A new companion of elongating RNA polymerase II: TINTIN, an independent sub-module of NuA4/TIP60 for nucleosome transactions

Transcription

Volumn 5, Issue 5, 2014, Pages

  Cheng, Xue ^a   Côté, Jacques ^a  

^a University Laval   (Canada)

Author keywords

Acetylation; Chromatin; Eaf3; Eaf5; Eaf7; MRG15; MRGBP; NuA4; References; TINTIN; Transcription elongation

Indexed keywords

CHAPERONE; CHAPERONE ASF1; CHAPERONE FACT; CHAPERONE SPT6; HISTONE ACETYLTRANSFERASE; HISTONE ACETYLTRANSFERASE NUA4; HISTONE METHYLTRANSFERASE SET2; REGULATOR PROTEIN; RNA POLYMERASE II; TRANSCRIPTION ELONGATION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG; VEZF1 PROTEIN; KAT5 PROTEIN, HUMAN; NUA4 PROTEIN, S CEREVISIAE; NUCLEOSOME; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; DNA DAMAGE; HISTONE METHYLATION; HUMAN; NONHUMAN; NUCLEOSOME; PROTEIN DOMAIN; PROTEIN PROCESSING; PROTEIN SUBUNIT; PROTEOMICS; SEQUENCE HOMOLOGY; TINTIN SUBMODULE; TRANSCRIPTION ELONGATION; ANIMAL; METABOLISM; SACCHAROMYCES CEREVISIAE;

ANIMALS; HISTONE ACETYLTRANSFERASES; HUMANS; NUCLEOSOMES; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION ELONGATION, GENETIC; TRANSCRIPTION FACTORS;

EID: 84922232260     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.1080/21541264.2014.995571     Document Type: Article

References (36)

1. Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007a; 128:707-19; http://dx.doi.org/10.1016/j.cell.2007.01.015
2. Lee TI, Young RA. Transcriptional regulation and its misregulation in disease. Cell 2013; 152:1237-51; PMID:23498934; http://dx.doi.org/10.1016/j.cell.2013.02.014
3. Fuchs SM, Laribee RN, Strahl BD. Protein modifications in transcription elongation. Biochim Biophys Acta 2009; 1789:26-36; PMID:18718879; http://dx.doi.org/10.1016/j.bbagrm.2008.07.008
4. Avvakumov N, Nourani A, Cote J. Histone chaperones: modulators of chromatin marks. 2011; Mol Cell 41:502-14; PMID:21362547; http://dx.doi.org/10.1016/j.molcel.2011.02.013
5. Eick D, Geyer M. The RNA polymerase II carboxy-terminal domain (CTD) code. Chem Rev 2013; 113:8456-90; PMID:23952966; http://dx.doi.org/10.1021/cr400071f
6. Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DF et al. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol 2002; 22:1298-306; PMID:11839797; http://dx.doi.org/10.1128/MCB.22.5.1298-1306.2002
7. Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KM, Stewart AF. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res 2003; 31:2475-82; PMID:12736296; http://dx.doi.org/10.1093/nar/gkg372
8. Li B, Howe L, Anderson S, Yates JR 3rd, Workman JL. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 2003; 278: 8897-903; PMID:12511561; http://dx.doi.org/10.1074/jbc.M212134200
9. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, Strahl BD. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 2003; 17:654-63; PMID:12629047; http://dx.doi.org/10.1101/gad.1055503
10. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005; 123:581-92; PMID:16286007; http://dx.doi.org/10.1016/j. cell.2005.10.023
11. Joshi AA, Struhl K. Eaf3 Chromodomain Interaction with Methylated H3-K36 Links Histone Deacetylation to Pol II Elongation. Mol Cell 2005; 20:971-78; PMID:16364921
12. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 2005; 123:593-605; PMID:16286008; http://dx.doi.org/10.1016/j.cell.2005.10.025
13. Venkatesh S, Smolle M, Li H, Gogol MM, Saint M, Kumar S, Natarajan K, Workman JL. Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes. Nature 2012; 489:452-5; PMID:22914091; http://dx.doi.org/10.1038/nature11326
14. Utley RT, Ikeda K, Grant PA, Cote J, Steger DJ, Eberharter A, John S, Workman JL. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 1998; 394:498-502; PMID:9697775; http://dx.doi.org/10.1038/28886
15. Reid JL, Iyer VR, Brown PO, Struhl K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol Cell 2000; 6:1297-307; PMID:11163204; http:// dx.doi.org/10.1016/S1097-2765(00)00128-3
16. Brown CE, Howe L, Sousa K, Alley SC, Carrozza MJ, Tan S, Workman JL. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science 2001; 292:2333-7.
17. Nourani A, Utley RT, Allard S, Cote J. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J 2004; 23:2597-607; PMID:15175650; http://dx.doi.org/10.1038/sj.emboj.7600230
18. Li B, Gogol M, Carey M, Lee D, Seidel C, Workman JL. Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 2007b; 316:1050-4; PMID:17510366
19. Drouin S, Laramee L, Jacques PE, Forest A, Bergeron M, Robert F. DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS Genet 2010; 6: e1001173
20. Govind CK, Qiu H, Ginsburg DS, Ruan C, Hofmeyer K, Hu C, Swaminathan V, Workman JL, Li B, Hinnebusch AG. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation dependent deacetylation of ORF nucleosomes. Mol Cell 2010; 39:234-46; PMID:20670892; http://dx.doi.org/10.1016/j.molcel.2010.07.003
21. Ginsburg DS, Govind CK, Hinnebusch AG. NuA4 lysine acetyltransferase Esa1 is targeted to coding regions and stimulates transcription elongation with Gcn5. Mol Cell Biol 2009; 29:6473-87; PMID:19822662; http://dx.doi.org/10.1128/MCB.01033-09
22. Ginsburg DS, Anlembom TE, Wang J, Patel SR, Li B, Hinnebusch AG. NuA4 Links Methylation of Histone H3 Lysines 4 and 36 to Acetylation of Histones H4 and H3. J Biol Chem 2014; 289:32656-70; PMID:25301943; http://dx.doi.org/10.1074/jbc.M114.585588
23. Rossetto D, Cramet M, Wang AY, Steunou AL, Lacoste N, Schulze JM, Cote V, Monnet-Saksouk J, Piquet S, Nourani A et al. Eaf5/7/3 form a functionally independent NuA4 submodule linked to RNA polymerase II coupled nucleosome recycling. EMBO J 2014; 33:1397-15; PMID:24843044
24. Smolle M, Venkatesh S, Gogol MM, Li H, Zhang Y, Florens L, Washburn MP, Workman JL. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol 2012; 19:884-92; PMID:22922743; http://dx.doi.org/10.1038/nsmb.2312
25. Cai Y, Jin J, Tomomori-Sato C, Sato S, Sorokina I, Parmely TJ, Conaway RC, Conaway JW. Identification of new subunits of the multiprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex. J Biol Chem 2003; 278:42733-6; PMID:12963728; http://dx.doi.org/10.1074/jbc.C300389200
26. Kirkwood KJ, Ahmad Y, Larance M, Lamond AI. Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Mol Cell Proteomics 2013; 12:3851-73; PMID:24043423
27. Gowher H, Brick K, Camerini-Otero RD, Felsenfeld G. Vezf1 protein binding sites genome-wide are associated with pausing of elongating RNA polymerase II. Proc Nat Acad Sci U S A 2012; 109:2370-5.
28. Smolka MB, Albuquerque CP, Chen SH, Zhou H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Nat Acad Sci U S A 2007; 104:10364-9; PMID:17563356
29. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 2008; 7:1389-96; PMID:18407956
30. Chen SH, Albuquerque CP, Liang J, Suhandynata RT, Zhou H. A proteome-wide analysis of kinase-substrate network in the DNA damage response. J Biol Chem 2010; 285:12803-12; PMID:20190278;http://dx.doi.org/10.1074/jbc.M110.106989
31. Ohouo PY, Bastos de Oliveira FM, Liu Y, Ma CJ, Smolka MB. DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9. Nature 2013; 493:120-4; PMID:23160493; http://dx.doi.org/10.1038/nature11658
32. Sy SM, Huen MS, Chen J. MRG15 is a novel PALB2-interacting factor involved in homologous recombination. J Biol Chem 2009; 284:21127-31; PMID:19553677; http://dx.doi.org/10.1074/jbc.C109.023937
33. Hayakawa T, Zhang F, Hayakawa N, Ohtani Y, Shinmyozu K, Nakayama J, Andreassen PR. MRG15 binds directly to PALB2 and stimulates homology-directed repair of chromosomal breaks. J Cell Sci 2010; 123:1124-30; PMID:20332121; http://dx.doi.org/10.1242/jcs.060178
34. Boudreault AA, Cronier D, Selleck W, Lacoste N, Utley RT, Allard S, Savard J, Lane WS, Tan S, Cote J. Yeast Enhancer of Polycomb defines global Esa1-dependent acetylation of chromatin. Genes Dev 2003; 17:1415-28; PMID:12782659
35. Auger A, Galarneau L, Altaf M, Nourani A, Doyon Y, Utley RT, Cronier D, Allard S, Cote J. Eaf1 is the plat-form for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Mol Cell Biol 2008; 28:2257-70; PMID:18212047; http://dx.doi.org/10.1128/MCB.01755-07
36. Mitchell L, Lambert JP, Gerdes M, Al-Madhoun AS, Skerjanc IS, Figeys D, Baetz K. Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity. Mol Cell Biol 2008; 28:2244-56; PMID:18212056; http://dx.doi.org/10.1128/MCB.01653-07