Srr2-dependent SOX2 levels govern the chromatin and transcriptional landscape of adult neural stem cell fate decisions in mouse More about Open Access at the Crick

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 Srr2del/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.