The 3' end processing factor PCF11 regulates gene expression based on gene size and intronic polyadenylation

Genes with different sizes have distinct expression patterns and functions. Here we show that the 3' end processing PCF11 modulates gene expression according to gene size. Gene density and polyA site strength, but not orientation between neighboring genes, impact short gene regulation by PCF11. In contrast, long gene modulation involves intronic polyadenylation (IPA), which is widespread in large introns. Downregulation of PCF11, which takes place in cell differentiation, contributes to short and long gene expressions with functions related to cell proliferation, cell morphology, adhesion, and migration. Mild, exogenous upregulation of PCF11 perturbs the gene expression program in cell differentiation. Further, PCF11 is auto-regulated through a highly conserved IPA site, the removal of which leads to PCF11 overexpression and global activation of proximal PASs sites. Together, our data indicate that PCF11 level impacts gene expression based on size and its autoregulation maintains homeostasis of PAS usage in the cell. In total 2 RNA-seq libraries from 3T3-L1 cells for gene expression analysis; In total 4 3'READS libraries for the analysis of APA during C2C12 cell differentiation; In total 4 3'READS libraries for analysis of APA isoform stability under siPcf11 using 4sU metabolic labeling in C2C12 cells; In total 4 3'READS libraries for analysis of APA under siPcf11 using total RNA from C2C12 cells; In total 4 3'READS libraries for analysis of APA under Pcf11-IPAKO using total RNA from 4T1 cells; In total 4 3'READS libraries for analysis of APA under siPcf11 using total RNA from NIH3T3 cells;