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Volumn 22, Issue 18, 2008, Pages 2550-2563

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

Author keywords

Comparative genomics; Fox 2 RBM9; Fox l A2BP1; Splicing regulatory network; Tissue specific alternative splicing; UGCAUG

Indexed keywords

FOX 1 PROTEIN; FOX 2 PROTEIN; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

EID: 51949111100     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1703108     Document Type: Article
Times cited : (252)

References (60)
  • 1
    • 33847327313 scopus 로고    scopus 로고
    • Mapping autism risk loci using genetic linkage and chromosomal rearrangements
    • The Autism Genome Project Consortium
    • The Autism Genome Project Consortium. 2007. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet. 39: 319-328.
    • (2007) Nat Genet , vol.39 , pp. 319-328
  • 3
    • 32044467372 scopus 로고    scopus 로고
    • Fox-2 mediates epithelial cell-specific fibroblast growth factor receptor 2 exon choice
    • Baraniak, A.P., Chen, J.R., and Garcia-Blanco, M.A. 2006. Fox-2 mediates epithelial cell-specific fibroblast growth factor receptor 2 exon choice. Mol. Cell. Biol. 26: 1209-1222.
    • (2006) Mol. Cell. Biol , vol.26 , pp. 1209-1222
    • Baraniak, A.P.1    Chen, J.R.2    Garcia-Blanco, M.A.3
  • 5
    • 0013394889 scopus 로고    scopus 로고
    • Mechanisms of alternative pre-messenger RNA splicing
    • Black, D.L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291-336.
    • (2003) Annu. Rev. Biochem , vol.72 , pp. 291-336
    • Black, D.L.1
  • 6
    • 33745899048 scopus 로고    scopus 로고
    • Alternative splicing: New insights from global analyses
    • Blencowe, B.J. 2006. Alternative splicing: New insights from global analyses. Cell 126: 37-47.
    • (2006) Cell , vol.126 , pp. 37-47
    • Blencowe, B.J.1
  • 7
    • 33846135109 scopus 로고    scopus 로고
    • MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development
    • Boutz, P.L., Chawla, G., Stoilov, P., and Black, D.L. 2007a. MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. Genes & Dev. 21: 71-84.
    • (2007) Genes & Dev , vol.21 , pp. 71-84
    • Boutz, P.L.1    Chawla, G.2    Stoilov, P.3    Black, D.L.4
  • 8
    • 34347384211 scopus 로고    scopus 로고
    • A post-transcriptional regulatory switch in polypyrimidine tractbinding proteins reprograms alternative splicing in developing neurons
    • Boutz, P.L., Stoilov, P., Li, Q., Lin, C.-H., Chawla, G., Ostrow, K., Shiue, L., Ares Jr., M., and Black, D.L. 2007b. A post-transcriptional regulatory switch in polypyrimidine tractbinding proteins reprograms alternative splicing in developing neurons. Genes & Dev. 21: 1636-1652.
    • (2007) Genes & Dev , vol.21 , pp. 1636-1652
    • Boutz, P.L.1    Stoilov, P.2    Li, Q.3    Lin, C.-H.4    Chawla, G.5    Ostrow, K.6    Shiue, L.7    Ares Jr., M.8    Black, D.L.9
  • 9
    • 0035369805 scopus 로고    scopus 로고
    • Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing
    • Brudno, M., Gelfand, M.S., Spengler, S., Zorn, M., Dubchak, I., and Conboy, J.G. 2001. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res. 29: 2338-2348.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2338-2348
    • Brudno, M.1    Gelfand, M.S.2    Spengler, S.3    Zorn, M.4    Dubchak, I.5    Conboy, J.G.6
  • 10
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • Cartegni, L., Chew, S.L., and Krainer, A.R. 2002. Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Genet. 3: 285-298.
    • (2002) Nat. Rev. Genet , vol.3 , pp. 285-298
    • Cartegni, L.1    Chew, S.L.2    Krainer, A.R.3
  • 12
    • 38949133822 scopus 로고    scopus 로고
    • The search for alternative splicing regulators: New approaches offer a path to a splicing code
    • David, C.J. and Manley, J.L. 2008. The search for alternative splicing regulators: New approaches offer a path to a splicing code. Genes & Dev. 22: 279-285.
    • (2008) Genes & Dev , vol.22 , pp. 279-285
    • David, C.J.1    Manley, J.L.2
  • 13
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for annotation, visualization, and integrated discovery
    • doi: 10.1186/gb-2003-4-5-p3
    • Dennis, G., Sherman, B., Hosack, D., Yang, J., Gao, W., Lane, H., and Lempicki, R. 2003. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol. 4: R60. doi: 10.1186/gb-2003-4-5-p3.
    • (2003) Genome Biol , vol.4
    • Dennis, G.1    Sherman, B.2    Hosack, D.3    Yang, J.4    Gao, W.5    Lane, H.6    Lempicki, R.7
  • 16
    • 34548764367 scopus 로고    scopus 로고
    • Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1γ gene
    • Fukumura, K., Kato, A., Jin, Y., Ideue, T., Hirose, T., Kataoka, N., Fujiwara, T., Sakamoto, H., and Inoue, K. 2007. Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1γ gene. Nucleic Acids Res. 35: 5303-5311.
    • (2007) Nucleic Acids Res , vol.35 , pp. 5303-5311
    • Fukumura, K.1    Kato, A.2    Jin, Y.3    Ideue, T.4    Hirose, T.5    Kataoka, N.6    Fujiwara, T.7    Sakamoto, H.8    Inoue, K.9
  • 17
    • 0028308631 scopus 로고
    • Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element
    • Huh, G.S. and Hynes, R.O. 1994. Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element. Genes & Dev. 8: 1561-1574.
    • (1994) Genes & Dev , vol.8 , pp. 1561-1574
    • Huh, G.S.1    Hynes, R.O.2
  • 18
    • 38649129366 scopus 로고    scopus 로고
    • Diverse roles of hnRNP L in mammalian mRNA processing: A combined microarray and RNAi analysis
    • Hung, L.-H., Heiner, M., Hui, J., Schreiner, S., Benes, V., and Bindereif, A. 2008. Diverse roles of hnRNP L in mammalian mRNA processing: A combined microarray and RNAi analysis. RNA 14: 284-296.
    • (2008) RNA , vol.14 , pp. 284-296
    • Hung, L.-H.1    Heiner, M.2    Hui, J.3    Schreiner, S.4    Benes, V.5    Bindereif, A.6
  • 19
    • 17044427579 scopus 로고    scopus 로고
    • Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers
    • Ibrahim, E.C., Schaal, T.D., Hertel, K.J., Reed, R., and Maniatis, T. 2005. Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc. Natl. Acad. Sci. 102: 5002-5007.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 5002-5007
    • Ibrahim, E.C.1    Schaal, T.D.2    Hertel, K.J.3    Reed, R.4    Maniatis, T.5
  • 20
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • The International HapMap Consortium
    • The International HapMap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
    • (2007) Nature , vol.449 , pp. 851-861
  • 21
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 22
    • 33947720465 scopus 로고    scopus 로고
    • Global analysis of alternative splicing during T-cell activation
    • Ip, J.Y., Tong, A., Pan, Q., Topp, J.D., Blencowe, B.J., and Lynch, K.W. 2007. Global analysis of alternative splicing during T-cell activation. RNA 13: 563-572.
    • (2007) RNA , vol.13 , pp. 563-572
    • Ip, J.Y.1    Tong, A.2    Pan, Q.3    Topp, J.D.4    Blencowe, B.J.5    Lynch, K.W.6
  • 23
    • 0037656313 scopus 로고    scopus 로고
    • Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism
    • Jamain, S. 2003. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nat. Genet. 34: 27-29.
    • (2003) Nat. Genet , vol.34 , pp. 27-29
    • Jamain, S.1
  • 24
    • 0037450704 scopus 로고    scopus 로고
    • A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG
    • Jin, Y., Suzuki, H., Maegawa, S., Endo, H., Sugano, S., Hashimoto, K., Yasuda, K., and Inoue, K. 2003. A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J. 22: 905-912.
    • (2003) EMBO J , vol.22 , pp. 905-912
    • Jin, Y.1    Suzuki, H.2    Maegawa, S.3    Endo, H.4    Sugano, S.5    Hashimoto, K.6    Yasuda, K.7    Inoue, K.8
  • 26
    • 0029952557 scopus 로고    scopus 로고
    • Neuron-specific alternative splicing of non-muscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence
    • Kawamoto, S. 1996. Neuron-specific alternative splicing of non-muscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence. J. Biol. Chem. 271: 17613-17616.
    • (1996) J. Biol. Chem , vol.271 , pp. 17613-17616
    • Kawamoto, S.1
  • 28
    • 33845275018 scopus 로고    scopus 로고
    • RTP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
    • Keene, J.D., Komisarow, J.M., and Friedersdorf, M.B. 2006. RTP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat. Protoc. 1: 302-307.
    • (2006) Nat. Protoc , vol.1 , pp. 302-307
    • Keene, J.D.1    Komisarow, J.M.2    Friedersdorf, M.B.3
  • 29
    • 0034919348 scopus 로고    scopus 로고
    • Identification and expression of a mouse ortholog of A2BP1
    • Kiehl, T.-R., Shibata, H., Vo, T., Huynh, D.P., and Pulst, S.-M. 2001. Identification and expression of a mouse ortholog of A2BP1. Mamm. Genome 12: 595-601.
    • (2001) Mamm. Genome , vol.12 , pp. 595-601
    • Kiehl, T.-R.1    Shibata, H.2    Vo, T.3    Huynh, D.P.4    Pulst, S.-M.5
  • 30
    • 37549047982 scopus 로고    scopus 로고
    • The Fox-1 family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo
    • Kuroyanagi, H., Ohno, G., Mitani, S., and Hagiwara, M. 2007. The Fox-1 family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo. Mol. Cell. Biol. 27: 8612-8621.
    • (2007) Mol. Cell. Biol , vol.27 , pp. 8612-8621
    • Kuroyanagi, H.1    Ohno, G.2    Mitani, S.3    Hagiwara, M.4
  • 31
    • 35548940665 scopus 로고    scopus 로고
    • Neuronal regulation of alternative pre-mRNA splicing
    • Li, Q., Lee, J.-A., and Black, D.L. 2007. Neuronal regulation of alternative pre-mRNA splicing. Nat. Rev. Neurosci. 8: 819-831.
    • (2007) Nat. Rev. Neurosci , vol.8 , pp. 819-831
    • Li, Q.1    Lee, J.-A.2    Black, D.L.3
  • 32
    • 0031806710 scopus 로고    scopus 로고
    • Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats
    • Lim, L.P. and Sharp, P.A. 1998. Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats. Mol. Cell. Biol. 18: 3900-3906.
    • (1998) Mol. Cell. Biol , vol.18 , pp. 3900-3906
    • Lim, L.P.1    Sharp, P.A.2
  • 33
    • 0032435862 scopus 로고    scopus 로고
    • Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation
    • Lopez, A.J. 1998. Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 32: 279-305.
    • (1998) Annu. Rev. Genet , vol.32 , pp. 279-305
    • Lopez, A.J.1
  • 34
    • 15544379277 scopus 로고    scopus 로고
    • Are splicing mutations the most frequent cause of hereditary disease?
    • López-Bigas, N., Audit, B., Ouzounis, C., Parra, G., and Guigó, R. 2005. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. 579: 1900-1903.
    • (2005) FEBS Lett , vol.579 , pp. 1900-1903
    • López-Bigas, N.1    Audit, B.2    Ouzounis, C.3    Parra, G.4    Guigó, R.5
  • 35
    • 34547212309 scopus 로고    scopus 로고
    • The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing
    • Makeyev, E.V., Zhang, J., Carrasco, M.A., and Maniatis, T. 2007. The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27: 435-448.
    • (2007) Mol. Cell , vol.27 , pp. 435-448
    • Makeyev, E.V.1    Zhang, J.2    Carrasco, M.A.3    Maniatis, T.4
  • 36
    • 0037041395 scopus 로고    scopus 로고
    • An extensive network of coupling among gene expression machines
    • Maniatis, T. and Reed, R. 2002. An extensive network of coupling among gene expression machines. Nature 416: 499-506.
    • (2002) Nature , vol.416 , pp. 499-506
    • Maniatis, T.1    Reed, R.2
  • 38
    • 48749124117 scopus 로고    scopus 로고
    • ChIPping away at gene regulation
    • Massie, C.E. and Mills, I.G. 2008. ChIPping away at gene regulation. EMBO Rep. 9: 337-343.
    • (2008) EMBO Rep , vol.9 , pp. 337-343
    • Massie, C.E.1    Mills, I.G.2
  • 39
    • 38649089551 scopus 로고    scopus 로고
    • Exon expression profiling reveals stimulus-mediated exon use in neural cells
    • doi: 10.1186/gb-2007-8-8-r159
    • McKee, A., Neretti, N., Carvalho, L., Meyer, C., Fox, E., Brodsky, A., and Silver, P. 2007. Exon expression profiling reveals stimulus-mediated exon use in neural cells. Genome Biol. 8: R159. doi: 10.1186/gb-2007-8-8-r159.
    • (2007) Genome Biol , vol.8
    • McKee, A.1    Neretti, N.2    Carvalho, L.3    Meyer, C.4    Fox, E.5    Brodsky, A.6    Silver, P.7
  • 41
    • 0034195219 scopus 로고    scopus 로고
    • Sex in the worm: Counting and compensating X-chromosome dose
    • Meyer, B.J. 2000. Sex in the worm: Counting and compensating X-chromosome dose. Trends Genet. 16: 247-253.
    • (2000) Trends Genet , vol.16 , pp. 247-253
    • Meyer, B.J.1
  • 43
    • 13844314248 scopus 로고    scopus 로고
    • The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons
    • Minovitsky, S., Gee, S.L., Schokrpur, S., Dubchak, I., and Conboy, J.G. 2005. The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. Nucleic Acids Res. 33: 714-724.
    • (2005) Nucleic Acids Res , vol.33 , pp. 714-724
    • Minovitsky, S.1    Gee, S.L.2    Schokrpur, S.3    Dubchak, I.4    Conboy, J.G.5
  • 44
    • 38649125206 scopus 로고    scopus 로고
    • Global analysis of mRNA splicing
    • Moore, M.J. and Silver, P.A. 2008. Global analysis of mRNA splicing. RNA 14: 197-203.
    • (2008) RNA , vol.14 , pp. 197-203
    • Moore, M.J.1    Silver, P.A.2
  • 45
    • 17544367787 scopus 로고    scopus 로고
    • Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities
    • Nakahata, S. and Kawamoto, S. 2005. Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities. Nucleic Acids Res. 33: 2078-2089.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2078-2089
    • Nakahata, S.1    Kawamoto, S.2
  • 50
    • 2442694425 scopus 로고    scopus 로고
    • Transcriptome and genome conservation of alternative splicing events in humans and mice
    • Sugnet, C., Kent, W., Ares, M.J., and Haussler, D. 2004. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac. Symp. Biocomput. 2004: 66-77.
    • (2004) Pac. Symp. Biocomput , vol.2004 , pp. 66-77
    • Sugnet, C.1    Kent, W.2    Ares, M.J.3    Haussler, D.4
  • 51
    • 33645760966 scopus 로고    scopus 로고
    • Sugnet, C.W., Srinivasan, K., Clark, T.A., Brien, G., Cline, M.S., Wang, H., Williams, A., Kulp, D., Blume, J.E., Haussler, D., et al. 2006. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Computat. Biol. 2: e4. doi: 10.1371/journal.pcbi.0020004.
    • Sugnet, C.W., Srinivasan, K., Clark, T.A., Brien, G., Cline, M.S., Wang, H., Williams, A., Kulp, D., Blume, J.E., Haussler, D., et al. 2006. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Computat. Biol. 2: e4. doi: 10.1371/journal.pcbi.0020004.
  • 53
    • 27944508215 scopus 로고    scopus 로고
    • CLIP: A method for identifying protein-RNA interaction sites in living cells
    • Ule, J., Jensen, K., Mele, A., and Darnell, R.B. 2005a. CLIP: A method for identifying protein-RNA interaction sites in living cells. Methods 37: 376-386.
    • (2005) Methods , vol.37 , pp. 376-386
    • Ule, J.1    Jensen, K.2    Mele, A.3    Darnell, R.B.4
  • 56
    • 27644455141 scopus 로고    scopus 로고
    • Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals
    • Underwood, J.G., Boutz, P.L., Dougherty, J.D., Stoilov, P., and Black, D.L. 2005. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol. Cell. Biol. 25: 10005-10016.
    • (2005) Mol. Cell. Biol , vol.25 , pp. 10005-10016
    • Underwood, J.G.1    Boutz, P.L.2    Dougherty, J.D.3    Stoilov, P.4    Black, D.L.5
  • 57
    • 34347379534 scopus 로고    scopus 로고
    • A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing
    • Voelker, R.B. and Berglund, J.A. 2007. A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Res. 17: 1023-1033.
    • (2007) Genome Res , vol.17 , pp. 1023-1033
    • Voelker, R.B.1    Berglund, J.A.2
  • 58
    • 14544277546 scopus 로고    scopus 로고
    • Identification and analysis of alternative splicing events conserved in human and mouse
    • Yeo, G.W., Van Nostrand, E., Holste, D., Poggio, T., and Burge, C.B. 2005. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. 102: 2850-2855.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 2850-2855
    • Yeo, G.W.1    Van Nostrand, E.2    Holste, D.3    Poggio, T.4    Burge, C.B.5
  • 59
    • 34249696543 scopus 로고    scopus 로고
    • Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements
    • doi: 10.1371/journal.pgen.0030085
    • Yeo, G.W., Van Nostrand, E.L., and Liang, T.Y. 2007. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet. 3: e85. doi: 10.1371/journal.pgen.0030085.
    • (2007) PLoS Genet , vol.3
    • Yeo, G.W.1    Van Nostrand, E.L.2    Liang, T.Y.3
  • 60
    • 35448950862 scopus 로고    scopus 로고
    • Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites
    • Zhang, C., Hastings, M.L., Krainer, A.R., and Zhang, M.Q. 2007. Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites. Proc. Natl. Acad. Sci. 104: 15028-15033.
    • (2007) Proc. Natl. Acad. Sci , vol.104 , pp. 15028-15033
    • Zhang, C.1    Hastings, M.L.2    Krainer, A.R.3    Zhang, M.Q.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.