Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast

Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 39 untranslated region in order to regulate mRNA function. Here we present a systematic analysis of 39 end formation factors, which revealed 39 UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 39UTRs. We show that the anti-cancer drug cordycepin, 39 deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 39 end processing and controlled by the availability of 39 end factors, nucleotide levels and chromatin landscape.