YTHDF2/3 are required for somatic reprogramming through different RNA deadenylation pathways

N6-methyladenosine (m6A), the most abundant reversible modification on eukaryote messenger RNA, is recognized by a series of readers, including the YT521-B homology domain family (YTHDF) proteins, which are coupled to perform physiological functions. Here, we report that YTHDF2 and YTHDF3, but not YTHDF1, are required for the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). Mechanistically, we found that YTHDF3 recruits the PAN2-PAN3 deadenylase complex and conduces to reprogramming by promoting mRNA clearance of somatic genes, including Tead2 and Tgfb1 , which parallels the activity of the YTHDF2-CCR4-NOT deadenylase complex. Ythdf2/3 deficiency further represses mesenchymal-to-epithelial transition (MET) and chromatin silencing at loci containing the TEAD motif, contributing to decreased reprogramming efficiency. Moreover, we reveal that RNA interference of Tgfb1 or the Hippo signaling effectors Yap1 , Taz , and Tead2 rescues Ythdf2/3 deficiency-initiated defects in reprogramming. Overall, the compensatory mechanism by which YTHDF2/3 couple RNA deadenylation and regulation with the clearance of genes, in particular, Tead2 and Tgfb1 , in somatic cells provides novel insights into iPSC reprogramming at the posttranscriptional level.N6-甲基腺嘌呤（N6-methyladenosine, m6A）是真核生物信使RNA上最为丰富的可逆修饰，可被一系列阅读蛋白识别，其中包括YT521-B同源结构域家族（YT521-B homology domain family, YTHDF）蛋白，这类蛋白可协同发挥生理功能。本研究报道，YTHDF2与YTHDF3（而非YTHDF1）是体细胞重编程为诱导多能干细胞（induced pluripotent stem cells, iPSCs）过程所必需的。从机制层面来看，研究发现YTHDF3可招募PAN2-PAN3脱腺苷酶复合物，并通过促进包括Tead2与Tgfb1在内的体细胞相关基因的mRNA降解，协同YTHDF2-CCR4-NOT脱腺苷酶复合物的活性，从而助力重编程进程。Ythdf2/3基因缺陷会进一步抑制间质-上皮转化（mesenchymal-to-epithelial transition, MET）以及含TEAD基序位点的染色质沉默，进而导致重编程效率下降。此外，研究表明，对Tgfb1或Hippo信号通路效应因子Yap1、Taz与Tead2进行RNA干扰，可挽救Ythdf2/3基因缺陷引发的重编程缺陷。综上，YTHDF2/3通过协同RNA脱腺苷化与基因调控，清除体细胞中的特定基因（尤其是Tead2与Tgfb1）的补偿机制，为转录后水平的iPSC重编程研究提供了全新视角。