Ash1l Methylates Lys36 of Histone H3 Independently of Transcriptional Elongation to Counteract Polycomb Silencing
Molecular mechanisms for the establishment of transcriptional memory are poorly understood. 5,6-dichloro-1-D-ribofuranosyl-benzimidazole (DRB) is a P-TEFb kinase inhibitor that artificially induces the poised RNA polymerase II (RNAPII), thereby manifesting intermediate steps for the establishment of transcriptional activation. Here, using genetics and DRB, we show that mammalian Absent, small, or homeotic discs 1-like (Ash1l), a member of the trithorax group proteins, methylates Lys36 of histone H3 to promote the establishment of Hox gene expression by counteracting Polycomb silencing. Importantly, we found that Ash1l-dependent Lys36 di-, tri-methylation of histone H3 in a coding region and exclusion of Polycomb group proteins occur independently of transcriptional elongation in embryonic stem (ES) cells, although both were previously thought to be consequences of transcription. Genome-wide analyses of histone H3 Lys36 methylation under DRB treatment have suggested that binding of the retinoic acid receptor (RAR) to a certain genomic region promotes trimethylation in the RAR-associated gene independent of its ongoing transcription. Moreover, DRB treatment unveils a parallel response between Lys36 methylation of histone H3 and occupancy of either Tip60 or Mof in a region-dependent manner. We also found that Brg1 is another key player involved in the response. Our results uncover a novel regulatory cascade orchestrated by Ash1l with RAR and provide insights into mechanisms underlying the establishment of the transcriptional activation that counteracts Polycomb silencing.
Vyšlo v časopise:
Ash1l Methylates Lys36 of Histone H3 Independently of Transcriptional Elongation to Counteract Polycomb Silencing. PLoS Genet 9(11): e32767. doi:10.1371/journal.pgen.1003897
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003897
Souhrn
Molecular mechanisms for the establishment of transcriptional memory are poorly understood. 5,6-dichloro-1-D-ribofuranosyl-benzimidazole (DRB) is a P-TEFb kinase inhibitor that artificially induces the poised RNA polymerase II (RNAPII), thereby manifesting intermediate steps for the establishment of transcriptional activation. Here, using genetics and DRB, we show that mammalian Absent, small, or homeotic discs 1-like (Ash1l), a member of the trithorax group proteins, methylates Lys36 of histone H3 to promote the establishment of Hox gene expression by counteracting Polycomb silencing. Importantly, we found that Ash1l-dependent Lys36 di-, tri-methylation of histone H3 in a coding region and exclusion of Polycomb group proteins occur independently of transcriptional elongation in embryonic stem (ES) cells, although both were previously thought to be consequences of transcription. Genome-wide analyses of histone H3 Lys36 methylation under DRB treatment have suggested that binding of the retinoic acid receptor (RAR) to a certain genomic region promotes trimethylation in the RAR-associated gene independent of its ongoing transcription. Moreover, DRB treatment unveils a parallel response between Lys36 methylation of histone H3 and occupancy of either Tip60 or Mof in a region-dependent manner. We also found that Brg1 is another key player involved in the response. Our results uncover a novel regulatory cascade orchestrated by Ash1l with RAR and provide insights into mechanisms underlying the establishment of the transcriptional activation that counteracts Polycomb silencing.
Zdroje
1. GuentherMG, LevineSS, BoyerLA, JaenischR, YoungRA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 77–88.
2. ChengB, PriceDH (2007) Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J Biol Chem 282: 21901–21912.
3. GilmourDS (2009) Promoter proximal pausing on genes in metazoans. Chromosoma 118: 1–10.
4. ChibaK, YamamotoJ, YamaguchiY, HandaH (2010) Promoter-proximal pausing and its release: Molecular mechanisms and physiological functions. Exp Cell Res 316: 2723–2730.
5. RahlPB, LinCY, SeilaAC, FlynnRA, McCuineS, et al. (2010) c-Myc regulates transcriptional pause release. Cell 141: 432–445.
6. MavrichTN, JiangC, IoshikhesIP, LiX, VentersBJ, et al. (2008) Nucleosome organization in the Drosophila genome. Nature 453: 358–362.
7. SimonJA, KingstonRE (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 10: 697–708.
8. PappB, MüllerJ (2006) Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev 20: 2041–2054.
9. GregoryGD, VakocCR, RozovskaiaT, ZhengX, PatelS, et al. (2007) Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes. Mol Cell Biol 27: 8466–8479.
10. BeiselC, ImhofA, GreeneJ, KremmerE, SauerF (2002) Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1. Nature 419: 857–862.
11. TanakaY, KatagiriZ, KawahashiK, KioussisD, KitajimaS (2007) Trithorax-group protein ASH1 methylates histone H3 lysine 36. Gene 397: 161–168.
12. CabiancaDS, CasaV, BodegaB, XynosA, GinelliE, et al. (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149: 819–831.
13. KroganNJ, KimM, TongA, GolshaniA, CagneyG, et al. (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23: 4207–4218.
14. LiB, HoweL, AndersonS, YatesJR3rd, WorkmanJL (2003) The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 278: 8897–8903.
15. XiaoT, HallH, KizerKO, ShibataY, HallMC, et al. (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 17: 654–663.
16. KuzinB, TillibS, SedkovY, MizrokhiL, MazoA (1994) The Drosophila trithorax gene encodes a chromosomal protein and directly regulates the region-specific homeotic gene fork head. Genes Dev 8: 2478–2490.
17. RozovskaiaT, TillibS, SmithS, SedkovY, Rozenblatt-RosenO, et al. (1999) Trithorax and ASH1 interact directly and associate with the trithorax group-responsive bxd region of the Ultrabithorax promoter. Mol Cell Biol 19: 6441–6447.
18. MikkelsenTS, KuM, JaffeDB, IssacB, LiebermanE, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553–560.
19. TanakaY, KawahashiK, KatagiriZ-I, NakayamaY, MahajanM, et al. (2011) Dual Function of Histone H3 Lysine 36 Methyltransferase ASH1 in Regulation of Hox Gene Expression. PLoS ONE 6(11): e28171.
20. CarrozzaMJ, LiB, FlorensL, SuganumaT, SwansonSK, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581–592.
21. KeoghMC, KurdistaniSK, MorrisSA, AhnSH, PodolnyV, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593–605.
22. MahonyS, MazzoniEO, McCuineS, YoungRA, WichterleH, et al. (2011) Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol 12: R2.
23. SchmittS, PrestelM, ParoR (2005) Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19: 697–708.
24. BellO, WirbelauerC, HildM, ScharfAN, SchwaigerM, et al. (2007) Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. EMBO J 26: 4974–4984.
25. SmithER, CayrouC, HuangR, LaneWS, CôtéJ, et al. (2005) A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16. Mol Cell Biol 25: 9175–9188.
26. HayakawaT, OhtaniY, HayakawaN, ShinmyozuK, SaitoM, et al. (2007) RBP2 is an MRG15 complex component and down-regulates intragenic histone H3 lysine 4 methylation. Genes Cells 12: 811–826.
27. ZhangP, DuJ, SunB, DongX, XuG, et al. (2006) Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res 34: 6621–6628.
28. LarschanE, AlekseyenkoAA, GortchakovAA, PengS, LiB, et al. (2007) MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell 28: 121–133.
29. Shogren-KnaakM, IshiiH, SunJM, PazinMJ, DavieJR, et al. (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311: 844–847.
30. SinghM, PopowiczGM, KrajewskiM, HolakTA (2007) Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex. Chembiochem 8: 1308–1316.
31. ZippoA, SerafiniR, RocchigianiM, PennacchiniS, KrepelovaA, et al. (2009) Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138: 1122–1136.
32. HoranGS, Ramírez-SolisR, FeatherstoneMS, WolgemuthDJ, BradleyA, et al. (1995) Compound mutants for the paralogous hoxa-4, hoxb-4, and hoxd-4 genes show more complete homeotic transformations and a dose-dependent increase in the number of vertebrae transformed. Genes Dev 9: 1667–1677.
33. LagarouA, Mohd-SaripA, MoshkinYM, ChalkleyGE, BezstarostiK, et al. (2008) dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group silencing. Genes Dev 22: 2799–2810.
34. YuanW, XuM, HuangC, LiuN, ChenS, et al. (2011) H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J Biol Chem 286: 7983–7989.
35. FrancisNJ, KingstonRE, WoodcockCL (2004) Chromatin compaction by a polycomb group protein complex. Science 306: 1574–1577.
36. AshburnerM (1972) Ecdysone induction of puffing in polytene chromosomes of Drosophila melanogaster. Effects of inhibitors of RNA synthesis. Exp Cell Res 71: 433–440.
37. OrphanidesG, ReinbergD (2000) RNA polymerase II elongation through chromatin. Nature 407: 471–475.
38. TerranovaR, AgherbiH, BonedA, MeresseS, DjabaliM (2006) Histone and DNA methylation defects at Hox genes in mice expressing a SET domain-truncated form of Mll. Proc Natl Acad Sci U S A 103: 6629–6634.
39. AkasakaT, KannoM, BallingR, MiezaMA, TaniguchiM, et al. (1996) A role for mel-18, a Polycomb group-related vertebrate gene, during the anteroposterior specification of the axial skeleton. Development 122: 1513–2215.
40. IsonoK, FujimuraY, ShingaJ, YamakiM, O-WangJ, et al. (2005) Mammalian polyhomeotic homologues Phc2 and Phc1 act in synergy to mediate polycomb repression of Hox genes. Mol Cell Biol 25: 6694–6706.
41. KesselM, GrussP (1991) Homeotic transformations of murine vertebrae and concomitant alteration of Hox codes induced by retinoic acid. Cell 67: 89–104.
42. WilkinsonDG, NietoMA (1993) Detection of messenger RNA by in situ hybridization to tissue sections and whole mounts. Methods Enzymol 225: 361–373.
43. PatroneG, PuppoF, CusanoR, ScaranariM, CeccheriniI, et al. (2000) Nuclear run-on assay using biotin labeling, magnetic bead capture and analysis by fluorescence-based RT-PCR. Biotechniques 29: 1012–1017, 1012-1014, 1016-1017.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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