title: Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2.
abstract: The precise regulation of many alternative splicing (AS) events by specific splicing factors is essential to determine tissue types and developmental stages. However, the molecular basis of tissue-specific AS regulation and the properties of splicing regulatory networks (SRNs) are poorly understood. Here we comprehensively predict the targets of the brain- and muscle-specific splicing factor Fox-1 (A2BP1) and its paralog Fox-2 (RBM9) and systematically define the corresponding SRNs genome-wide. Fox-1/2 are conserved from worm to human, and specifically recognize the RNA element UGCAUG. We integrate Fox-1/2-binding specificity with phylogenetic conservation, splicing microarray data, and additional computational and experimental characterization. We predict thousands of Fox-1/2 targets with conserved binding sites, at a false discovery rate (FDR) of approximately 24%, including many validated experimentally, suggesting a surprisingly extensive SRN. The preferred position of the binding sites differs according to AS pattern, and determines either activation or repression of exon recognition by Fox-1/2. Many predicted targets are important for neuromuscular functions, and have been implicated in several genetic diseases. We also identified instances of binding site creation or loss in different vertebrate lineages and human populations, which likely reflect fine-tuning of gene expression regulation during evolution.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
authors.forename: Chaolin
authors.initials: C
authors.lastname: Zhang
authors.forename: Zuo
authors.initials: Z
authors.lastname: Zhang
authors.forename: John
authors.initials: J
authors.lastname: Castle
authors.forename: Shuying
authors.initials: S
authors.lastname: Sun
authors.forename: Jason
authors.initials: J
authors.lastname: Johnson
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D001665:Binding Sites; D005786:Gene Expression Regulation / Q000502:physiology*; D006367:HeLa Cells; D006801:Humans; D000072260:RNA Splicing Factors; D016601:RNA-Binding Proteins / Q000378:metabolism / Q000502:physiology*; D012097:Repressor Proteins / Q000378:metabolism / Q000502:physiology*
chemical_list: C455479:RBFOX1 protein, human; C454924:RBFOX2 protein, human; D000072260:RNA Splicing Factors; D016601:RNA-Binding Proteins; D012097:Repressor Proteins
references.citation: Genome Res. 2007 Dec;17(12):1797-808
references.pmid: 17984227
references.citation: Mol Cell Biol. 2005 Nov;25(22):10005-16
references.pmid: 16260614
references.citation: Nature. 2002 Apr 4;416(6880):499-506
references.pmid: 11932736
references.citation: Nucleic Acids Res. 2007;35(14):4845-57
references.pmid: 17626050
references.citation: Genome Biol. 2003;4(5):P3
references.pmid: 12734009
references.citation: Mol Cell Biol. 2006 Feb;26(4):1209-22
references.pmid: 16449636
references.citation: RNA. 2007 Apr;13(4):563-72
references.pmid: 17307815
references.citation: Nat Protoc. 2006;1(1):302-7
references.pmid: 17406249
references.citation: Methods. 2005 Dec;37(4):376-86
references.pmid: 16314267
references.citation: Annu Rev Genet. 1998;32:279-305
references.pmid: 9928482
references.citation: Nat Genet. 2007 Mar;39(3):319-28
references.pmid: 17322880
references.citation: EMBO J. 2006 Jan 11;25(1):163-73
references.pmid: 16362037
references.citation: Nucleic Acids Res. 2007;35(16):5303-11
references.pmid: 17686786
references.citation: J Biol Chem. 2006 May 5;281(18):12468-74
references.pmid: 16537540
references.citation: Nat Rev Neurosci. 2007 Nov;8(11):819-31
references.pmid: 17895907
references.citation: Genome Res. 2007 Jul;17(7):1023-33
references.pmid: 17525134
references.citation: Genes Dev. 2007 Jan 1;21(1):71-84
references.pmid: 17210790
references.citation: Cell. 2006 Jul 14;126(1):37-47
references.pmid: 16839875
references.citation: Genes Dev. 1994 Jul 1;8(13):1561-74
references.pmid: 7958840
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2850-5
references.pmid: 15708978
references.citation: Nucleic Acids Res. 2005 Feb 03;33(2):714-24
references.pmid: 15691898
references.citation: Annu Rev Biochem. 2003;72:291-336
references.pmid: 12626338
references.citation: Nature. 2006 Nov 30;444(7119):580-6
references.pmid: 17065982
references.citation: Circulation. 2003 May 20;107(19):2467-74
references.pmid: 12742993
references.citation: RNA. 2008 Feb;14(2):197-203
references.pmid: 18083834
references.citation: Nucleic Acids Res. 2001 Jun 1;29(11):2338-48
references.pmid: 11376152
references.citation: Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):15028-33
references.pmid: 17848517
references.citation: J Hum Genet. 2004;49(6):308-311
references.pmid: 15148587
references.citation: Genome Biol. 2007;8(8):R159
references.pmid: 17683528
references.citation: Mol Cell. 2007 Aug 3;27(3):435-48
references.pmid: 17679093
references.citation: EMBO J. 2003 Feb 17;22(4):905-12
references.pmid: 12574126
references.citation: EMBO Rep. 2008 Apr;9(4):337-43
references.pmid: 18379585
references.citation: Nat Genet. 2005 Nov;37(11):1289-95
references.pmid: 16200064
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):5002-7
references.pmid: 15753297
references.citation: Nucleic Acids Res. 2005 Apr 11;33(7):2078-89
references.pmid: 15824060
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D64-9
references.pmid: 14681360
references.citation: Nat Rev Genet. 2002 Apr;3(4):285-98
references.pmid: 11967553
references.citation: Genes Dev. 2008 Feb 1;22(3):279-85
references.pmid: 18245441
references.citation: Science. 2003 Dec 19;302(5653):2141-4
references.pmid: 14684825
references.citation: FEBS Lett. 2005 Mar 28;579(9):1900-3
references.pmid: 15792793
references.citation: RNA. 2008 Feb;14(2):284-96
references.pmid: 18073345
references.citation: Nature. 2007 Oct 18;449(7164):851-61
references.pmid: 17943122
references.citation: Mol Cell Biol. 1998 Jul;18(7):3900-6
references.pmid: 9632774
references.citation: PLoS Genet. 2007 May 25;3(5):e85
references.pmid: 17530930
references.citation: Trends Genet. 2000 Jun;16(6):247-53
references.pmid: 10827451
references.citation: Nat Genet. 2003 May;34(1):27-9
references.pmid: 12669065
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Genes Dev. 2007 Jul 1;21(13):1636-52
references.pmid: 17606642
references.citation: Am J Med Genet B Neuropsychiatr Genet. 2007 Oct 5;144B(7):869-76
references.pmid: 17503474
references.citation: Mol Endocrinol. 2002 Mar;16(3):459-68
references.pmid: 11875103
references.citation: Mamm Genome. 2001 Aug;12(8):595-601
references.pmid: 11471052
references.citation: Nat Genet. 2005 Aug;37(8):844-52
references.pmid: 16041372
references.citation: Mol Cell Biol. 2007 Dec;27(24):8612-21
references.pmid: 17923701
references.citation: Science. 2007 Apr 20;316(5823):445-9
references.pmid: 17363630
references.citation: Nature. 2007 Nov 8;450(7167):219-32
references.pmid: 17994088
references.citation: Pac Symp Biocomput. 2004;:66-77
references.pmid: 14992493
references.citation: Genome Biol. 2007;8(6):R108
references.pmid: 17565696
references.citation: J Biol Chem. 1996 Jul 26;271(30):17613-6
references.pmid: 8663598
references.citation: PLoS Comput Biol. 2006 Jan;2(1):e4
references.pmid: 16424921