Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2.

Cohesin organizes 3D genome architecture yet its acute depletion in vitro minimally affects transcription, leaving its regulatory role puzzling. We hypothesized that cohesin function is relevant when first encounters chromatin after mitosis. Using in vivo labeling and cell-cycle synchronization in human cells, we demonstrate that cohesin complexes persist through mitosis. This inherited pool dominates over newly translated cohesin during telophase-G1, highlighting the relevance of such transmission. Acute depletion of cohesin Rad21 at mitotic exit impairs the expression of hundreds of genes, mostly downregulated, enriched on functions related to tissue growth and development. Rad21 binds the promoter of this group of genes. Remarkably, we uncover a direct interaction during the M-G1 transition between Rad21 and Cdk9, the kinase component of transcription elongation factor b (pTEFb) complex. Rad21 loss impairs Cdk9 chromatin association, reducing active-elongating RNAPol2 at down-regulated genes. Overall, preserving cohesin across mitosis enables post-mitotic transcriptional reactivation via Cdk9, establishing tissue-specific expression programs.