title: Selection preserves Ubiquitin Specific Protease 4 alternative exon skipping in therian mammals.
abstract: Ubiquitin specific protease 4 (USP4) is a highly networked deubiquitinating enzyme with reported roles in cancer, innate immunity and RNA splicing. In mammals it has two dominant isoforms arising from inclusion or skipping of exon 7 (E7). We evaluated two plausible mechanisms for the generation of these isoforms: (A) E7 skipping due to a long upstream intron and (B) E7 skipping due to inefficient 5' splice sites (5'SS) and/or branchpoint sites (BPS). We then assessed whether E7 alternative splicing is maintained by selective pressure or arose from genetic drift. Both transcript variants were generated from a USP4-E7 minigene construct with short flanking introns, an observation consistent with the second mechanism whereby differential splice signal strengths are the basis of E7 skipping. Optimization of the downstream 5'SS eliminated E7 skipping. Experimental validation of the correlation between 5'SS identity and exon skipping in vertebrates pinpointed the +6 site as the key splicing determinant. Therian mammals invariably display a 5'SS configuration favouring alternative splicing and the resulting isoforms have distinct subcellular localizations. We conclude that alternative splicing of mammalian USP4 is under selective maintenance and that long and short USP4 isoforms may target substrates in various cellular compartments.
authors.affiliation: Ottawa Hospital Research Institute, Ottawa, K1H 8L6, Canada.|Ottawa Institute of Systems Biology, Ottawa, K1H 8M5, Canada.|Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5, Canada.
authors.forename: Caitlyn
authors.initials: C
authors.lastname: Vlasschaert
authors.affiliation: Department of Biology, University of Ottawa, Ottawa, K1N 6N5, Canada.|Ottawa Institute of Systems Biology, Ottawa, K1H 8M5, Canada.
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
authors.affiliation: Ottawa Hospital Research Institute, Ottawa, K1H 8L6, Canada.|Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5, Canada.
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Gray
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D005091:Exons; D007438:Introns; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008322:Mammals / Q000235:genetics* / Q000378:metabolism; D043222:Ubiquitin Thiolesterase / Q000235:genetics* / Q000378:metabolism
chemical_list: D007527:Isoenzymes; D043222:Ubiquitin Thiolesterase
references.citation: PLoS One. 2012;7(2):e31003
references.pmid: 22347420
references.citation: J Cell Mol Med. 2009 Aug;13(8B):1886-95
references.pmid: 20141612
references.citation: RNA. 2008 Nov;14(11):2261-73
references.pmid: 18796579
references.citation: Bioinformatics. 2005 Oct 1;21(19):3701-3
references.pmid: 16091412
references.citation: Hum Mutat. 2013 Apr;34(4):572-7
references.pmid: 23348830
references.citation: RNA. 2007 May;13(5):661-70
references.pmid: 17369312
references.citation: EMBO J. 2011 Jun 1;30(11):2177-89
references.pmid: 21522127
references.citation: Nucleic Acids Res. 2007;35(1):125-31
references.pmid: 17158149
references.citation: Cell. 2009 Jul 23;138(2):389-403
references.pmid: 19615732
references.citation: Nat Cell Biol. 2012 Jul;14(7):656-7
references.pmid: 22743709
references.citation: Nat Rev Mol Cell Biol. 2005 May;6(5):386-98
references.pmid: 15956978
references.citation: Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15081-5
references.pmid: 8986767
references.citation: EMBO J. 2011 May 18;30(10):1965-76
references.pmid: 21468032
references.citation: J Biol Chem. 2012 Mar 30;287(14):11002-10
references.pmid: 22262844
references.citation: Nucleic Acids Res. 2008 Apr;36(7):2257-67
references.pmid: 18285363
references.citation: Nat Cell Biol. 2012 Jul;14(7):717-26
references.pmid: 22706160
references.citation: J Virol. 2013 Apr;87(8):4507-15
references.pmid: 23388719
references.citation: Genes Dev. 2010 Jul 1;24(13):1434-47
references.pmid: 20595234
references.citation: Int J Cancer. 2001 Sep 1;93(5):623-8
references.pmid: 11477570
references.citation: PLoS Comput Biol. 2008;4(8):e1000147
references.pmid: 18688268
references.citation: EMBO J. 2002 Dec 16;21(24):6882-92
references.pmid: 12486009
references.citation: RNA. 2005 Dec;11(12):1777-87
references.pmid: 16251388
references.citation: PLoS Genet. 2013;9(10):e1003856
references.pmid: 24146627
references.citation: PLoS Comput Biol. 2006 Jan;2(1):e4
references.pmid: 16424921
references.citation: BMC Genet. 2009;10:67
references.pmid: 19840385
references.citation: Nature. 2002 Sep 5;419(6902):86-90
references.pmid: 12214237
references.citation: Nat Rev Mol Cell Biol. 2003 Dec;4(12):960-70
references.pmid: 14685174
references.citation: PLoS Genet. 2007 Nov;3(11):e203
references.pmid: 18020709
references.citation: Mol Cell Biol. 1998 Oct;18(10):5930-41
references.pmid: 9742110
references.citation: Biochem J. 2012 Feb 1;441(3):979-86
references.pmid: 22029577
references.citation: Oncogene. 1998 Jan 15;16(2):153-65
references.pmid: 9464533
references.citation: Nucleic Acids Res. 2004;32(5):1792-7
references.pmid: 15034147
references.citation: Front Genet. 2014 Jul 23;5:245
references.pmid: 25101120
references.citation: Cell Death Differ. 2011 Oct;18(10):1547-60
references.pmid: 21331078
references.citation: J Mol Biol. 2012 Jan 27;415(4):727-40
references.pmid: 22154808
references.citation: Nucleic Acids Res. 2009 Aug;37(14):4873-86
references.pmid: 19546110
references.citation: PLoS Genet. 2010;6(12):e1001236
references.pmid: 21151575
references.citation: Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16176-81
references.pmid: 16260721
references.citation: Nat Rev Genet. 2010 May;11(5):345-55
references.pmid: 20376054
references.citation: Oncogene. 1993 Aug;8(8):2307-10
references.pmid: 8336951
references.citation: Nat Commun. 2014;5:5399
references.pmid: 25404403
references.citation: J Biol Chem. 2014 Mar 28;289(13):8916-30
references.pmid: 24526689
references.citation: Mol Cell Biol. 2011 Mar;31(5):935-54
references.pmid: 21189287
references.citation: Oncogene. 1994 Jun;9(6):1729-31
references.pmid: 8183569
references.citation: BMC Genomics. 2006;7:311
references.pmid: 17156453
references.citation: Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):9926-31
references.pmid: 26216990
references.citation: Mol Biol Evol. 2013 Jul;30(7):1720-8
references.pmid: 23564938
references.citation: J Biol Chem. 2005 Jan 7;280(1):745-52
references.pmid: 15494318
references.citation: Proc Natl Acad Sci U S A. 1999 May 25;96(11):6307-11
references.pmid: 10339583
references.citation: Am J Hum Genet. 1999 May;64(5):1340-56
references.pmid: 10205265
references.citation: BMC Evol Biol. 2015;15:230
references.pmid: 26503449