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

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. 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.
Wellcome Trust [9340/Z/09/Z, 202115/Z/16/Z]; Royal Society [RG170246]; DBT Ramalingaswami Grant [BT/RHD/35/02/2006]; Biotechnology and Biological Sciences Research Council [BBSRC BB/M022757/1, BBSRC BB/S017984/1, BBSRC BB/M]; Bangabandhu Science and Technology Fellowship Trust. Funding for open access charge: Fellowship Trust.