Fig. 3

The speed of RNA polymerase II influences APA. (A) Model for how polymerase speed can affect alternative polyadenylation. During the time between transcription of proximal and distal polyadenylation sites, the proximal site can be recognized and used but the proximal site cannot. Increasing this time of proximal site exclusivity by decreasing the speed of RNA polymerase may increase the likelihood of the proximal site being used. (B) Read coverage and ψ values for the gene PAFAH1B1 in cells expressing wildtype (orange) and slow (purple) RNA polymerase II. (C) Comparison of ψ values in cells expressing wildtype and slow RNA polymerase II for genes whose ψ value was significantly different between these samples (FDR < 0.05). (D) Distance between alternative polyadenylation sites for genes that displayed increased upstream APA (orange), increased downstream APA (purple), or whose APA did not change (gray) in cells expressing a slow RNA polymerase II compared to cells expressing wildtype RNA polymerase II. (E-F) As in D, comparison of ψ values in cells expressing wildtype and slow RNA polymerase II for tandem UTR (E) and ALE (F) genes whose ψ value was significantly different between these samples (FDR < 0.05)