Coordination of RNA Polymerase II Pausing and 3’ end processing factor recruitment with alternative polyadenylation

Sites of RNA polymerase II (pol II) pausing and processing factor recruitment change depending on which alternative poly(A) site is utilized at the IgM locus. In contrast, the extent of pol II CTD Ser2 phosphorylation did not closely correlate with poly(A) site selection. We conclude that changes in properties of the transcription elongation complex closely correlate with utilization of different poly(A) sites. Overall design: The function of co-transcriptional events in the selection of alternative poly(A) sites was investigated. RNA polymerase II pausing, Ser2 CTD phosphorylation and processing factor CstF recruitment at WT and mutant mouse IgM transgenes that use alternative poly(A) sites to produce mRNAs encoding the secreted and membrane-bound forms of the Ig heavy chain. The mutants used were pA21 a 21 bp deletion of the uS polyA site consensus and 5''SP which mutates 3 bases in the 5'' splice site of the Cu4-M1 intron to strengthen it.