CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation

Cancer cells usually exhibit shortened 3′ untranslated regions (UTRs) due to alternative polyadenylation (APA) to promote cell proliferation and migration. Upregulated CPSF6 leads to a systematic prolongation of 3′ UTRs, but CPSF6 expression in tumors is typically higher than that in healthy tissues. This contradictory observation suggests that it is necessary to investigate the underlying mechanism by which CPSF6 regulates APA switching in cancer. Here, we find that CPSF6 can undergo liquid-liquid phase separation (LLPS), and elevated LLPS is associated with the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs CPSF6 LLPS by phosphorylating its arginine/serine-like domain. The reduction of CPSF6 LLPS can lead to a shortened 3′ UTR of cell-cycle-related genes and accelerate cell proliferation. These results suggest that CPSF6 LLPS, rather than its expression level, may be responsible for APA regulation in cancer cells. [Display omitted] •CPSF6 undergoes liquid-liquid phase separation (LLPS) and recruits CPSF5 into foci•CPSF6 LLPS is disrupted by phosphorylation mediated through CLK2 in cancer cells•CPSF6 LLPS is associated with APA regulation and cell proliferation in cancer cells Liu et al. show that the reduction of CPSF6 liquid-liquid phase separation (LLPS) through CLK2-mediated phosphorylation is associated with the shortened 3′ UTR and accelerated proliferation of cancer cells, dissecting a mechanism of APA regulation involving the alteration of CPSF6 LLPS through post-translational modification.