Nascent Connections: R-Loops and Chromatin Patterning

Trends Genet. 2016 Dec;32(12):828-838. doi: 10.1016/j.tig.2016.10.002. Epub 2016 Oct 25.


RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed.

Keywords: R-loop; RNA:DNA hybrids; chromatin; gene regulation; genomics; transcription.

Publication types

  • Review
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Chromatin / genetics*
  • Chromatin Assembly and Disassembly / genetics
  • Gene Expression Regulation / genetics*
  • Mammals
  • RNA, Long Noncoding / genetics*


  • Chromatin
  • RNA, Long Noncoding