Home LiteratureArticle Details
PMID: 20300060 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis.

The EMBO journal ·Vol. 29 ·No. 8 ·2010-04-21 ·Pages 1401-11

Seenundun S, Rampalli S, Liu QC, Aziz A, Palii C, Hong S, Blais A, Brand M, Ge K, Dilworth FJ

Abstract

Polycomb (PcG) and Trithorax (TrxG) group proteins act antagonistically to establish tissue-specific patterns of gene expression. The PcG protein Ezh2 facilitates repression by catalysing histone H3-Lys27 trimethylation (H3K27me3). For expression, H3K27me3 marks are removed and replaced by TrxG protein catalysed histone H3-Lys4 trimethylation (H3K4me3). Although H3K27 demethylases have been identified, the mechanism by which these enzymes are targeted to specific genomic regions to remove H3K27me3 marks has not been established. Here, we demonstrate a two-step mechanism for UTX-mediated demethylation at muscle-specific genes during myogenesis. Although the transactivator Six4 initially recruits UTX to the regulatory region of muscle genes, the resulting loss of H3K27me3 marks is limited to the region upstream of the transcriptional start site. Removal of the repressive H3K27me3 mark within the coding region then requires RNA Polymerase II (Pol II) elongation. Interestingly, blocking Pol II elongation on transcribed genes leads to increased H3K27me3 within the coding region, and formation of bivalent (H3K27me3/H3K4me3) chromatin domains. Thus, removal of repressive H3K27me3 marks by UTX occurs through targeted recruitment followed by spreading across the gene.

MeSH Terms
Animals Cell Line Creatine Kinase/metabolism Genes Histone Demethylases/metabolism Histones/metabolism Homeodomain Proteins/metabolism Methylation Mice Muscle Development Myoblasts/cytology,metabolism Myogenin/genetics Nuclear Proteins/metabolism RNA Polymerase II/antagonists & inhibitors,metabolism Trans-Activators/metabolism
Chemicals
Histones Homeodomain Proteins Myogenin Nuclear Proteins Six4 protein, mouse Trans-Activators Histone Demethylases Utx protein, mouse Creatine Kinase RNA Polymerase II
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Seenundun Shayesta
Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.
Rampalli Shravanti
Liu Qi-Cai
Aziz Arif
Palii Carmen
Hong SunHwa
Blais Alexandre
Brand Marjorie
Ge Kai
Dilworth Francis Jeffrey
References (64)
64 references, click to expand
  1. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development.
    Nature. 2007 Oct 11;449(7163):731-4 PMID: 17713478
  2. Biochemical mechanisms of gene regulation by polycomb group protein complexes.
    Curr Opin Genet Dev. 2009 Apr;19(2):150-8 PMID: 19345089
  3. Six1 and Six4 homeoproteins are required for Pax3 and Mrf expression during myogenesis in the mouse embryo.
    Development. 2005 May;132(9):2235-49 PMID: 15788460
  4. Dual role for the methyltransferase G9a in the maintenance of beta-globin gene transcription in adult erythroid cells.
    Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18303-8 PMID: 19822740
  5. The inhibition by DRB (5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole) of hnRNA and mRNA production in HeLa cells.
    Cell. 1976 Nov;9(3):473-80 PMID: 1086720
  6. Maintenance of gene expression patterns.
    Dev Dyn. 2005 Mar;232(3):633-55 PMID: 15704101
  7. Drosophila Kismet regulates histone H3 lysine 27 methylation and early elongation by RNA polymerase II.
    PLoS Genet. 2008 Oct;4(10):e1000217 PMID: 18846226
  8. Global transcription in pluripotent embryonic stem cells.
    Cell Stem Cell. 2008 May 8;2(5):437-47 PMID: 18462694
  9. Six3 and Six6 activity is modulated by members of the groucho family.
    Development. 2003 Jan;130(1):185-95 PMID: 12441302
  10. Knockdown of ALR (MLL2) reveals ALR target genes and leads to alterations in cell adhesion and growth.
    Mol Cell Biol. 2007 Mar;27(5):1889-903 PMID: 17178841
  11. Divergent transcription from active promoters.
    Science. 2008 Dec 19;322(5909):1849-51 PMID: 19056940
  12. Transgenic and tissue culture analyses of the muscle creatine kinase enhancer Trex control element in skeletal and cardiac muscle indicate differences in gene expression between muscle types.
    Transgenic Res. 2003 Jun;12(3):337-49 PMID: 12779122
  13. p38 pathway targets SWI-SNF chromatin-remodeling complex to muscle-specific loci.
    Nat Genet. 2004 Jul;36(7):738-43 PMID: 15208625
  14. An initial blueprint for myogenic differentiation.
    Genes Dev. 2005 Mar 1;19(5):553-69 PMID: 15706034
  15. Modifications of RNA polymerase II are pivotal in regulating gene expression states.
    EMBO Rep. 2009 Nov;10(11):1213-9 PMID: 19834511
  16. The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.
    Cell. 1988 Sep 9;54(6):795-804 PMID: 3136931
  17. MyoD recruits the cdk9/cyclin T2 complex on myogenic-genes regulatory regions.
    J Cell Physiol. 2006 Mar;206(3):807-13 PMID: 16245309
  18. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.
    Nat Genet. 2009 Aug;41(8):941-5 PMID: 19633671
  19. Muscle creatine kinase sequence elements regulating skeletal and cardiac muscle expression in transgenic mice.
    Mol Cell Biol. 1989 Aug;9(8):3393-9 PMID: 2796990
  20. Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II.
    Mol Cell Biol. 2008 Feb;28(3):1041-6 PMID: 18039863
  21. Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II.
    Nature. 1998 May 14;393(6681):187-91 PMID: 9603525
  22. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei.
    Nucleic Acids Res. 1983 Mar 11;11(5):1475-89 PMID: 6828386
  23. Turnover and function of noncoding RNA polymerase II transcripts.
    Cold Spring Harb Symp Quant Biol. 2006;71:275-84 PMID: 17381307
  24. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination.
    Science. 2007 Oct 19;318(5849):447-50 PMID: 17761849
  25. p38 MAPK signaling regulates recruitment of Ash2L-containing methyltransferase complexes to specific genes during differentiation.
    Nat Struct Mol Biol. 2007 Dec;14(12):1150-6 PMID: 18026121
  26. A histone H3 lysine 27 demethylase regulates animal posterior development.
    Nature. 2007 Oct 11;449(7163):689-94 PMID: 17851529
  27. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.
    Annu Rev Genet. 2004;38:413-43 PMID: 15568982
  28. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions.
    Genes Dev. 2006 May 1;20(9):1123-36 PMID: 16618801
  29. Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II.
    Mol Cell Biol. 2009 Nov;29(22):6074-85 PMID: 19703992
  30. An alpha motif at Tas3 C terminus mediates RITS cis spreading and promotes heterochromatic gene silencing.
    Mol Cell. 2009 Apr 24;34(2):155-67 PMID: 19394293
  31. The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation.
    Genes Dev. 2004 Nov 1;18(21):2627-38 PMID: 15520282
  32. Identification of TATA-binding protein-free TAFII-containing complex subunits suggests a role in nucleosome acetylation and signal transduction.
    J Biol Chem. 1999 Jun 25;274(26):18285-9 PMID: 10373431
  33. Functional integration of transcriptional and RNA processing machineries.
    Curr Opin Cell Biol. 2008 Jun;20(3):260-5 PMID: 18436438
  34. Serial passaging and differentiation of myogenic cells isolated from dystrophic mouse muscle.
    Nature. 1977 Dec 22-29;270(5639):725-7 PMID: 563524
  35. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.
    Science. 2008 Dec 19;322(5909):1845-8 PMID: 19056941
  36. Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression.
    Mol Cell. 2002 Mar;9(3):587-600 PMID: 11931766
  37. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors.
    Mol Cell. 2008 Jun 20;30(6):755-66 PMID: 18514006
  38. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing.
    Cell. 2007 Sep 21;130(6):1083-94 PMID: 17825402
  39. A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
    Cell. 2006 Apr 21;125(2):315-26 PMID: 16630819
  40. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells.
    Nature. 1986 Jun 12-18;321(6071):702-6 PMID: 3520340
  41. Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer.
    Mol Cell Biol. 2004 Mar;24(5):2132-43 PMID: 14966291
  42. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing.
    Mol Cell. 2004 Jan 16;13(1):67-76 PMID: 14731395
  43. Groucho/transducin-like enhancer of split (TLE) family members interact with the yeast transcriptional co-repressor SSN6 and mammalian SSN6-related proteins: implications for evolutionary conservation of transcription repression mechanisms.
    Biochem J. 1999 Jan 1;337 ( Pt 1):13-7 PMID: 9854018
  44. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.
    Nat Genet. 2007 Dec;39(12):1512-6 PMID: 17994019
  45. Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography.
    Nat Protoc. 2008;3(3):398-409 PMID: 18323811
  46. RNA polymerase is poised for activation across the genome.
    Nat Genet. 2007 Dec;39(12):1507-11 PMID: 17994021
  47. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases.
    Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18439-44 PMID: 18003914
  48. High-resolution profiling of histone methylations in the human genome.
    Cell. 2007 May 18;129(4):823-37 PMID: 17512414
  49. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.
    EMBO J. 2004 Jan 28;23(2):354-64 PMID: 14739930
  50. Dynamic regulation of nucleosome positioning in the human genome.
    Cell. 2008 Mar 7;132(5):887-98 PMID: 18329373
  51. Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins.
    Genes Dev. 2006 Aug 1;20(15):2041-54 PMID: 16882982
  52. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region.
    Genes Dev. 1992 Nov;6(11):2201-13 PMID: 1427080
  53. Nucleosome arrays reveal the two-start organization of the chromatin fiber.
    Science. 2004 Nov 26;306(5701):1571-3 PMID: 15567867
  54. Genetics and epigenetics: stability and plasticity during cellular differentiation.
    Trends Genet. 2009 Mar;25(3):129-36 PMID: 19185382
  55. p38 mitogen-activated protein kinase pathway promotes skeletal muscle differentiation. Participation of the Mef2c transcription factor.
    J Biol Chem. 1999 Feb 19;274(8):5193-200 PMID: 9988769
  56. A model for transmission of the H3K27me3 epigenetic mark.
    Nat Cell Biol. 2008 Nov;10(11):1291-300 PMID: 18931660
  57. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics.
    Nat Struct Mol Biol. 2004 Jan;11(1):73-80 PMID: 14718926
  58. Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus.
    Mol Cell. 2007 Aug 17;27(4):573-84 PMID: 17707229
  59. Expression of myogenin during embryogenesis is controlled by Six/sine oculis homeoproteins through a conserved MEF3 binding site.
    Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14220-5 PMID: 9826681
  60. Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme.
    BMC Genomics. 2007 Jun 01;8:140 PMID: 17540040
  61. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation.
    Genes Dev. 1995 Mar 1;9(5):559-72 PMID: 7698646
  62. PLD regulates myoblast differentiation through the mTOR-IGF2 pathway.
    J Cell Sci. 2008 Feb 1;121(Pt 3):282-9 PMID: 18198186
  63. Tissue and developmental distribution of Six family gene products.
    Int J Dev Biol. 1998 Mar;42(2):141-8 PMID: 9551859
  64. PTIP associates with MLL3- and MLL4-containing histone H3 lysine 4 methyltransferase complex.
    J Biol Chem. 2007 Jul 13;282(28):20395-406 PMID: 17500065
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
1460-2075
Published
2010-04-21
Epub
2010-00-18
Pages
1401-11
Language
English
Region
England
NLM ID
8208664
PMCID
PMC2868576
Subset
IM
Grants
NIDDK NIH HHS · ZIADK047055-03 · United States
Intramural NIH HHS · ZIA DK075003-08 · United States
CIHR · Canada
NIDDK NIH HHS · ZIADK075017-01 · United States
NIDDK NIH HHS · ZIADK075003-06 · United States
Intramural NIH HHS · Z01 DK047055-01 · United States
Intramural NIH HHS · Z01 DK075003-04 · United States
Intramural NIH HHS · Z01 DK047055-02 · United States
Intramural NIH HHS · Z99 DK999999 · United States
Intramural NIH HHS · Z01 DK075003-05 · United States
Intramural NIH HHS · ZIA DK075017-03 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com