m(6)A RNA methylation promotes XIST-mediated transcriptional repression

Nature. 2016 Sep 15;537(7620):369-373. doi: 10.1038/nature19342. Epub 2016 Sep 7.

Abstract

The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome. Here we show that, in human cells, XIST is highly methylated with at least 78 N6-methyladenosine (m6A) residues-a reversible base modification of unknown function in long non-coding RNAs. We show that m6A formation in XIST, as well as in cellular mRNAs, is mediated by RNA-binding motif protein 15 (RBM15) and its paralogue RBM15B, which bind the m6A-methylation complex and recruit it to specific sites in RNA. This results in the methylation of adenosine nucleotides in adjacent m6A consensus motifs. Furthermore, we show that knockdown of RBM15 and RBM15B, or knockdown of methyltransferase like 3 (METTL3), an m6A methyltransferase, impairs XIST-mediated gene silencing. A systematic comparison of m6A-binding proteins shows that YTH domain containing 1 (YTHDC1) preferentially recognizes m6A residues on XIST and is required for XIST function. Additionally, artificial tethering of YTHDC1 to XIST rescues XIST-mediated silencing upon loss of m6A. These data reveal a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression.

Publication types

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

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / metabolism
  • Animals
  • Cell Line
  • Embryonic Stem Cells / metabolism
  • Female
  • Gene Silencing*
  • HEK293 Cells
  • Humans
  • Male
  • Methylation
  • Methyltransferases / metabolism
  • Mice
  • Nerve Tissue Proteins / metabolism
  • Nuclear Proteins / metabolism
  • RNA Splicing Factors / metabolism
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism*
  • RNA-Binding Proteins / metabolism
  • Transcription, Genetic*

Substances

  • Nerve Tissue Proteins
  • Nuclear Proteins
  • RBM15 protein, human
  • RNA Splicing Factors
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • WTAP protein, human
  • XIST non-coding RNA
  • YTHDC1 protein, human
  • N(6)-methyladenosine
  • Methyltransferases
  • METTL3 protein, human
  • Adenosine