R loops regulate promoter-proximal chromatin architecture and cellular differentiation

Nat Struct Mol Biol. 2015 Dec;22(12):999-1007. doi: 10.1038/nsmb.3122. Epub 2015 Nov 9.


Numerous chromatin-remodeling factors are regulated by interactions with RNA, although the contexts and functions of RNA binding are poorly understood. Here we show that R loops, RNA-DNA hybrids consisting of nascent transcripts hybridized to template DNA, modulate the binding of two key chromatin-regulatory complexes, Tip60-p400 and polycomb repressive complex 2 (PRC2) in mouse embryonic stem cells (ESCs). Like PRC2, the Tip60-p400 histone acetyltransferase complex binds to nascent transcripts; however, transcription promotes chromatin binding of Tip60-p400 but not PRC2. Interestingly, we observed higher Tip60-p400 and lower PRC2 levels at genes marked by promoter-proximal R loops. Furthermore, disruption of R loops broadly decreased Tip60-p400 occupancy and increased PRC2 occupancy genome wide. In agreement with these alterations, ESCs partially depleted of R loops exhibited impaired differentiation. These results show that R loops act both positively and negatively in modulating the recruitment of key pluripotency regulators.

Publication types

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

MeSH terms

  • Animals
  • Cell Differentiation*
  • Chromatin / chemistry*
  • Chromatin / metabolism*
  • DNA / metabolism*
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism
  • Histone Acetyltransferases / analysis
  • Inositol 1,4,5-Trisphosphate Receptors / analysis
  • Lysine Acetyltransferase 5
  • Mice
  • Molecular Sequence Data
  • Polycomb Repressive Complex 2 / analysis
  • Promoter Regions, Genetic*
  • RNA, Messenger / metabolism*
  • Sequence Analysis, DNA
  • Trans-Activators / analysis


  • Chromatin
  • Inositol 1,4,5-Trisphosphate Receptors
  • Itpr1 protein, mouse
  • RNA, Messenger
  • Trans-Activators
  • DNA
  • Polycomb Repressive Complex 2
  • Histone Acetyltransferases
  • Kat5 protein, mouse
  • Lysine Acetyltransferase 5

Associated data

  • GEO/GSE67584