The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from transcription sites

Abstract

UPF1 is an RNA helicase that is required for efficient nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3'UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm and that it has multiple functions in the nucleus. It is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary gland and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNA transcripts, and cells depleted of UPF1 show defects in several processes essential to correct gene expressionincluding Pol II pausing, the release of mRNAs from transcription sites, and mRNA export from the nucleus. *Corresponding author: s.brogna@bham.ac.uk Running title: UPF1 also acts on nuclear RNAs

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

“…The data we have presented are in agreement with the recent report that Upf1 is associated genome-wide with nascent transcripts in Drosophila (Singh et al, 2019). Taken together, the findings from these two highly divergent organisms predict that the roles of Upf1 in transcription-coupled processes are conserved in eukaryotes.…”

“…To remove proteins from the DNA, 5 µl Proteinase K (20 mg/ml) was added and samples were incubated at 50°C for two hours. DNA was then extracted using the Monarch PCR purification kit, as previously described (Singh et al, 2019).…”

An intron proximal to a PTC enhances NMD inSaccharomyces cerevisiae

“…In the absence of a coherent mechanism and many conflicting observations it has been proposed that eukaryotes perhaps do not possess any such surveillance mechanism (Brogna et al, 2016). Moreover, recent evidence indicates that UPF1 plays broad roles in fundamental processes of gene expression, in the nucleus as well as in the cytoplasm, and these more than its requirement in NMD might explain UPF1 conservation in eukaryotes (Singh et al, 2019).…”