Srr2-dependent SOX2 levels govern the chromatin and transcriptional landscape of adult neural stem cell fate decisions in mouse

Abstract Background Stem cell maintenance and lineage commitment in the nervous system require precise regulation of transcription factors, with SOX2 serving as a pivotal regulator. SOX2 expression is controlled by multiple enhancers, including the Sox2 regulatory region 2 ( Srr2 ). However, the specific role of Srr2 in adult neurogenesis and chromatin regulation during neural lineage commitment remains incompletely understood. Results To dissect the function of Srr2 , we generate a CRISPR-Cas9 mouse model harboring a targeted deletion of this enhancer. Srr2 deletion reduce SOX2 levels in proliferating, but not differentiating, neurosphere cultures, while impairing both neuronal and oligodendroglial differentiation. Paired bulk RNA-seq and ATAC-seq during proliferation and early differentiation reveal that loss of Srr2 induces widespread chromatin compaction during proliferation, which partially converges toward wild-type states upon early differentiation. Multi-omic integration identifies a subset of neurogenic genes exhibiting persistent promoter closure and impaired transcriptional induction in proliferating mutant cells, despite being normally translated during neural differentiation. In vivo, subependymal zone cells of Srr2 del/del mice exhibit lower SOX2 and FOXG1 expression, fewer ASCL1/OLIG2 progenitors, and reduced neuronal and oligodendroglial marker expression. Conclusions These findings establish Srr2 as a critical enhancer of Sox2 required to maintain a chromatin environment permissive for neural differentiation during stem cell proliferation. Our study underscores the essential role of non-coding regulatory elements in coordinating chromatin accessibility, transcriptional programs, and stem cell fate decisions during adult neurogenesis.