Proximity of pre-mRNA 3' end processing and transcription termination predicts enhanced gene expression

Abstract

Two key factors required for pre-mRNA 3 end cleavage and polyadenylation, CPSF73 and PCF11, exhibit oncogenic properties: their elevated expression is associated with poor cancer patient prognosis. However, both proteins are also transcription termination factors, and it is unclear which of the processes they promote might contribute to carcinogenesis. Here, we employ a cellular model of colorectal cancer (CRC) progression and find that cells from primary tumor are addicted to high levels of CPSF73 and PCF11, while metastatic cells become less sensitive to their levels. We find no association between alternative polyadenylation (APA) and cell dependence on CPSF73 and PCF11, and no impact of their downregulation on transcription-replication collisions. Instead, we uncover an uncoupling of changes in 3 cleavage and termination during CRC progression: primary tumor-derived cells display a global shift to more proximal termination, yet a tendency for distal APA, compared to normal cells. Metastatic cells display partial reversion toward termination patterns observed in normal cells, and opposite tendency favoring proximal APA. This prompts us to measure the distance between the site of 3 cleavage and transcription termination for active protein-coding genes and find it almost halved in cells from primary tumor compared to normal cells. Interestingly, this distance becomes critically short for oncogenes. Closer proximity of 3 cleavage to termination correlates with higher gene expression, both across genes within a cell line and when distance and expression change in parallel. This uncovers a new relationship of transcription termination with gene expression regulation. SIGNIFICANCE STATEMENTAt the 3 end of genes two processes occur, which are often treated as one: pre-mRNA 3 processing and transcription termination. In fact, they are promoted by a common set of protein factors, with oncogenic properties. Here, we employ a cellular model of colorectal cancer (CRC) progression, to study changes in both pre-mRNA 3 processing and transcription termination. Unexpectedly, we uncover that those changes occur in opposite directions: mRNA tends to be lengthened, while termination is accelerated in cells from primary tumors. We show that the cleavage-termination distance is strongly reduced in these cells compared to normal and metastatic cells, and further determine that cleavage-termination proximity correlates with enhanced gene expression. This uncovers a new layer of gene expression regulation.