Identification of YTH Domain-Containing Proteins as the Readers for N1-Methyladenosine in RNA

Abstract

N1-methyladenosine (m¹A) is an important post-transcriptional modification in RNA; however, the exact biological role of m¹A remains to be determined. By employing a quantitative proteomics method, we identified multiple putative protein readers of m¹A in RNA, including several YTH domain family proteins. We showed that YTHDF1-3 and YTHDC1, but not YTHDC2, could bind directly to m¹A in RNA. We also found that Trp⁴³² in YTHDF2, a conserved residue in the hydrophobic pocket of the YTH domain that is necessary for its binding to N⁶-methyladenosine (m⁶A), is required for its recognition of m¹A. An analysis of previously published data revealed transcriptome-wide colocalization of YTH domain-containing proteins and m¹A sites in HeLa cells, suggesting that YTH domain-containing proteins can bind to m¹A in cells. Together, our results uncovered YTH domain-containing proteins as readers for m¹A in RNA and provided new insight into the functions of m¹A in RNA biology.