Genome-wide chromosomal association of Upf1 is linked to Pol II transcription inSchizosaccharomyces pombe

Abstract

Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive and it correlates with Pol II transcription and mRNA expression levels. While changes in Pol II occupancy were detected at only some genes in a Upf1-deficient (upf1Δ strain, there is an increased Ser2 Pol II signal at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil and display Pol II abnormalities suggestive of Pol II hyperphosphorylation. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript Upf1 might influence Pol II phosphorylation and transcription.

Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting

“…from 2k bp upstream of the TSS to the TES) for each gene, so a single value is obtained per gene per HM. Metagene plots were produced by averaging the coverage values for each position through/around the gene across all specified genes, similarly to the metagene analysis described in [53].…”