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PMID: 21172659 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Genome-wide identification of polycomb-associated RNAs by RIP-seq.

Molecular cell ·Vol. 40 ·No. 6 ·2010-12-22 ·Pages 939-53

Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT

Abstract

Polycomb proteins play essential roles in stem cell renewal and human disease. Recent studies of HOX genes and X inactivation have provided evidence for RNA cofactors in Polycomb repressive complex 2 (PRC2). Here we develop a RIP-seq method to capture the PRC2 transcriptome and identify a genome-wide pool of >9000 PRC2-interacting RNAs in embryonic stem cells. The transcriptome includes antisense, intergenic, and promoter-associated transcripts, as well as many unannotated RNAs. A large number of transcripts occur within imprinted regions, oncogene and tumor suppressor loci, and stem cell-related bivalent domains. We provide evidence for direct RNA-protein interactions, most likely via the Ezh2 subunit. We also identify Gtl2 RNA as a PRC2 cofactor that directs PRC2 to the reciprocally imprinted Dlk1 coding gene. Thus, Polycomb proteins interact with a genome-wide family of RNAs, some of which may be used as biomarkers and therapeutic targets for human disease.

MeSH Terms
Animals Embryonic Stem Cells/metabolism Epigenesis, Genetic Gene Expression Profiling Gene Expression Regulation Genome/genetics Humans Immunoprecipitation/methods Mice Polycomb-Group Proteins Protein Binding Proteins/genetics RNA/genetics,metabolism RNA, Long Noncoding RNA-Binding Proteins/genetics,metabolism Repressor Proteins/genetics,metabolism Reproducibility of Results Transcription, Genetic/genetics
Chemicals
MEG3 non-coding RNA, mouse Polycomb-Group Proteins Proteins RNA, Long Noncoding RNA-Binding Proteins Repressor Proteins RNA
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Zhao Jing
Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
Ohsumi Toshiro K
Kung Johnny T
Ogawa Yuya
Grau Daniel J
Sarma Kavitha
Song Ji Joon
Kingston Robert E
Borowsky Mark
Lee Jeannie T
References (59)
59 references, click to expand
  1. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.
    Mol Cell. 2010 Jun 11;38(5):662-74 PMID: 20541999
  2. A region of the human HOXD cluster that confers polycomb-group responsiveness.
    Cell. 2010 Jan 8;140(1):99-110 PMID: 20085705
  3. Stem cell transcriptome profiling via massive-scale mRNA sequencing.
    Nat Methods. 2008 Jul;5(7):613-9 PMID: 18516046
  4. Genome regulation by polycomb and trithorax proteins.
    Cell. 2007 Feb 23;128(4):735-45 PMID: 17320510
  5. Concise review: roles of polycomb group proteins in development and disease: a stem cell perspective.
    Stem Cells. 2007 Oct;25(10):2498-510 PMID: 17600113
  6. Polycomb complexes and epigenetic states.
    Curr Opin Cell Biol. 2008 Jun;20(3):266-73 PMID: 18439810
  7. The evolution of the DLK1-DIO3 imprinted domain in mammals.
    PLoS Biol. 2008 Jun 3;6(6):e135 PMID: 18532878
  8. The Notch signaling cascade in neuroblastoma: role of the basic helix-loop-helix proteins HASH-1 and HES-1.
    Cancer Lett. 2004 Feb 20;204(2):171-8 PMID: 15013216
  9. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome.
    Genes Dev. 2009 Aug 15;23(16):1831-42 PMID: 19684108
  10. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.
    Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72 PMID: 19571010
  11. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.
    Cell. 2009 Dec 24;139(7):1290-302 PMID: 20064375
  12. Jarid2 and PRC2, partners in regulating gene expression.
    Genes Dev. 2010 Feb 15;24(4):368-80 PMID: 20123894
  13. Genome-wide analysis of Polycomb targets in Drosophila melanogaster.
    Nat Genet. 2006 Jun;38(6):700-5 PMID: 16732288
  14. Reconstitution of a functional core polycomb repressive complex.
    Mol Cell. 2001 Sep;8(3):545-56 PMID: 11583617
  15. RNA maps reveal new RNA classes and a possible function for pervasive transcription.
    Science. 2007 Jun 8;316(5830):1484-8 PMID: 17510325
  16. Long non-coding RNAs: insights into functions.
    Nat Rev Genet. 2009 Mar;10(3):155-9 PMID: 19188922
  17. Mechanisms regulating imprinted genes in clusters.
    Curr Opin Cell Biol. 2007 Jun;19(3):281-9 PMID: 17467259
  18. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells.
    Cell. 2009 Dec 24;139(7):1303-14 PMID: 20064376
  19. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency.
    Mol Cell. 2008 Nov 21;32(4):491-502 PMID: 19026780
  20. Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing.
    EMBO J. 2006 Jul 12;25(13):3110-22 PMID: 16763550
  21. Tiny RNAs associated with transcription start sites in animals.
    Nat Genet. 2009 May;41(5):572-8 PMID: 19377478
  22. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation.
    Mol Cell. 2008 Oct 24;32(2):232-46 PMID: 18951091
  23. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.
    Annu Rev Genet. 2004;38:413-43 PMID: 15568982
  24. Control of developmental regulators by Polycomb in human embryonic stem cells.
    Cell. 2006 Apr 21;125(2):301-13 PMID: 16630818
  25. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
    Nature. 2007 Aug 2;448(7153):553-60 PMID: 17603471
  26. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.
    Science. 2008 Dec 19;322(5909):1845-8 PMID: 19056941
  27. Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12.
    Nat Genet. 2003 Sep;35(1):97-102 PMID: 12937418
  28. Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies.
    Nat Rev Mol Cell Biol. 2007 Dec;8(12):1006-16 PMID: 17928811
  29. Roles of the EZH2 histone methyltransferase in cancer epigenetics.
    Mutat Res. 2008 Dec 1;647(1-2):21-9 PMID: 18723033
  30. Point mutations in the WD40 domain of Eed block its interaction with Ezh2.
    Mol Cell Biol. 1998 Oct;18(10):5634-42 PMID: 9742080
  31. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
    PLoS Genet. 2008 Oct;4(10):e1000242 PMID: 18974828
  32. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation.
    Curr Biol. 2005 May 24;15(10):942-7 PMID: 15916951
  33. The transcriptional landscape of the mammalian genome.
    Science. 2005 Sep 2;309(5740):1559-63 PMID: 16141072
  34. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.
    Cell. 2007 Jun 29;129(7):1311-23 PMID: 17604720
  35. A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
    Cell. 2006 Apr 21;125(2):315-26 PMID: 16630819
  36. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.
    Nature. 2010 Apr 15;464(7291):1071-6 PMID: 20393566
  37. Polycomb silencers control cell fate, development and cancer.
    Nat Rev Cancer. 2006 Nov;6(11):846-56 PMID: 17060944
  38. Regulation of imprinting in clusters: noncoding RNAs versus insulators.
    Adv Genet. 2008;61:207-23 PMID: 18282507
  39. SnapShot: imprinted gene clusters.
    Cell. 2007 Sep 7;130(5):958 PMID: 17803916
  40. CLIP: a method for identifying protein-RNA interaction sites in living cells.
    Methods. 2005 Dec;37(4):376-86 PMID: 16314267
  41. ARACHNE: a whole-genome shotgun assembler.
    Genome Res. 2002 Jan;12(1):177-89 PMID: 11779843
  42. Mapping and quantifying mammalian transcriptomes by RNA-Seq.
    Nat Methods. 2008 Jul;5(7):621-8 PMID: 18516045
  43. RNA meets chromatin.
    Genes Dev. 2005 Jul 15;19(14):1635-55 PMID: 16024654
  44. Stem cell regulation by polycomb repressors: postponing commitment.
    Curr Opin Cell Biol. 2008 Apr;20(2):201-7 PMID: 18291635
  45. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome.
    Science. 2008 Oct 31;322(5902):750-6 PMID: 18974356
  46. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.
    Mol Cell. 2010 Jun 11;38(5):675-88 PMID: 20542000
  47. Epigenetic properties and identification of an imprint mark in the Nesp-Gnasxl domain of the mouse Gnas imprinted locus.
    Mol Cell Biol. 2003 Aug;23(16):5475-88 PMID: 12897124
  48. The X as model for RNA's niche in epigenomic regulation.
    Cold Spring Harb Perspect Biol. 2010 Sep;2(9):a003749 PMID: 20739414
  49. Polycomb complexes repress developmental regulators in murine embryonic stem cells.
    Nature. 2006 May 18;441(7091):349-53 PMID: 16625203
  50. A vertebrate Polycomb response element governs segmentation of the posterior hindbrain.
    Cell. 2009 Sep 4;138(5):885-97 PMID: 19737517
  51. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells.
    Nature. 2010 Mar 11;464(7286):306-10 PMID: 20075857
  52. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
    Nature. 2009 Mar 12;458(7235):223-7 PMID: 19182780
  53. Cancer genetics of epigenetic genes.
    Hum Mol Genet. 2007 Apr 15;16 Spec No 1:R28-49 PMID: 17613546
  54. Divergent transcription from active promoters.
    Science. 2008 Dec 19;322(5909):1849-51 PMID: 19056940
  55. Identification of an imprinting control region affecting the expression of all transcripts in the Gnas cluster.
    Nat Genet. 2006 Mar;38(3):350-5 PMID: 16462745
  56. Deletion of Gtl2, imprinted non-coding RNA, with its differentially methylated region induces lethal parent-origin-dependent defects in mice.
    Hum Mol Genet. 2009 May 15;18(10):1879-88 PMID: 19264764
  57. Targeted mutagenesis of Tsix leads to nonrandom X inactivation.
    Cell. 1999 Oct 1;99(1):47-57 PMID: 10520993
  58. Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin.
    Mol Cell Biol. 2006 Apr;26(7):2560-9 PMID: 16537902
  59. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity.
    EMBO J. 2004 Oct 13;23(20):4061-71 PMID: 15385962
Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-4164
DOI
10.1016/j.molcel.2010.12.011
Published
2010-12-22
Pages
939-53
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC3021903
Subset
IM
Grants
NIGMS NIH HHS · R01 GM043901 · United States
NIGMS NIH HHS · GM43901 · United States
NIGMS NIH HHS · R01-GM090278 · United States
NIGMS NIH HHS · R01 GM090278 · United States
Howard Hughes Medical Institute · United States
NIGMS NIH HHS · R01 GM110090 · United States
NIGMS NIH HHS · R01 GM090278-01 · United States
External Links
PubMed source DOI: 10.1016/j.molcel.2010.12.011 PMC Full Text View journal details
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