Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

BMC Genomics
Nicholas J McGlincyChristopher W J Smith

Abstract

In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD) plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate. In order to achieve a greater understanding of NMD regulated gene expression we used 2D-DiGE proteomics technology to examine the changes in protein expression induced in HeLa cells by UPF1 knockdown. QPCR based validation of the corresponding mRNAs, in response to both UPF1 knockdown and cycloheximide treatment, identified 17 bona fide NMD targets. Most of these were associated with bioinformatically predicted NMD activating features, predominantly upstream open reading frames (uORFs). Strikingly, however, the majority of transcripts up-regulated by UPF1 knockdown were either insensitive to, or even down-regulated by, cycloheximide treatment. Furthermore, the mRNA abundance of several down-regulated proteins failed to change upon UPF1 knockdown, indicating that UPF1's role in regulating mRNA and protein abundance is more complex than previously appreciated. Among the bona fide NMD targets, we identified a highly conserved A...Continue Reading

References

Aug 1, 1993·Molecular and Cellular Biology·C W SmithB Nadal-Ginard
Aug 5, 1997·Proceedings of the National Academy of Sciences of the United States of America·C HeintzenD Staiger
Sep 2, 1997·Proceedings of the National Academy of Sciences of the United States of America·M MorrisonM B Roth
Jul 8, 1999·Current Opinion in Cell Biology·A M Krecic, M S Swanson
Nov 14, 2000·Molecular and Cellular Biology·D R Morris, A P Geballe
Jan 5, 2002·Journal of Neural Transmission. Supplementum·S H KimG Lubec
Mar 19, 2002·Genome Biology·Flavio MignoneGraziano Pesole
Apr 5, 2002·Genome Research·W James Kent
Sep 6, 2002·Genome Research·Mihaela ZavolanTerry Gaasterland
Nov 7, 2002·Molecular Cell·Eric J Wagner, Mariano A Garcia-Blanco
Jan 10, 2003·Nucleic Acids Research·D KarolchikUNKNOWN University of California Santa Cruz
Jan 22, 2003·The Plant Journal : for Cell and Molecular Biology·Dorothee StaigerLuca Eckstein
Mar 11, 2003·Annual Review of Biochemistry·Douglas L Black
May 20, 2003·Immunity·Emmanuel DonnadieuJean-Pierre Kinet
Aug 5, 2003·Nature Reviews. Genetics·Scott Kuersten, Elizabeth B Goodwin
Sep 23, 2003·Nucleic Acids Research·Brian J HaasOwen White
Oct 8, 2003·Nucleic Acids Research·Ales TichopadMichael W Pfaffl
Nov 25, 2003·The EMBO Journal·Natalia GromakChristopher W J Smith
Dec 5, 2003·Nucleic Acids Research·Xiaowei Wang, Brian Seed
Feb 5, 2004·Genome Biology·R Tyler HillmanSteven E Brenner
Apr 3, 2004·Genome Biology·Gabriele Neu-YilikAndreas E Kulozik
Apr 21, 2004·The Journal of Biological Chemistry·Teresa R PachecoMaria Carmo-Fonseca
Apr 23, 2004·Current Opinion in Biotechnology·Gert Van den Bergh, Lutgarde Arckens
May 8, 2004·Science·Gill BejeranoDavid Haussler
Jul 31, 2004·Nature Genetics·Jill A HolbrookAndreas E Kulozik

❮ Previous
Next ❯

Citations

Jun 18, 2011·Journal of Molecular Neuroscience : MN·Mauricio Budini, Emanuele Buratti
Feb 7, 2012·Nature Structural & Molecular Biology·Mo ChenJames L Manley
Jul 19, 2013·Nucleic Acids Research·Serena BonomiGiuseppe Biamonti
May 2, 2012·Molecular and Cellular Biology·Igor Y MorozovMark X Caddick
Aug 21, 2013·PLoS Genetics·Cristina BarbosaLuísa Romão
May 7, 2013·Journal of Proteome Research·Meike J OchsPer-Johan Jakobsson
Oct 27, 2015·Seminars in Cell & Developmental Biology·Stefan Mockenhaupt, Eugene V Makeyev
Mar 11, 2016·Nucleic Acids Research·Satomi TakeiHidehito Kuroyanagi
Nov 15, 2011·Journal of Neurochemistry·Barbara RoigElisabet Vilella
Aug 12, 2014·Biochemical Society Transactions·Fursham M Hamid, Eugene V Makeyev
Aug 12, 2014·Biochemical Society Transactions·Christopher R Sibley
May 18, 2016·Trends in Genetics : TIG·Saverio BrognaMarija Petric
Feb 21, 2016·Molecular & Cellular Proteomics : MCP·Jana SieberAndreas E Kulozik
Aug 2, 2017·Human Genetics·Katannya KapeliGene W Yeo
Oct 17, 2017·Frontiers in Molecular Biosciences·Erik Dassi
Mar 20, 2020·International Journal of Molecular Sciences·Ken-Ichi FujitaSeiji Masuda
Jun 27, 2020·Wiley Interdisciplinary Reviews. RNA·Yu Liu, Song-Lin Shi
Dec 17, 2020·International Journal of Molecular Sciences·Juan F García-Moreno, Luísa Romão
May 1, 2021·Molecular Cancer·Gonçalo NogueiraLuísa Romão

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Methods Mentioned

BETA
electrophoresis
transfection
flow cytometry
PCR
protein assay
FCS

Software Mentioned

PASA
UCSC genome browser
It ( LS Image Analysis
UCSC browser
Primer3 plus
Primerbank
Doc
BLAT
Gene
SPA

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