Alternative polyadenylation mediated by CPSF5 regulates pro-inflammatory gene expression

The majority of mammalian genes contains more than one functional cleavage and polyadenylation site, so that selection of alternative sites leads to different 3 ends of the mature transcripts. This mechanism can lead to the exclusion or retention of regulatory sequence elements, which affects post-transcriptional regulation of gene expression, such as RNA stability, localization or translation efficiency. We used 3 end sequencing to assess alternative polyadenylation during the response of macrophages to LPS, and observed a strong global shift towards proximal polyadenylation sites. This was accompanied by a decreased expression of cleavage and polyadenylation factors, including CPSF5, which is known to favor selection of distal polyadenylation sites. Upon depletion of CPSF5 in macrophage, we observed global transcript shortening, and an induction of TNF and other pro-inflammatory cytokines without LPS-stimulation. Analysis of RNA-seq data from monocytes of sepsis patients revealed that CPSF5 expression and alternative polyadenylation are also affected in vivo. Usage of distal polyadenylation sites showed a negative correlation with TNF mRNA expression in human monocytes. Our data suggest that transcript shortening mediated by CPSF5 repression contributes to the induction of pro-inflammatory genes.