The 3’-untranslated region (3’-UTR) marks an important landscape for regulation of mRNA fate. Through the binding of key regulatory elements such as microRNAs and RNA binding proteins, the 3’-UTR can influence the stability, localisation and translatability of mRNA. In eukaryotes, up to 80% of genes regulate 3’-UTR length by encoding multiple locations for cleavage and polyadenylation (CPA) within the nascent transcript, a process known as alternative polyadenylation (APA). A naturally occurring adenosine analogue, cordycepin (3’-deoxyadenosine), is known to cause bulk mRNA shortening through chain termination due to its lack of a reactive hydroxyl group at the 3’ position. Using poly(A)-tail-focused deep sequencing, PAT-seq, we show that, unexpectedly, treatment with cordycepin induces bulk transcript lengthening and increased usage of distal CPA sites in yeast. A similar result was found for yeast strains with defective CPA machinery, implicating CPA complex stoichiometry as a key determinant of CPA site choice. Using yeast nucleosome occupancy data, we also show that genes that are able to undergo alternative polyadenylation have a wider nucleosome depleted region at the 3’-end of the gene suggesting that the higher ordering of the gene itself plays a significant role in CPA site usage.