title: Compensatory signals associated with the activation of human GC 5' splice sites.
abstract: GC 5' splice sites (5'ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5'ss activated by a mutation in BTK intron 3. This GC 5'ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5'ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5'ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5'ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5'ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5'ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5'ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.
authors: University of Southampton School of Medicine, Division of Human Genetics, Southampton SO16 6YD, UK.
authors: Jana
authors: J
authors: Kralovicova
authors: Gyulin
authors: G
authors: Hwang
authors: A Charlotta
authors: AC
authors: Asplund
authors: Alexander
authors: A
authors: Churbanov
authors: C I Edvard
authors: CI
authors: Smith
authors: Igor
authors: I
authors: Vorechovsky
references: Cell. 1990 Jul 13;62(1):35-42
references: 2364434
references: Nucleic Acids Res. 2011 Mar;39(4):1538-53
references: 20926394
references: Cell. 2009 Feb 20;136(4):688-700
references: 19239889
references: Hum Genet. 2010 Oct;128(4):383-400
references: 20628762
references: Mol Cell Biol. 2004 Feb;24(3):1387-400
references: 14729981
references: Nature. 1996 Jun 6;381(6582):535-8
references: 8632829
references: Science. 1994 Sep 23;265(5180):1866-9
references: 8091213
references: Mol Cell. 2004 Apr 23;14(2):221-31
references: 15099521
references: EMBO J. 1993 Sep;12(9):3607-17
references: 8253084
references: Exp Cell Res. 2008 Oct 15;314(17):3130-41
references: 18775696
references: BMC Mol Biol. 2010 Apr 30;11:32
references: 20433698
references: Hum Mutat. 2008 Sep;29(9):E173-93
references: 18546366
references: Am J Hum Genet. 1999 Aug;65(2):336-44
references: 10417276
references: Nat Genet. 2003 Aug;34(4):460-3
references: 12833158
references: Hum Mol Genet. 2004 Dec 15;13(24):3189-202
references: 15496424
references: Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13427-32
references: 16938881
references: J Mol Biol. 2000 Dec 1;304(3):335-54
references: 11090278
references: PLoS Comput Biol. 2009 Mar;5(3):e1000300
references: 19266014
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W187-90
references: 15215377
references: BMC Bioinformatics. 2010 Mar 15;11:129
references: 20230624
references: J Mol Cell Cardiol. 2005 Apr;38(4):555-60
references: 15808832
references: Eur J Hum Genet. 2009 Jun;17(6):759-65
references: 19142208
references: Nucleic Acids Res. 2001 Jan 1;29(1):255-9
references: 11125105
references: Hum Mutat. 2007 Jun;28(6):599-612
references: 17311297
references: Mol Cell Biol. 1997 Apr;17(4):2143-50
references: 9121463
references: FEBS Lett. 2002 Sep 11;527(1-3):274-8
references: 12220673
references: EMBO J. 1995 Jul 3;14(13):3236-46
references: 7621835
references: J Comput Biol. 2004;11(2-3):377-94
references: 15285897
references: Genome Biol. 2007;8(2):R29
references: 17326827
references: Trends Biochem Sci. 2010 Mar;35(3):169-78
references: 19959365
references: J Bioinform Comput Biol. 2004 Jun;2(2):309-31
references: 15297984
references: Mol Cell Biol. 1997 Aug;17(8):4562-71
references: 9234714
references: Cell. 1986 Sep 12;46(6):827-35
references: 3757028
references: Cell. 2004 Dec 17;119(6):831-45
references: 15607979
references: Hum Mol Genet. 2003 Jun 1;12(11):1337-48
references: 12761049
references: BMC Genomics. 2011 Jan 19;12:45
references: 21247441
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D86-91
references: 20929868
references: Nucleic Acids Res. 2000 Nov 1;28(21):4364-75
references: 11058137
references: Nucleic Acids Res. 2006;34(16):4630-41
references: 16963498
references: Hum Mol Genet. 2004 Mar 1;13(5):509-24
references: 14709600
references: RNA. 2001 Mar;7(3):342-50
references: 11333015
references: Nucleic Acids Res. 2006;34(14):3955-67
references: 16914448
references: Mol Cell Biol. 1992 Mar;12(3):962-70
references: 1532050
references: Blood. 2002 Dec 15;100(13):4478-84
references: 12393540
references: Nucleic Acids Res. 2001 Jun 15;29(12):2581-93
references: 11410667
references: Nucleic Acids Res. 2005 Jul 14;33(12):3897-906
references: 16027113
references: Nat Struct Mol Biol. 2011 Apr;18(4):443-50
references: 21399644
references: Nucleic Acids Res. 2003 Jul 1;31(13):3568-71
references: 12824367
references: Am J Hum Genet. 1995 May;56(5):1052-9
references: 7726158
references: Mol Cell. 2009 Jul 10;35(1):1-10
references: 19595711
references: Nat Rev Genet. 2004 Oct;5(10):773-82
references: 15510168
references: Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9618-23
references: 10931943
references: Nat Struct Biol. 2001 Apr;8(4):339-43
references: 11276255
references: Nucleic Acids Res. 2007;35(13):4250-63
references: 17576681
references: Cell. 2009 Feb 20;136(4):701-18
references: 19239890
references: J Invest Dermatol. 2005 Aug;125(2):244-6
references: 16098033
references: Hum Genet. 1999 Feb;104(2):135-42
references: 10190324
references: Nucleic Acids Res. 2005 Sep 01;33(15):4882-98
references: 16141195
references: J Invest Dermatol. 2004 May;122(5):1321-4
references: 15140237
references: Cell. 1987 Jul 17;50(2):237-46
references: 3647844
references: Nucleic Acids Res. 1991 Jul 25;19(14):3795-8
references: 1713664
references: Hum Genet. 2010 Feb;127(2):135-54
references: 19823873
references: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903
references: 11296253
references: Mol Cell. 2004 Jan 16;13(1):91-100
references: 14731397
references: Nucleic Acids Res. 2004 Apr 15;32(7):2113-22
references: 15087490
references: Cell. 1990 Sep 7;62(5):889-99
references: 2168293
references: Trends Genet. 1994 Jun;10(6):188-93
references: 8073532
references: Nat Genet. 2002 Apr;30(4):426-9
references: 11889466
references: Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13266-71
references: 16141323
references: Genome Res. 2005 Jan;15(1):111-9
references: 15590946
references: Am J Hum Genet. 1993 Feb;52(2):414-24
references: 8430702
references: Am J Hum Genet. 2000 Oct;67(4):788-92
references: 10986039
references: Science. 2002 Aug 9;297(5583):1007-13
references: 12114529
references: PLoS Genet. 2008 Sep 26;4(9):e1000204
references: 18818740
references: Mol Cell. 2007 Aug 3;27(3):420-34
references: 17679092
references: Genes Dev. 2004 Jun 1;18(11):1241-50
references: 15145827
references: Nature. 1999 May 6;399(6731):75-80
references: 10331393
references: Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7582-7
references: 8755518
references: Nature. 2001 Feb 15;409(6822):860-921
references: 11237011
references: Genes Dev. 1996 Aug 15;10(16):2089-101
references: 8769651
references: Science. 2003 Dec 5;302(5651):1727-36
references: 14605208
references: PLoS Med. 2008 Apr 22;5(4):e88
references: 18433292
references: Nucleic Acids Res. 2007;35(13):4359-68
references: 17576688
references: Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5797-802
references: 18391195
references: Hum Mol Genet. 2000 Jan 22;9(2):237-47
references: 10607834
references: Mol Cell Biol. 2010 Apr;30(8):1878-86
references: 20123971
references: RNA. 2005 May;11(5):683-98
references: 15840817
references: Bioinformatics. 2010 Jul 15;26(14):1772-6
references: 20547637
references: Oncogene. 2005 Jun 30;24(28):4604-8
references: 15856016
references: Science. 2003 May 23;300(5623):1288-91
references: 12764196
references: RNA. 2006 Dec;12(12):2047-56
references: 17053087
references: Nature. 1993 Jan 21;361(6409):226-33
references: 8380905
references: Hum Mol Genet. 1992 Apr;1(1):11-7
references: 1284466
references: Cell. 1998 Apr 3;93(1):139-48
references: 9546399
references: PLoS Genet. 2007 Nov;3(11):e204
references: 18020710
references: Nucleic Acids Res. 2007;35(19):6399-413
references: 17881373
references: Hum Mutat. 2011 Apr;32(4):436-44
references: 21309043
references: Hum Genet. 2001 Nov;109(5):559-63
references: 11735032
references: BMC Bioinformatics. 2010 Jan 12;11:22
references: 20067640
references: Biol Direct. 2008 Jul 09;3:30
references: 18613975
references: Mol Cell Biol. 1995 Sep;15(9):4898-907
references: 7651409
references: Hum Mol Genet. 2006 Aug 15;15(16):2490-508
references: 16825284
references: Mol Cell Biol. 2005 Aug;25(16):6912-20
references: 16055705