Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylation

Abstract

Transcription by RNA polymerase II (RNAPII) is a dynamic process with frequent variations in the elongation rate. However, the physiological relevance of variations in RNAPII elongation kinetics has remained unclear. Here we show in yeast that a RNAPII mutant that reduces the transcription elongation rate causes widespread changes in alternative polyadenylation (APA). We unveil two mechanisms by which APA affects gene expression in the slow mutant: 3 ′ UTR shortening and gene derepression by premature transcription termination of upstream interfering noncoding RNAs. Strikingly, the genes affected by these mechanisms are enriched for functions involved in phosphate uptake and purine synthesis, processes essential for maintenance of the intracellular nucleotide pool. As nucleotide concentration regulates transcription elongation, our findings argue that RNAPII is a sensor of nucleotide availability and that genes important for nucleotide pool maintenance have adopted regulatory mechanisms responsive to reduced rates of transcription elongation.

Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq

“…1 c). Following immunoprecipitation and extraction of TRAP RNA (2 animals pooled per sample), we used an unbiased RNA sequencing approach and the MUGQIC RNA-seq pipeline [ 45 ] to identify and analyze differential gene expression. Using a stringent criterion for significance (False Discovery Rate (FDR) < 0.05) to avoid false positives, we found differentially expressed transcripts representing 200 genes, with 132 significantly upregulated and 68 significantly downregulated (Fig.…”

Transcriptional interference at tandem lncRNA and protein-coding genes: an emerging theme in regulation of cellular nutrient homeostasis

“…A very recent study from the Bachand lab approaches this issue from a different angle, by surveying the effects of a N494D mutation in the Rpb1 subunit of fission yeast Pol2 that slows its rate of elongation ( 46 ). Genome-wide RNA-seq revealed that the slow Pol2 mutation resulted in up-regulation of the tgp1 mRNA in phosphate-replete cells, which was associated with a shift in nc-tgp1 poly(A) site utilization in favor of the short isoform and a concomitant increase in Pho7 ChIP signal over the tgp1 promoter.…”

“…The slow Pol2 mutation also leads to de-repression of pho1 and pho84 , albeit to a lesser extent than tgp1 . Relevance of poly(A) site choice to phosphate nutrient sensing was suggested by the finding that ChIP signals for 3′ processing factor Rna14 and the termination factor Seb1 increased over the short nc-tgp1 poly(A) site 4 hours after acute phosphate starvation ( 46 ).…”

Functional profiling of long intergenic non-coding RNAs in fission yeast

“…Notably, both lincRNAs are located upstream of genes regulated by the Pho7 transcription factor (Schwer et al ., 2017), which functions during phosphate starvation and other stresses (Carter-O’Connell et al ., 2012): SPNCRNA.989 and SPNCRNA.1343 are divergently expressed to atd1 and tgp1, respectively (Supplemental Figure 7). SPNCRNA.1343 partially overlaps with the nc-tgp1 RNA that regulates phosphate homeostasis by repressing the adjacent tgp1 gene via transcriptional interference; deletion of SPNCRNA.1343 has been shown to increase tgp1 expression by inhibiting nc-tgp1 expression (Ard, Tong and Allshire, 2014; Ard and Allshire, 2016; Shah et al ., 2014; Garg et al ., 2018; Yague-Sanz et al ., 2020). Inspection of the region upstream of SPNCRNA.989 suggested a regulatory mechanism similar to tgp1 , with divergent transcripts towards atd1 likely driven by a bi-directional promoter from the nucleosome-depleted region upstream of SPNCRNA.989 (Supplemental Figure 7).…”