Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program [RNA-seq]

Senescence —the end-point of the replicative life span of normal cells— is characterized by a complex sequence of molecular and biochemical events. One of these is the dramatic reorganization of CTCF into large senescence-induced CTCF clusters (SICCs). However, the molecular determinants, genomic consequences, and functional purpose of SICCs remained unknown. Here, we combine super-resolution imaging, 3D genomics, and functional assays with computational modelling to address all aspects of SICC emergence. First, we used modelling and data from the overexpression of nuclear factors lost upon senescence entry to explain how changes in the nuclear environment allow for CTCF clustering. Second, we discovered that cells entering senescence repurpose SRRM2 —a key component of nuclear speckles— and BANF1 —a protein known to act as 'molecular glue' for chromosomes during mitosis— to cluster CTCF on the surface of speckles, while rewiring higher-order genome architecture. Last, we could show that SICCs are required for the faithful execution of the senescence splicing program as their disruption by SRRM2 or BANF1 depletion reverts splicing choices. Together, the senescence-specific clustering of CTCF on nuclear speckles is a new paradigm of a change in the biochemical environment of the nucleus being translated into its architectural reorganization to allow for the deployment of a splicing program driving homeostatic deregulation. Overall design: To invstigate the function of SICCs in the senescence splicing program, we performed RNA-seq on the IMR90 cell lines of wild type (WT), ICM-induced senescence (ICM), siRNA-mediated HMGB2 knockdown on the wild type background (siHMGB2), SRRM2 knockdown and BANF1 knockdown on the background of ICM (siSRRM2 and siBANF1). Next, we compared the expression profile and the splicing profile of ICM vs WT, siHMGB2 vs WT, siSRRM2 vs ICM, and siBANF1 vs ICM.