Ythdf2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells via Cooperation with Cnot1 [RNA-seq_siCNOT1]

Mouse embryonic stem cells (ESCs) consist of a rare population of heterogeneous cells which express 2-cell-stage-specific transcripts and are referred to as 2-cell-like cells (2CLCs). Accumulating evidence has demonstrated that transcription factors and epigenetic modifications exert crucial functions in the transition of ESCs to 2CLCs. However, the roles of RNA modification in the regulation of 2C-like state remain elusive. Using Dux-induced 2CLCs system, we examine N6-methyladenosine (m6A) modification landscape in transcriptome-wide, and find that m6A is dynamically regulated during Dux-driven 2C-like reprogramming. Intriguingly, many of 2C-specific transcripts are highly methylated, including Dux and Zscan4 cluster genes. We further identify the m6A reader protein Ythdf2 as a critical regulator of 2C-like state. Depletion of Ythdf2 facilitates robust expressions of 2C transcripts and the transition of ESCs to 2CLCs. Mechanically, Ythdf2 binds to the Dux/Zscan4 transcripts and promotes their degradation through recruiting the key component of RNA deadenylase complex, Cnot1. Consistent with the phenotype of Ythdf2 deficiency, silencing of Cnot1 induces the 2C gene expressions and the transition of ESCs into the 2C-like state. Collectively, our findings reveal novel insights into the epitranscriptomic regulation of the 2C-like state in mouse ESCs.