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

Authors: Dai, Xiaoxia; Gonzalez, Gwendolyn; Li, Lin; Li, Jie; You, Changjun; Miao, Weili; Hu, Junchi; Fu, Lijuan; Zhao, Yonghui; Li, Ruidong; Li, Lichao; Chen, Xuemei; Xu, Yanhui; Gu, Weifeng; Wang, Yinsheng

Published In Anal Chem, (2020 Jan 07)

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 N6-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 YTHDF2 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.

PubMed ID: 31815440

MeSH Terms: 5-Methylcytosine/chemistry*; 5-Methylcytosine/metabolism; Binding Sites; Cells, Cultured; HEK293 Cells; HeLa Cells; Humans; Methylation; Molecular Structure; RNA Processing, Post-Transcriptional/genetics; RNA, Ribosomal/chemistry*; RNA, Ribosomal/metabolism; RNA-Binding Proteins/chemistry*; RNA-Binding Proteins/genetics; RNA-Binding Proteins/metabolism