Functional consequences of shifting transcript boundaries in glucose starvation

Abstract

Glucose is a major source of carbon and essential for the survival of many organisms, ranging from yeast to human. A sudden 60-fold reduction of glucose in exponentially growing fission yeast induces transcriptome-wide changes in gene expression. This regulation is multilayered, and the boundaries of transcripts are known to vary, with functional consequences at the protein level. By combining direct RNA sequencing with 5-CAGE and short-read sequencing, we accurately defined the 5- and 3-ends of transcripts that are both poly(A) tailed and 5-capped in glucose starvation, followed by proteome analysis. Our results confirm previously experimentally validated loci with alternative isoforms and reveal several transcriptome-wide patterns. First, we show that sense-antisense gene pairs are more strongly anti-correlated when a time lag is taken into account. Secondly, we show that the glucose starvation response initially elicits a shortening of 3-UTRs and poly(A) tails, followed by a shortening of the 5-UTRs at later time points. These result in domain gains and losses in proteins involved in the stress response. Finally, the relatively poor overlap both between differentially expressed genes (DEGs), differential transcript usage events (DTUs), and differentially detected proteins (DDPs) highlight the need for further study on post-transcriptional regulation mechanisms in glucose starvation.