Developmentally regulated alternate 3′ end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage

Alternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3′ cleavage site, resulting in the production of mRNA isoforms with different length 3′ UTRs. Although widespread, the role of APA in the biology of cells, tissues, and organisms has been controversial. We identified >500 Drosophila genes that express mRNA isoforms with a long 3′ UTR in proliferating spermatogonia but a short 3′ UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3′ end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3′ UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed >250 genes where the long 3′ UTR versus short 3′ UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3′ end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.