5-Aza-Cytidine Enhances Terminal Polyadenylation Site Usage for Full-Length Transcripts in Cells

As an inhibitor of DNA methyltransferases (DNMT) and anti-cancer drug, the many effects of 5-aza-cytidine (5-azaC) on gene expression remains unknown. Here we show that 5-azaC treatment of cultured pituitary tumour cells increases the relative usage of the genomic terminal exons (GTE) across the transcriptome. This effect is largely achieved by switching mRNA polyadenylation (poly(A)) from proximal sites to the GTE, which have a more optimal poly(A) signal consensus motif. Consistently, 5-azaC upregulates mRNA anti-terminators Scaf4 and Scaf8 while downregulating the early termination enhancer E2f2. In MOLM-13 leukaemia cells, 5-azaC similarly promotes full-length transcript production, regulating alternative polyadenylation factors in both common and cell-specific ways. Unexpectedly, PCF11, known to promote proximal poly(A) site usage, is upregulated in both cell lines, reminiscent of a homeostatic effort by the tumour/cancer cells to maintain their shortened transcripts during the 5-azaC treatment. This study highlights a previously unknown aspect of 5-azaC’s effect on gene expression as a DNMT inhibitor and anti-cancer drug: to directionally promote the terminal polyadenylation site usage to switch from the shortened to full-length transcripts of cancer cells and consequently the alternative usage of strings of 3’ exons.