HMGB2 Loss Upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering Across Cell Types

Ageing-relevant processes, like cellular senescence, are characterized by complex events giving rise to heterogeneous cell populations. However, the early molecular events that trigger such cascades remain elusive. We hypothesized that senescence entry by primary human cells is characterized by an early disruption of the cells' three-dimensional genome organization. To test this, we combined Hi-C, single-cell and population transcriptomics, super-resolution imaging, in silico simulations, and functional analyses on proliferating and replicatively-senescent cells from three distinct lineages. We discovered a cluster of genes involved in DNA conformation maintenance being suppressed upon senescence entry across all cell types. Of these, the abundant non-histone-like HMGB2 is depleted from nuclei before typical senescence markers appear, and is involved in loop formation. Its loss coincides with a reorganization of chromatin interactions via dramatic spatial clustering of CTCF foci. Upon HMGB2 knock-down this senescence-induced CTCF clustering is recapitulated and CTCF loops are reshuffled, as HMGB2 appears to confer local insulation both at TAD boundaries and within TADs. Our data suggest that the HMGB-mediated deregulation of genomic organization constitutes a primer for the ensuing senescent program across cell lineages.