YTH domain-containing family protein 2
C5-methylcytidine-containing RNA reader activity
YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA.
5-Methylcytosine is found in both DNA and RNA; although its functions in DNA are well established, the exact role of 5-methylcytidine (m<sup>5</sup>C) in RNA remains poorly defined. Here we identified, by employing a quantitative proteomics method, multiple candidate recognition proteins of m<sup>5</sup>C in RNA, including several YTH domain-containing family (YTHDF) proteins. We showed that YTHDF2 could bind directly to m<sup>5</sup>C in RNA, albeit at a lower affinity than that toward <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A) in RNA, and this binding involves Trp<sup>432</sup>, a conserved residue located in the hydrophobic pocket of YTHDF2 that is also required for m<sup>6</sup>A recognition. RNA bisulfite sequencing results revealed that, after CRISPR-Cas9-mediated knockout of the <i>YTHDF2</i> gene, the majority of m<sup>5</sup>C 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 m<sup>5</sup>C in RNA biology.