Cohesin regulation of genome organization in mature granule neurons in the mouse cerebellum

BACKGROUND: Proper control of gene expression is important for the development and functions of neurons in the brain. The three-dimensional organization of the genome facilitates gene expression by regulating interactions between gene promoters and their enhancers. Notably, the cohesin complex drives genome folding through loop extrusion, thereby increasing promoter-enhancer interactions. Although cohesin's roles have been well-characterized in proliferating cells and cultured developing neurons, its functions in nuclear organization and gene transcription in mature mammalian brain neurons in vivo remain incompletely understood. RESULTS: To investigate cohesin's functions in the brain, we induced the conditional knockout of the core cohesin subunit RAD21 specifically in cerebellar granule neurons during late development or in adulthood. We then performed RNA-seq and Hi-C approaches to determine the effects of RAD21 depletion on gene expression and 3D genome organization. We found that cohesin was required for the expression of genes that become active in mature granule neurons, and this was linked to its functions in increasing local genomic interactions that bring target gene promoters into spatial proximity with their enhancers. Moreover, for target genes with distal intergenic enhancers, cohesin also maintained those intergenic enhancers within the transcriptionally active A compartment. CONCLUSIONS: Our results reveal the essential functions of cohesin in gene transcription by regulating genome folding across multiple length scales in cerebellar granule neurons. Its roles in orchestrating both local and compartment-level genomic interactions highlight the additional layers of regulation for genes selectively expressed in mature post-mitotic neurons in vivo.