citedreferenceGuise AJ, Greco TM, Zhang IY, Yu F, Cristea IM ( 2012 ) Aurora B‐dependent regulation of class IIa histone deacetylases by mitotic nuclear localization signal phosphorylation. Mol Cell Proteomics 11: 1220 – 1229en_US
dc.identifier.citedreferenceHa CH, Wang W, Jhun BS, Wong C, Hausser A, Pfizenmaier K, McKinsey TA, Olson EN, Jin ZG ( 2008 ) Protein kinase D‐dependent phosphorylation and nuclear export of histone deacetylase 5 mediates vascular endothelial growth factor‐induced gene expression and angiogenesis. J Biol Chem 283: 14590 – 14599en_US
dc.identifier.citedreferenceHan Z, Guo L, Wang H, Shen Y, Deng XW, Chai J ( 2006 ) Structural basis for the specific reconition of methylated histone H3 lysine 4 by the WD‐40 protein WDR5. Mol Cell 22: 137 – 144en_US
dc.identifier.citedreferenceHubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP ( 2002 ) HDAC6 is a microtubule‐associated deacetylase. Nature 417: 455 – 458en_US
dc.identifier.citedreferenceInoue A, Fujimoto D ( 1969 ) Enzymatic deacetylation of histone. Biochem Biophys Res Commun 36: 146 – 150en_US
dc.identifier.citedreferenceKao HY, Verdel A, Tsai CC, Simon C, Juguilon H, Khochbin S ( 2001 ) Mechanism for nucleocytoplasmic shuttling of histone deacetylase 7. J Biol Chem 276: 47496 – 47507en_US
dc.identifier.citedreferenceKeedy KS, Archin NM, Gates AT, Espeseth A, Hazuda DJ, Margolis DM ( 2009 ) A limited group of class I histone deacetylases acts to repress human immunodeficiency virus type 1 expression. J Virol 83: 4749 – 4756en_US
dc.identifier.citedreferenceKim J, Sif S, Jones B, Jackson A, Koipally J, Heller E, Winandy S, Viel A, Sawyer A, Ikeda T, Kingston R, Georgopoulos K ( 1999 ) Ikaros DNA‐binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity 10: 345 – 355en_US
dc.identifier.citedreferenceKim JE, Chen J, Lou Z ( 2008 ) DBC1 is a negative regulator of SIRT1. Nature 451: 583 – 586en_US
dc.identifier.citedreferenceKramer T, Greco TM, Enquist LW, Cristea IM ( 2011 ) Proteomic characterization of pseudorabies virus extracellular virions. J Virol 85: 6427 – 6441en_US
dc.identifier.citedreferenceLebreton A, Lakisic G, Job V, Fritsch L, Tham TN, Camejo A, Mattei PJ, Regnault B, Nahori MA, Cabanes D, Gautreau A, Ait‐Si‐Ali S, Dessen A, Cossart P, Bierne H ( 2011 ) A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response. Science 331: 1319 – 1321en_US
dc.identifier.citedreferenceLin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD ( 2012 ) Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature 482: 251 – 255en_US
dc.identifier.citedreferenceLiu P, Keller JR, Ortiz M, Tessarollo L, Rachel RA, Nakamura T, Jenkins NA, Copeland NG ( 2003 ) Bcl11a is essential for normal lymphoid development. Nat Immunol 4: 525 – 532en_US
dc.identifier.citedreferenceLu J, McKinsey TA, Zhang CL, Olson EN ( 2000 ) Regulation of skeletal myogenesis by association of the MEF2 transcription factor with class II histone deacetylases. Mol Cell 6: 233 – 244en_US
dc.identifier.citedreferenceMcKinsey TA, Zhang CL, Lu J, Olson EN ( 2000a ) Signal‐dependent nuclear export of a histone deacetylase regulates muscle differentiation. Nature 408: 106 – 111en_US
dc.identifier.citedreferenceMcKinsey TA, Zhang CL, Olson EN ( 2000b ) Activation of the myocyte enhancer factor‐2 transcription factor by calcium/calmodulin‐dependent protein kinase‐stimulated binding of 14‐3‐3 to histone deacetylase 5. Proc Natl Acad Sci USA 97: 14400 – 14405en_US
dc.identifier.citedreferenceMeister G, Buhler D, Laggerbauer B, Zobawa M, Lottspeich F, Fischer U ( 2000 ) Characterization of a nuclear 20S complex containing the survival of motor neurons (SMN) protein and a specific subset of spliceosomal Sm proteins. Hum Mol Genet 9: 1977 – 1986en_US
dc.identifier.citedreferenceMeister G, Buhler D, Pillai R, Lottspeich F, Fischer U ( 2001 ) A multiprotein complex mediates the ATP‐dependent assembly of spliceosomal U snRNPs. Nat Cell Biol 3: 945 – 949en_US
dc.identifier.citedreferenceMinucci S, Pelicci PG ( 2006 ) Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer 6: 38 – 51en_US
dc.identifier.citedreferenceMiska EA, Karlsson C, Langley E, Nielsen SJ, Pines J, Kouzarides T ( 1999 ) HDAC4 deacetylase associates with and represses the MEF2 transcription factor. Embo J 18: 5099 – 5107en_US
dc.identifier.citedreferenceMiteva YV, Budayeva HG, Cristea IM ( 2013 ) Proteomics‐based methods for discovery, quantification, and validation of protein‐protein interactions. Anal Chem 85: 749 – 768en_US
dc.identifier.citedreferenceMunoz IM, Macartney T, Sanchez‐Pulido L, Ponting CP, Rocha S, Rouse J ( 2012 ) FAM60A (Family with sequence similarity 60A) is a cell cycle‐fluctuating regulator of the SIN3‐HDAC1 histone deacetylase complex. J Biol Chem 287: 32346 – 32353en_US
dc.identifier.citedreferenceMurphy JC, Fischle W, Verdin E, Sinclair JH ( 2002 ) Control of cytomegalovirus lytic gene expression by histone acetylation. Embo J 21: 1112 – 1120en_US
dc.identifier.citedreferenceOng SE, Kratchmarova I, Mann M ( 2003 ) Properties of 13C‐substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2: 173 – 181en_US
dc.identifier.citedreferenceParoni G, Fontanini A, Cernotta N, Foti C, Gupta MP, Yang XJ, Fasino D, Brancolini C ( 2007 ) Dephosphorylation and caspase processing generate distinct nuclear pools of histone deacetylase 4. Mol Cell Biol 27: 6718 – 6732en_US
dc.identifier.citedreferencePatsialou A, Wilsker D, Moran E ( 2005 ) DNA‐binding properties of ARID family proteins. Nucleic Acids Res 33: 66 – 80en_US
dc.identifier.citedreferencePeters JM, Tedeschi A, Schmitz J ( 2008 ) The cohesin complex and its roles in chromosome biology. Genes Dev 22: 3089 – 3114en_US
dc.identifier.citedreferenceRappsilber J, Mann M, Ishihama Y ( 2007 ) Protocol for micro‐purification, enrichment, pre‐fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2: 1896 – 1906en_US
dc.identifier.citedreferenceRenthal W, Maze I, Krishnan V, Covington HE 3rd, Xiao G, Kumar A, Russo SJ, Graham A, Tsankova N, Kippin TE, Kerstetter KA, Neve RL, Haggarty SJ, McKinsey TA, Bassel‐Duby R, Olson EN, Nestler EJ ( 2007 ) Histone deacetylase 5 epigenetically controls behavioral adaptations to chronic emotional stimuli. Neuron 56: 517 – 529en_US
dc.identifier.citedreferenceSatterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B, Oscier DG, Siebert R, Tucker PW, Dyer MJ ( 2001 ) The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood 98: 3413 – 3420en_US
dc.identifier.citedreferenceSeigneurin‐Berny D, Verdel A, Curtet S, Lemercier C, Garin J, Rousseaux S, Khochbin S ( 2001 ) Identification of components of the murine histone deacetylase 6 complex: link between acetylation and ubiquitination signaling pathways. Mol Cell Biol 21: 8035 – 8044en_US
dc.identifier.citedreferenceShi Y, Sawada J, Sui G, Affar el B, Whetstine JR, Lan F, Ogawa H, Luke MP, Nakatani Y ( 2003 ) Coordinated histone modifications mediated by a CtBP co‐repressor complex. Nature 422: 735 – 738en_US
dc.identifier.citedreferenceShi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y ( 2005 ) Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell 19: 857 – 864en_US
dc.identifier.citedreferenceSmith KT, Sardiu ME, Martin‐Brown SA, Seidel C, Mushegian A, Egidy R, Florens L, Washburn MP, Workman JL ( 2012 ) Human family with sequence similarity 60 member A (FAM60A) protein: a new subunit of the Sin3 deacetylase complex. Mol Cell Proteomics 11: 1815 – 1828en_US
dc.identifier.citedreferenceSmoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T ( 2011 ) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431 – 432en_US
dc.identifier.citedreferenceStark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M ( 2006 ) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535 – D539en_US
dc.identifier.citedreferenceSwanson KA, Knoepfler PS, Huang K, Kang RS, Cowley SM, Laherty CD, Eisenman RN, Radhakrishnan I ( 2004 ) HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations. Nat Struct Mol Biol 11: 738 – 746en_US
dc.identifier.citedreferenceTackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP, Chait BT ( 2005 ) I‐DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res 4: 1752 – 1756en_US
dc.identifier.citedreferenceTerhune SS, Moorman NJ, Cristea IM, Savaryn JP, Cuevas‐Bennett C, Rout MP, Chait BT, Shenk T ( 2010 ) Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate‐early RNA. Plos Pathog 6: e1000965en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
msb201326-sup-0001.pdf
Size:
1.933MB
Format:
PDF
View/Open
Name:
msb201326.pdf
Size:
1.071MB
Format:
PDF
View/Open
Name:
msb201326.reviewer_comments.pdf
Size:
637.8KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.