Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

Cell. 2019 Jun 27;178(1):107-121.e18. doi: 10.1016/j.cell.2019.06.001.


Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also show strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping, and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.

Keywords: RBP-TF co-occupancy; RNA-based transcriptional control; RNA-binding proteins; YY1-mediated DNA looping; chromatin binding; functional genomics.

Publication types

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

MeSH terms

  • Binding Sites
  • Chromatin / metabolism*
  • Gene Expression Regulation
  • Genome, Human / genetics
  • Hep G2 Cells
  • Humans
  • K562 Cells
  • Nuclear Proteins
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • RNA / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • RNA-Seq
  • Transcription, Genetic / genetics*
  • Transcriptome
  • YY1 Transcription Factor / genetics
  • YY1 Transcription Factor / metabolism*


  • Chromatin
  • LUC7L3 protein, human
  • Nuclear Proteins
  • RNA-Binding Proteins
  • YY1 Transcription Factor
  • YY1 protein, human
  • RNA