eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci

Mol Cell. 2013 Sep 12;51(5):606-17. doi: 10.1016/j.molcel.2013.07.022. Epub 2013 Aug 29.


Transcription factors and DNA regulatory binding motifs are fundamental components of the gene regulatory network. Here, by using genome-wide binding profiling, we show extensive occupancy of transcription factors of myogenesis (MyoD and Myogenin) at extragenic enhancer regions coinciding with RNA synthesis (i.e., eRNA). In particular, multiple regions were transcribed to eRNA within the regulatory region of MYOD1, including previously characterized distal regulatory regions (DRR) and core enhancer (CE). While (CE)RNA enhanced RNA polymerase II (Pol II) occupancy and transcription at MYOD1, (DRR)RNA acted to activate the downstream myogenic genes. The deployment of transcriptional machinery to appropriate loci is contingent on chromatin accessibility, a rate-limiting step preceding Pol II assembly. By nuclease sensitivity assay, we found that eRNAs regulate genomic access of the transcriptional complex to defined regulatory regions. In conclusion, our data suggest that eRNAs contribute to establishing a cell-type-specific transcriptional circuitry by directing chromatin-remodeling events.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • Cell Line
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Chromatin Assembly and Disassembly
  • Enhancer Elements, Genetic / genetics*
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Mice
  • MyoD Protein / genetics
  • MyoD Protein / metabolism*
  • Myogenin / genetics
  • Myogenin / metabolism*
  • Promoter Regions, Genetic
  • RNA / biosynthesis
  • RNA / genetics
  • RNA / metabolism*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism


  • Chromatin
  • MyoD Protein
  • MyoD1 myogenic differentiation protein
  • Myog protein, mouse
  • Myogenin
  • RNA
  • RNA Polymerase II

Associated data

  • GEO/GSE49313