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ATAC-seq of SRR2KO

ABSTRACT: Stem cell maintenance and lineage commitment in the nervous system require precise regulation of transcription factors, among which SOX2 plays a central role. Its expression is controlled by multiple enhancers, including the Sox2 regulatory region 2 (Srr2), located downstream of the Sox2 locus. To dissect the role of Srr2 during neural development, we generated a CRISPR-Cas9 mouse model harboring a targeted deletion of this enhancer. We find reduced SOX2 in SEZ/SGZ niches and diminished ASCL1/OLIG2 progenitors, accompanied by fewer neurons and oligodendrocytes in vitro. Paired bulk RNA-seq and ATAC-seq at two defined transitions as 2 DIV (proliferation) and 2+1 DIV (early commitment) show that Srr2 loss causes widespread chromatin compaction during proliferation (6,393 DARs; 6,319 less accessible) that phenocopies wild-type differentiation, while accessibility largely converges by 2+1 DIV. Multi-omic integration reveals 115 neurogenic genes with persistent promoter closure and reduced induction at the transcriptional level in mutants, consistent with failure to activate proneural programs upon early differentiation. In vivo, SEZ cells of Srr2del/del mice exhibit lower SOX2 and FOXG1, fewer ASCL1/OLIG2 progenitors, and reduced neuronal and oligodendroglial markers. Together, our results uncover Srr2 as a critical enhancer of Sox2, required for establishing a chromatin environment permissive to neural differentiation, and underscore the importance of non-coding regulatory elements in controlling stem cell fate.

ORGANISM(S): Mus musculus

PROVIDER: GSE319464 | GEO | 2026/05/09

REPOSITORIES: GEO

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Project description:Stem cell maintenance and lineage commitment in the nervous system require precise regulation of transcription factors, among which SOX2 plays a central role. Its expression is controlled by multiple enhancers, including the Sox2 regulatory region 2 (Srr2), located downstream of the Sox2 locus. To dissect the role of Srr2 during neural development, we generated a CRISPR-Cas9 mouse model harboring a targeted deletion of this enhancer. We find reduced SOX2 in SEZ/SGZ niches and diminished ASCL1/OLIG2 progenitors, accompanied by fewer neurons and oligodendrocytes in vitro. Paired bulk RNA-seq and ATAC-seq at two defined transitions as 2 DIV (proliferation) and 2+1 DIV (early commitment) show that Srr2 loss causes widespread chromatin compaction during proliferation (6,393 DARs; 6,319 less accessible) that phenocopies wild-type differentiation, while accessibility largely converges by 2+1 DIV. Multi-omic integration reveals 115 neurogenic genes with persistent promoter closure and reduced induction at the transcriptional level in mutants, consistent with failure to activate proneural programs upon early differentiation. In vivo, SEZ cells of Srr2del/del mice exhibit lower SOX2 and FOXG1, fewer ASCL1/OLIG2 progenitors, and reduced neuronal and oligodendroglial markers. Together, our results uncover Srr2 as a critical enhancer of Sox2, required for establishing a chromatin environment permissive to neural differentiation, and underscore the importance of non-coding regulatory elements in controlling stem cell fate.

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