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

Sandip De,Peter Baumann,Vibha Dwivedi,Wazeer Varsally,Jianming Wang,Kayoko Tanaka,Francesco Falciani,Saverio Brogna,Daniel Hebenstreit,Precious O Owuamalam,Marco Saponaro,Nikolas J Hodges ,Matthew Wright ,Hannah L Dixon ,Marcin W Wojewodzic ,Claus M Azzalin ,David M Edwards ,Nazmul Hossain ,Emily Price ,R Summers ,Anand Kumar Singh

doi:10.1093/nar/gkab1249

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, 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.

Highlights

Upf1 is a conserved protein of eukaryotes that has so far been primarily studied for its key role in nonsense-mediated mRNA decay (NMD)
To explore what role it might play in the nucleus, we examined whether Upf1 is associated with individual genes by chromatin immunoprecipitation (ChIP)
This allowed for genome-wide enrichment profiles which were determined by hybridisation of the immunoprecipitated DNA to genomic tiling chip arrays (Affymetrix, see Materials and Methods)

Summary

Introduction

Upf is a conserved protein of eukaryotes that has so far been primarily studied for its key role in nonsense-mediated mRNA decay (NMD). The precise role of Upf in NMD as well as NMD significance and mechanisms remain unclear [9,10]. Upf belongs to the 1B superfamily (SF1B) of helicases that are involved in a diverse range of cellular activities in all domains of life. These are characterised by conserved sequence motifs and the ability to translocate in a 5 to 3 direction on both RNA and DNA [11,12]. There is evidence that Upf uses ATP hydrolysis to translocate on RNA and to displace RNA-bound proteins [13,14,15,16,17]

Methods

Results

Conclusion