Ythdf2-Setd1b axis mediates H3K4me3 is required for cerebellar development
Ythdf2 is a well-characterized m6A reader that promotes degradation of methylated transcripts and thereby maintains transcriptome balance. Although this role is established, whether Ythdf2 also links epitranscriptomic regulation to chromatin remodeling during brain development remains unknown. To address this, we generated a Ythdf2 knockout (Ythdf2KO) mouse and examined cerebellar development at embryonic day 13.5 (E13.5) and postnatal day 3 (P3).Ythdf2KO mice developed severe cerebellar ataxia with tremors and abnormal gait. Loss of Ythdf2 impaired neural progenitor self-renewal and accelerated neuronal differentiation, reflected by reduced Sox2 and Nestin and increased Tuj1 and Skor2 expression. Neuronal functional genes, including Map2, Calb1, and Gfap, were also downregulated, confirming defective lineage progression.m6A RIP-seq revealed that Ythdf2 knockout caused a global reduction in m6A levels, and the affected transcripts were enriched for regulators of histone modification and chromatin stability. Chromatin profiling showed that Ythdf2 deletion reduced H3K4me3 at promoters of neurodevelopmental genes, leading to decreased chromatin accessibility and suppressed transcriptional activity in neuronal pathways. Co-immunoprecipitation assays further demonstrated that Ythdf2 specifically interacts with the H3K4 methyltransferase Setd1b, but not Cxxc1 or Setd1a, to regulate transcription in early cerebellar development. Importantly, Setd1b knockdown partially rescued the defects in progenitor maintenance and neuronal differentiation observed in Ythdf2KO mice.These findings establish that Ythdf2 not only controls RNA stability through its canonical m6A-dependent decay function but also couples m6A signaling to Setd1b-mediated H3K4me3 modification. This dual role maintains chromatin accessibility and transcriptional programs required for proper cerebellar formation. Our study expands the functional scope of Ythdf2 beyond RNA decay and uncovers a mechanistic connection between m6A regulation, histone modification, and transcriptional control in neurodevelopment.