YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA

Abstract

5-Methylcytosine is found in both DNA and RNA; although its functions in DNA are well established, the exact role of 5-methylcytidine (m⁵C) in RNA remains poorly defined. Here we identified, by employing a quantitative proteomics method, multiple candidate recognition proteins of m⁵C in RNA, including several YTH domain-containing family (YTHDF) proteins. We showed that YTHDF2 could bind directly to m⁵C in RNA, albeit at a lower affinity than that toward <i>N</i>⁶-methyladenosine (m⁶A) in RNA, and this binding involves Trp⁴³², a conserved residue located in the hydrophobic pocket of YTHDF2 that is also required for m⁶A recognition. RNA bisulfite sequencing results revealed that, after CRISPR-Cas9-mediated knockout of the <i>YTHDF2</i> gene, the majority of m⁵C sites in rRNA (rRNA) exhibited substantially augmented levels of methylation. Moreover, we found that YTHDF2 is involved in pre-rRNA processing in cells. Together, our data expanded the functions of the YTHDF2 protein in post-transcriptional regulations of RNA and provided novel insights into the functions of m⁵C in RNA biology.