Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-chromatin Interactions

Mol Cell. 2011 Nov 18;44(4):667-78. doi: 10.1016/j.molcel.2011.08.027. Epub 2011 Sep 29.

Abstract

Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lncRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3' end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lncRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome wide.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Breast Neoplasms / genetics
  • Breast Neoplasms / metabolism
  • Cell Line, Tumor
  • Chromatin / chemistry*
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Assembly and Disassembly / genetics*
  • Chromosome Mapping / methods*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • Enhancer of Zeste Homolog 2 Protein
  • Female
  • Genome-Wide Association Study
  • Genomics*
  • High-Throughput Screening Assays*
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Male
  • Molecular Sequence Data
  • Nucleotide Motifs / genetics
  • Polycomb Repressive Complex 2
  • RNA / genetics
  • RNA / metabolism
  • RNA, Long Noncoding
  • RNA, Untranslated* / chemistry
  • RNA, Untranslated* / genetics
  • RNA, Untranslated* / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Telomerase / genetics
  • Telomerase / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Wnt Signaling Pathway / genetics

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Drosophila Proteins
  • HOTAIR long untranslated RNA, human
  • Histones
  • Pabp2 protein, Drosophila
  • RNA, Long Noncoding
  • RNA, Untranslated
  • RNA-Binding Proteins
  • Transcription Factors
  • telomerase RNA
  • RNA
  • EZH2 protein, human
  • Enhancer of Zeste Homolog 2 Protein
  • Polycomb Repressive Complex 2
  • Telomerase

Associated data

  • GEO/GSE31332