title: Regulation of alternative splicing within the supraspliceosome.
abstract: Alternative splicing is a fundamental feature in regulating the eukaryotic transcriptome, as ~95% of multi-exon human Pol II transcripts are subject to this process. Regulated splicing operates through the combinatorial interplay of positive and negative regulatory signals present in the pre-mRNA, which are recognized by trans-acting factors. All these RNA and protein components are assembled in a gigantic, 21 MDa, ribonucleoprotein splicing machine - the supraspliceosome. Because most alternatively spliced mRNA isoforms vary between different cell and tissue types, the ability to perform alternative splicing is expected to be an integral part of the supraspliceosome, which constitutes the splicing machine in vivo. Here we show that both the constitutively and alternatively spliced mRNAs of the endogenous human pol II transcripts: hnRNP A/B, survival of motor neuron (SMN) and ADAR2 are predominantly found in supraspliceosomes. This finding is consistent with our observations that the splicing regulators hnRNP G as well as all phosphorylated SR proteins are predominantly associated with supraspliceosomes. We further show that changes in alternative splicing of hnRNP A/B, affected by up regulation of SRSF5 (SRp40) or by treatment with C6-ceramide, occur within supraspliceosomes. These observations support the proposed role of the supraspliceosome in splicing regulation and alternative splicing.
authors.affiliation: Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Naama
authors.initials: N
authors.lastname: Sebbag-Sznajder
authors.forename: Oleg
authors.initials: O
authors.lastname: Raitskin
authors.forename: Minna
authors.initials: M
authors.lastname: Angenitzki
authors.forename: Taka-Aki
authors.initials: TA
authors.lastname: Sato
authors.forename: Joseph
authors.initials: J
authors.lastname: Sperling
authors.forename: Ruth
authors.initials: R
authors.lastname: Sperling
mesh_terms: D017398:Alternative Splicing; D002518:Ceramides / Q000378:metabolism; D005091:Exons; D006367:HeLa Cells; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008854:Microscopy, Electron; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D010766:Phosphorylation; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry; D000068103:Serine-Arginine Splicing Factors; D017381:Spliceosomes / Q000378:metabolism* / Q000648:ultrastructure; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D002518:Ceramides; D034441:Heterogeneous-Nuclear Ribonucleoproteins; D009687:Nuclear Proteins; D012322:RNA Precursors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins; D015534:Trans-Activators; C101954:N-caproylsphingosine; D000068103:Serine-Arginine Splicing Factors
references.citation: Curr Opin Cell Biol. 2008 Jun;20(3):260-5
references.pmid: 18436438
references.citation: FEBS Lett. 1991 Sep 23;290(1-2):159-61
references.pmid: 1717314
references.citation: Mol Cell. 2004 Sep 10;15(5):833-9
references.pmid: 15350226
references.citation: Biochem Soc Trans. 2008 Jun;36(Pt 3):483-90
references.pmid: 18481986
references.citation: Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6571-6
references.pmid: 11381114
references.citation: Nat Rev Genet. 2007 Oct;8(10):749-61
references.pmid: 17726481
references.citation: Exp Cell Res. 2006 Oct 15;312(17):3379-88
references.pmid: 16934801
references.citation: J Biol Chem. 2002 Apr 12;277(15):12587-95
references.pmid: 11801602
references.citation: Adv Exp Med Biol. 2007;623:107-22
references.pmid: 18380343
references.citation: J Mol Biol. 2006 Mar 3;356(4):955-66
references.pmid: 16386271
references.citation: J Biol Chem. 1997 Jan 17;272(3):1452-5
references.pmid: 8999813
references.citation: Nat Genet. 2008 Dec;40(12):1413-5
references.pmid: 18978789
references.citation: Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9155-60
references.pmid: 9689050
references.citation: Cell. 1991 Oct 4;67(1):11-9
references.pmid: 1717158
references.citation: Adv Exp Med Biol. 2007;623:175-89
references.pmid: 18380347
references.citation: Nat Genet. 2002 Jan;30(1):29-30
references.pmid: 11743582
references.citation: Eur J Immunol. 1999 Mar;29(3):823-37
references.pmid: 10092085
references.citation: Biochem J. 2009 Jan 1;417(1):15-27
references.pmid: 19061484
references.citation: Mol Cell Biol. 1985 Mar;5(3):569-75
references.pmid: 3990684
references.citation: Structure. 2008 Nov 12;16(11):1605-15
references.pmid: 19000813
references.citation: Genome Biol. 2009;10(10):242
references.pmid: 19857271
references.citation: Mol Cell. 2009 Oct 23;36(2):178-91
references.pmid: 19854129
references.citation: Nat Biotechnol. 2004 May;22(5):535-46
references.pmid: 15122293
references.citation: J Immunol. 2000 May 15;164(10):5287-95
references.pmid: 10799890
references.citation: Nucleic Acids Res. 2006 Jul 19;34(12):3421-33
references.pmid: 16855285
references.citation: Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8830-5
references.pmid: 8799112
references.citation: Nucleic Acids Res. 1994 Aug 11;22(15):3084-91
references.pmid: 7915031
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):5002-7
references.pmid: 15753297
references.citation: J Mol Biol. 2007 Apr 27;368(2):319-27
references.pmid: 17359996
references.citation: J Mol Biol. 1997 Apr 4;267(3):570-83
references.pmid: 9126839
references.citation: RNA. 1997 May;3(5):453-63
references.pmid: 9149227
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5277-82
references.pmid: 11959978
references.citation: EMBO J. 1997 Apr 1;16(7):1772-84
references.pmid: 9130721
references.citation: Nat Genet. 2002 Jan;30(1):13-9
references.pmid: 11753382
references.citation: J Cell Sci. 2006 Jul 1;119(Pt 13):2635-41
references.pmid: 16787944
references.citation: FEBS Lett. 2008 Jun 18;582(14):1971-6
references.pmid: 18435923
references.citation: Mol Cell Biol. 1997 May;17(5):2413-24
references.pmid: 9111310
references.citation: J Biol Chem. 2009 May 22;284(21):14303-15
references.pmid: 19282290
references.citation: J Biol Chem. 2001 Nov 30;276(48):44848-55
references.pmid: 11502750
references.citation: RNA. 2008 May;14(5):802-13
references.pmid: 18369186
references.citation: J Struct Biol. 2002 Apr-May;138(1-2):74-84
references.pmid: 12160703
references.citation: Mol Cell Biol. 2011 Feb;31(4):793-802
references.pmid: 21135118
references.citation: J Biol Chem. 2008 Aug 29;283(35):23619-26
references.pmid: 18586677
references.citation: EMBO J. 1995 Sep 1;14(17):4336-49
references.pmid: 7556075
references.citation: Cell. 1984 Apr;36(4):993-1005
references.pmid: 6323033
references.citation: Nucleic Acids Res. 2007;35(13):4359-68
references.pmid: 17576688
references.citation: Jpn J Cancer Res. 2000 Aug;91(8):802-10
references.pmid: 10965021
references.citation: J Struct Biol. 1999 Sep;127(2):113-9
references.pmid: 10527900
references.citation: Proc Natl Acad Sci U S A. 1999 May 25;96(11):6307-11
references.pmid: 10339583
references.citation: J Struct Biol. 2002 Oct-Dec;140(1-3):123-30
references.pmid: 12490160
references.citation: J Mol Biol. 1998 Oct 23;283(2):383-94
references.pmid: 9769212