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.

Plunging into a domain of silence Female mammals have two X chromosomes. One must be silenced to “balance” gene dosage with male XY cells. The Xist long noncoding RNA coats the inactive X chromosome in female mammalian cells. Chen et al. show that the Xist RNA helps recruit the X chromosome to the internal rim of the cell nucleus, a region where gene expression is silenced. Xist is recruited to the domain through an interaction with the Lamin B receptor. This recruitment allows the Xist RNA to spread across the future inactive X chromosome, shutting down gene expression. Science , this issue p. 468