Transcription factors interact with RNA to regulate genes

Mol Cell. 2023 Jul 20;83(14):2449-2463.e13. doi: 10.1016/j.molcel.2023.06.012. Epub 2023 Jul 3.

Abstract

Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.

Keywords: RNA; RNA-binding proteins; arginine-rich motif; chromatin; development; gene regulation; single-molecule imaging; transcription factor; zebrafish.

Publication types

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

MeSH terms

  • Binding Sites
  • DNA / genetics
  • Protein Binding
  • RNA* / metabolism
  • Transcription Factors* / metabolism

Substances

  • Transcription Factors
  • RNA
  • DNA