The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci.

Anand K Singh,Marija Petric,Vibha Dwivedi,Luisa Orsini,Preethi Ramanathan,Stephen Kissane,Sandip De,Jie Zhang,Subhendu Roy Choudhury,Saverio Brogna,Daniel Hebenstreit

doi:10.7554/elife.41444

Abstract

UPF1 is an RNA helicase that is required for 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 by a mechanism that requires its RNA helicase activity. UPF1 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 glands and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNAs, and cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and their export from the nucleus.

Highlights

UPF1 (UP-Frameshift-1) is a universally conserved eukaryotic protein that was first identified in a Saccharomyces cerevisiae genetic screen for mutations that enhance up-frameshift tRNA suppression (Culbertson et al, 1980; Leeds et al, 1992), and gained other names – including NAM7 (S. cerevisiae) and SMG2 (Caenorhabditis elegans) – from other genetic screens (Altamura et al, 1992; Hodgkin et al, 1989; Pulak and Anderson, 1993 )
Drosophila anti-UPF1 antibodies To explore the functions of UPF1, we generated three monoclonal anti-peptide antibodies that target regions of Drosophila UPF1 outside the RNA helicase domain: one epitope in the N-terminal flanking regions, and two near the C-terminus (Ab 7D17 vs. Pep11; and Ab 7B12 vs. Pep12)
UPF1 RNAi reduced the amount of UPF1 in S2 cells (Figure 1B) without affecting the levels of several other proteins we tested as controls (Figure 1B)

Summary

Introduction

UPF1 (UP-Frameshift-1) is a universally conserved eukaryotic protein that was first identified in a Saccharomyces cerevisiae genetic screen for mutations that enhance up-frameshift tRNA suppression (Culbertson et al, 1980; Leeds et al, 1992), and gained other names – including NAM7 (S. cerevisiae) and SMG2 (Caenorhabditis elegans) – from other genetic screens (Altamura et al, 1992; Hodgkin et al, 1989; Pulak and Anderson, 1993 ). Recent reports on mammalian translation systems have suggested, in contrast to earlier reports on other organisms (Czaplinski et al, 1998; Ivanov et al, 2008; Kashima et al, 2006; Keeling et al, 2004; Singh et al, 2008; Wang et al, 2001), that UPF1 does not bind to either of these They suggested, instead, that UPF3B may contact release factors, slow the termination of translation and facilitate post-termination release of ribosomes – and so fulfil the termination monitoring role that has been assigned to UPF1 (Gao and Wilkinson, 2017; Muhlemann and Karousis, 2017; Neu-Yilik et al, 2017)

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Discussion

Conclusion