A Combination of H2A.Z and H4 Acetylation Recruits Brd2 to Chromatin during Transcriptional Activation

English version České info

H2A.
Z is an essential histone variant that has been implicated to have multiple chromosomal functions. To understand how H2A.Z participates in such diverse activities, we sought to identify downstream effector proteins that are recruited to chromatin via H2A.Z. For this purpose, we developed a nucleosome purification method to isolate H2A.Z-containing nucleosomes from human cells and used mass spectrometry to identify the co-purified nuclear proteins. Through stringent filtering, we identified the top 21 candidates, many of which have conserved structural motifs that bind post-translationally modified histones. We further validated the biological significance of one such candidate, Brd2, which is a double-bromodomain-containing protein known to function in transcriptional activation. We found that Brd2's preference for H2A.Z nucleosomes is mediated through a combination of hyperacetylated H4 on these nucleosomes, as well as additional features on H2A.Z itself. In addition, comparison of nucleosomes containing either H2A.Z-1 or H2A.Z-2 isoforms showed that significantly more Brd2 co-purifies with the former, suggesting these two isoforms engage different downstream effector proteins. Consistent with these biochemical analyses, we found that Brd2 is recruited to AR–regulated genes in an H2A.Z-dependent manner and that chemical inhibition of Brd2 recruitment greatly inhibits AR–regulated gene expression. Taken together, we propose that Brd2 is a key downstream mediator that links H2A.Z and transcriptional activation of AR–regulated genes. Moreover, this study validates the approach of using proteomics to identify nucleosome-interacting proteins in order to elucidate downstream mechanistic functions associated with the histone variant H2A.Z.

Vyšlo v časopise: A Combination of H2A.Z and H4 Acetylation Recruits Brd2 to Chromatin during Transcriptional Activation. PLoS Genet 8(11): e32767. doi:10.1371/journal.pgen.1003047
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003047

Souhrn

Zdroje

1. LiuX, LiB, GorovskyMa (1996) Essential and nonessential histone H2A variants in Tetrahymena thermophila. Mol Cell Biol 16 : 4305–4311.

2. ClarksonMJ, WellsJR, GibsonF, SaintR, TremethickDJ (1999) Regions of variant histone His2AvD required for Drosophila development. Nature 399 : 694–697.

3. RidgwayP, BrownKD, RangasamyD, SvenssonU, TremethickDJ (2004) Unique residues on the H2A.Z containing nucleosome surface are important for Xenopus laevis development. J Biol Chem 279 : 43815–43820.

4. FaastR, ThonglairoamV, SchulzTC, BeallJ, WellsJR, et al. (2001) Histone variant H2A.Z is required for early mammalian development. Curr Biol 11 : 1183–1187.

5. RangasamyD, GreavesI, TremethickDJ (2004) RNA interference demonstrates a novel role for H2A.Z in chromosome segregation. Nat Struct Mol Biol 11 : 650–655.

6. AhmedS, DulB, QiuX, WalworthNC (2007) Msc1 acts through histone H2A.Z to promote chromosome stability in Schizosaccharomyces pombe. Genetics 177 : 1487–1497.

7. HouH, WangY, KallgrenSP, ThompsonJ, YatesJR3rd, et al. (2010) Histone variant H2A.Z regulates centromere silencing and chromosome segregation in fission yeast. J Biol Chem 285 : 1909–1918.

8. MeneghiniMD, WuM, MadhaniHD (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112 : 725–736.

9. DrakerR, CheungP (2009) Transcriptional and epigenetic functions of histone variant H2A.Z. Biochem Cell Biol 87 : 19–25.

10. GuillemetteB, GaudreauL (2006) Reuniting the contrasting functions of H2A.Z. Biochem Cell Biol 84 : 528–535.

11. BruceK, MyersFA, MantouvalouE, LefevreP, GreavesI, et al. (2005) The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken. Nucleic Acids Res 33 : 5633–5639.

12. MillarCB, XuF, ZhangK, GrunsteinM (2006) Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast. Genes Dev 20 : 711–722.

13. HalleyJE, KaplanT, WangAY, KoborMS, RineJ (2010) Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol 8: e1000401.

14. Valdes-MoraF, SongJZ, StathamAL, StrbenacD, RobinsonMD, et al. (2011) Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Res

15. DrakerR, SarcinellaE, CheungP (2011) USP10 deubiquitylates the histone variant H2A.Z and both are required for androgen receptor-mediated gene activation. Nucleic Acids Res 39 : 3529–3542.

16. SarcinellaE, ZuzartePC, LauPN, DrakerR, CheungP (2007) Monoubiquitylation of H2A.Z distinguishes its association with euchromatin or facultative heterochromatin. Mol Cell Biol 27 : 6457–6468.

17. SvotelisA, GevryN, GaudreauL (2009) Regulation of gene expression and cellular proliferation by histone H2A.Z. Biochem Cell Biol 87 : 179–188.

18. KoborMS, VenkatasubrahmanyamS, MeneghiniMD, GinJW, JenningsJL, et al. (2004) A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol 2: E131.

19. MizuguchiG, ShenX, LandryJ, WuWH, SenS, et al. (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303 : 343–348.

20. LukE, VuND, PattesonK, MizuguchiG, WuWH, et al. (2007) Chz1, a nuclear chaperone for histone H2AZ. Mol Cell 25 : 357–368.

21. StraubeK, BlackwellJSJr, PembertonLF (2010) Nap1 and Chz1 have separate Htz1 nuclear import and assembly functions. Traffic 11 : 185–197.

22. RuthenburgAJ, LiH, MilneTA, DewellS, McGintyRK, et al. (2011) Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 145 : 692–706.

23. NadyN, LemakA, WalkerJR, AvvakumovGV, KaretaMS, et al. (2011) Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem 286 : 24300–24311.

24. EustermannS, YangJC, LawMJ, AmosR, ChapmanLM, et al. (2011) Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nat Struct Mol Biol 18 : 777–782.

25. AgricolaE, RandallRA, GaarenstroomT, DupontS, HillCS (2011) Recruitment of TIF1gamma to chromatin via its PHD finger-bromodomain activates its ubiquitin ligase and transcriptional repressor activities. Mol Cell 43 : 85–96.

26. RuthenburgAJ, LiH, PatelDJ, AllisCD (2007) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8 : 983–994.

27. FlorenceB, FallerDV (2001) You bet-cha: a novel family of transcriptional regulators. Front Biosci 6: D1008–1018.

28. GyurisA, DonovanDJ, SeymourKA, LovascoLA, SmilowitzNR, et al. (2009) The chromatin-targeting protein Brd2 is required for neural tube closure and embryogenesis. Biochim Biophys Acta 1789 : 413–421.

29. ShangE, WangX, WenD, GreenbergDA, WolgemuthDJ (2009) Double bromodomain-containing gene Brd2 is essential for embryonic development in mouse. Dev Dyn 238 : 908–917.

30. WangF, LiuH, BlantonWP, BelkinaA, LebrasseurNK, et al. (2010) Brd2 disruption in mice causes severe obesity without Type 2 diabetes. Biochem J 425 : 71–83.

31. GreenwaldRJ, TumangJR, SinhaA, CurrierN, CardiffRD, et al. (2004) E mu-BRD2 transgenic mice develop B-cell lymphoma and leukemia. Blood 103 : 1475–1484.

32. DenisGV, VaziriC, GuoN, FallerDV (2000) RING3 kinase transactivates promoters of cell cycle regulatory genes through E2F. Cell Growth Differ 11 : 417–424.

33. CrowleyTE, KaineEM, YoshidaM, NandiA, WolgemuthDJ (2002) Reproductive cycle regulation of nuclear import, euchromatic localization, and association with components of Pol II mediator of a mammalian double-bromodomain protein. Mol Endocrinol 16 : 1727–1737.

34. DenisGV, McCombME, FallerDV, SinhaA, RomesserPB, et al. (2006) Identification of transcription complexes that contain the double bromodomain protein Brd2 and chromatin remodeling machines. J Proteome Res 5 : 502–511.

35. PengJ, DongW, ChenL, ZouT, QiY, et al. (2007) Brd2 is a TBP-associated protein and recruits TBP into E2F-1 transcriptional complex in response to serum stimulation. Mol Cell Biochem 294 : 45–54.

36. SinhaA, FallerDV, DenisGV (2005) Bromodomain analysis of Brd2-dependent transcriptional activation of cyclin A. Biochem J 387 : 257–269.

37. LeRoyG, RickardsB, FlintSJ (2008) The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol Cell 30 : 51–60.

38. HughesCM, Rozenblatt-RosenO, MilneTA, CopelandTD, LevineSS, et al. (2004) Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus. Mol Cell 13 : 587–597.

39. NakamuraT, MoriT, TadaS, KrajewskiW, RozovskaiaT, et al. (2002) ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation. Mol Cell 10 : 1119–1128.

40. WysockaJ, MyersMP, LahertyCD, EisenmanRN, HerrW (2003) Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev 17 : 896–911.

41. YokoyamaA, WangZ, WysockaJ, SanyalM, AufieroDJ, et al. (2004) Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol Cell Biol 24 : 5639–5649.

42. WysockaJ, SwigutT, MilneTA, DouY, ZhangX, et al. (2005) WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121 : 859–872.

43. SanchezR, ZhouMM (2011) The PHD finger: a versatile epigenome reader. Trends Biochem Sci 36 : 364–372.

44. Maurer-StrohS, DickensNJ, Hughes-DaviesL, KouzaridesT, EisenhaberF, et al. (2003) The Tudor domain ‘Royal Family’: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci 28 : 69–74.

45. MujtabaS, ZengL, ZhouMM (2007) Structure and acetyl-lysine recognition of the bromodomain. Oncogene 26 : 5521–5527.

46. ZengL, ZhouMM (2002) Bromodomain: an acetyl-lysine binding domain. FEBS Lett 513 : 124–128.

47. HuangH, ZhangJ, ShenW, WangX, WuJ, et al. (2007) Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC Struct Biol 7 : 57.

48. NakamuraY, UmeharaT, NakanoK, JangMK, ShirouzuM, et al. (2007) Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. J Biol Chem 282 : 4193–4201.

49. UmeharaT, NakamuraY, JangMK, NakanoK, TanakaA, et al. (2010) Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain. J Biol Chem 285 : 7610–7618.

50. UmeharaT, NakamuraY, WakamoriM, OzatoK, YokoyamaS, et al. (2010) Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2. FEBS Lett 584 : 3901–3908.

51. KannoT, KannoY, SiegelRM, JangMK, LenardoMJ, et al. (2004) Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol Cell 13 : 33–43.

52. WuWH, AlamiS, LukE, WuCH, SenS, et al. (2005) Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol 12 : 1064–1071.

53. Rafalska-MetcalfIU, PowersSL, JooLM, LeRoyG, JanickiSM (2010) Single cell analysis of transcriptional activation dynamics. PLoS One 5: e10272.

54. BonenfantD, CoulotM, TowbinH, SchindlerP, van OostrumJ (2006) Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry. Mol Cell Proteomics 5 : 541–552.

55. IshibashiT, DryhurstD, RoseKL, ShabanowitzJ, HuntDF, et al. (2009) Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome. Biochemistry 48 : 5007–5017.

56. BockI, KudithipudiS, TamasR, KungulovskiG, DhayalanA, et al. (2011) Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails. BMC Biochem 12 : 48.

57. CoonJJ, UeberheideB, SykaJE, DryhurstDD, AusioJ, et al. (2005) Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci U S A 102 : 9463–9468.

58. DryhurstD, IshibashiT, RoseKL, Eirin-LopezJM, McDonaldD, et al. (2009) Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates. BMC Biol 7 : 86.

59. Eirin-LopezJM, Gonzalez-RomeroR, DryhurstD, IshibashiT, AusioJ (2009) The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues. BMC Evol Biol 9 : 31.

60. MatsudaR, HoriT, KitamuraH, TakeuchiK, FukagawaT, et al. (2010) Identification and characterization of the two isoforms of the vertebrate H2A.Z histone variant. Nucleic Acids Res 38 : 4263–4273.

61. DryhurstD, McMullenB, FazliL, RenniePS, AusioJ (2012) Histone H2A.Z prepares the prostate specific antigen (PSA) gene for androgen receptor-mediated transcription and is upregulated in a model of prostate cancer progression. Cancer Lett 315 : 38–47.

62. HeemersHV, TindallDJ (2007) Androgen receptor (AR) coregulators: a diversity of functions converging on and regulating the AR transcriptional complex. Endocr Rev 28 : 778–808.

63. DenisGV (2010) Bromodomain coactivators in cancer, obesity, type 2 diabetes, and inflammation. Discov Med 10 : 489–499.

64. FilippakopoulosP, QiJ, PicaudS, ShenY, SmithWB, et al. (2010) Selective inhibition of BET bromodomains. Nature 468 : 1067–1073.

65. FujimotoS, SeebartC, GuastafierroT, PrenniJ, CaiafaP, et al. (2012) Proteome analysis of protein partners to nucleosomes containing canonical H2A or the variant histones H2A.Z or H2A.X. Biol Chem 393 : 47–61.

66. StrahlBD, AllisCD (2000) The language of covalent histone modifications. Nature 403 : 41–45.

67. SutoRK, ClarksonMJ, TremethickDJ, LugerK (2000) Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol 7 : 1121–1124.

68. TagamiH, Ray-GalletD, AlmouzniG, NakataniY (2004) Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116 : 51–61.

69. DraneP, OuararhniK, DepauxA, ShuaibM, HamicheA (2010) The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 24 : 1253–1265.

70. GoldbergAD, BanaszynskiLA, NohKM, LewisPW, ElsaesserSJ, et al. (2010) Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140 : 678–691.

71. LewisPW, ElsaesserSJ, NohKM, StadlerSC, AllisCD (2010) Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres. Proc Natl Acad Sci U S A 107 : 14075–14080.

72. BonischC, SchneiderK, PunzelerS, WiedemannSM, BielmeierC, et al. (2012) H2A.Z.2.2 is an alternatively spliced histone H2A.Z variant that causes severe nucleosome destabilization. Nucleic Acids Res 40 : 5951–5964.

73. DelmoreJE, IssaGC, LemieuxME, RahlPB, ShiJ, et al. (2011) BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146 : 904–917.

74. ZuberJ, ShiJ, WangE, RappaportAR, HerrmannH, et al. (2011) RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478 : 524–528.

75. VanDemarkAP, KastenMM, FerrisE, HerouxA, HillCP, et al. (2007) Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol Cell 27 : 817–828.

76. ZengL, ZhangQ, Gerona-NavarroG, MoshkinaN, ZhouMM (2008) Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure 16 : 643–652.

77. VoigtP, ReinbergD (2011) Histone tails: ideal motifs for probing epigenetics through chemical biology approaches. Chembiochem 12 : 236–252.

78. ShevchenkoA, TomasH, HavlisJ, OlsenJV, MannM (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1 : 2856–2860.

79. TaylorP, NielsenPA, TrelleMB, HorningOB, AndersenMB, et al. (2009) Automated 2D peptide separation on a 1D nano-LC-MS system. J Proteome Res 8 : 1610–1616.

80. DrakeRR, ElschenbroichS, Lopez-PerezO, KimY, IgnatchenkoV, et al. (2010) In-depth proteomic analyses of direct expressed prostatic secretions. J Proteome Res 9 : 2109–2116.

81. ElschenbroichS, IgnatchenkoV, ClarkeB, KallogerSE, BoutrosPC, et al. (2011) In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry. J Proteome Res 10 : 2286–2299.