GSE201217
A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and senescence
Cellular senescence is a program of permanent cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in mammalian cells.  Landmark studies in laboratory mice have established master senescence regulators, including p16INK4a, p21, NF-kB, p53, and C/EBPß.  To discover other molecular players in cellular senescence, we developed an approach that harnessed the natural divergence between distant mouse species.  We found that senescent primary cells from the Algerian mouse Mus spretus expressed a distinct, and largely muted, regulatory program relative to that of laboratory M. musculus.  We pinpointed which of these interspecies expression changes during senescence were under cis-regulatory control, via allele-specific expression profiling.  Then, in silico, we associated the latter with sequence variants in transcription factor binding sites.  Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, USF2, for molecular validation.  In acute irradiation experiments, cells lacking USF2 exhibited compromised DNA damage repair and response.  Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program—shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type.  We interpret these findings under a model of pro-repair, anti-senescence regulatory function by native USF2.  Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens. Overall design: Comparative gene expression profiling analysis of RNA-seq data for Mus musculus, M. spretus, and F1 hybrid primary cells and its KD derivatives (shUSF2).