Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [RNA-seq]. Homo sapiens

We hypothesized that entry into senescence of different primary human cells can be triggered by one early molecular event affecting the spatial organization of chromosomes. To test this, we combined whole-genome chromosome conformation capture, population and single-cell transcriptomics, super-resolution imaging, and functional analyses applied on proliferating and replicatively-senescent populations from three distinct human cell types. We found a number of genes involved in DNA conformation maintenance being suppressed upon senescence across cell types. Of these, the abundant high mobility group (HMG) B1 and B2 nuclear factors are quantitatively removed from cell nuclei before typical senescence markers appear, and mark a subset of topologically-associating domain (TAD) boundaries. Their loss coincides with obvious reorganization of chromatin interactions via the dramatic spatial clustering of CTCF foci. HMGB2 knock-down recapitulates this senescence-induced CTCF clustering, while also affecting insulation at TAD boundaries. Overall design: Gene expression profiles generated by sequencing total (ribodepleted) RNA from HUVEC (D1-D3), polyA-selected or nascent (factory) RNA from IMR90 (I10 and I79), polyA-selected RNA from MSC (donors A-D), or polyA-selected RNA from control (NTC) and HMGB2-knockdown (HMGB2-KD) HUVEC.