Isoform-specific regulation of rhythmic gene expression by alternative polyadenylation

Summary Alternative polyadenylation (APA) generates transcript isoforms with different 3’ ends. Differences in polyadenylation sites usage, which have been associated with diseases like cancer, regulate mRNA stability, subcellular localization, and translation. By characterizing APA across the 24-hour day in mouse liver, here we show that rhythmic gene expression occurs largely in an APA isoform-specific manner, and that hundreds of arrhythmically expressed genes surprisingly exhibit a rhythmic APA isoform. The underlying mechanisms comprise isoform-specific post-transcriptional regulation, transcription factor driven expression of specific isoform, co-transcriptional recruitment of RNA binding proteins that regulate mRNA cleavage and polyadenylation, and, to a lesser extent, cell subtype-specific expression. Remarkably, rhythmic expression of specific APA isoforms generates 24-hour rhythms in 3’ UTR length, with shorter UTRs in anticipation of the mouse active phase. Taken together, our findings demonstrate that cycling transcriptomes are regulated by APA, and suggest that APA strongly impacts the rhythmic regulation of biological functions.