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

Mol Cell. 2010 Dec 22;40(6):939-53. doi: 10.1016/j.molcel.2010.12.011.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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
  • RNA / metabolism*
  • RNA, Long Noncoding
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Reproducibility of Results
  • Transcription, Genetic / genetics


  • MEG3 non-coding RNA, mouse
  • Polycomb-Group Proteins
  • Proteins
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • Repressor Proteins
  • RNA