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YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA
- 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
- Analytical chemistry 2019 v.92 no.1 pp. 1346-1354
- DNA, DNA methylation, bisulfites, genes, hydrophobicity, proteins, proteomics, ribosomal RNA, sequence analysis
- 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.