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Volumn 11, Issue 6, 2015, Pages

Functional Assessment of Disease-Associated Regulatory Variants In Vivo Using a Versatile Dual Colour Transgenesis Strategy in Zebrafish

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON REGULATORY FACTOR 6; SONIC HEDGEHOG PROTEIN; TRANSCRIPTION FACTOR PAX6; TRANSCRIPTION FACTOR SOX9; EYE PROTEIN; GREEN FLUORESCENT PROTEIN; HOMEODOMAIN PROTEIN; INTERFERON REGULATORY FACTOR; IRF6 PROTEIN, ZEBRAFISH; PAIRED BOX TRANSCRIPTION FACTOR; PAX6 PROTEIN, HUMAN; PROTEIN BINDING; REPRESSOR PROTEIN; SHHA PROTEIN, ZEBRAFISH; ZEBRAFISH PROTEIN;

EID: 84937795136     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005193     Document Type: Article
Times cited : (22)

References (43)
  • 1
    • 84899450857 scopus 로고    scopus 로고
    • Transcriptional enhancers: from properties to genome-wide predictions
    • Shlyueva D, Stampfel G, Stark A, Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet. 2014;15: 272–286. doi: 10.1038/nrg3682 24614317
    • (2014) Nat Rev Genet , vol.15 , pp. 272-286
    • Shlyueva, D.1    Stampfel, G.2    Stark, A.3
  • 2
    • 84871688165 scopus 로고    scopus 로고
    • Characterization of enhancer function from genome-wide analyses
    • Maston GA, Landt SG, Snyder M, Green MR, Characterization of enhancer function from genome-wide analyses. Annu Rev Genomics Hum Genet. 2012; 13:29–57. doi: 10.1146/annurev-genom-090711-163723 22703170
    • (2012) Annu Rev Genomics Hum Genet , vol.13 , pp. 29-57
    • Maston, G.A.1    Landt, S.G.2    Snyder, M.3    Green, M.R.4
  • 3
    • 84904089628 scopus 로고    scopus 로고
    • Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences
    • Bhatia S, Kleinjan DA, Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet. 2014;133: 815–845. doi: 10.1007/s00439-014-1424-6 24496500
    • (2014) Hum Genet , vol.133 , pp. 815-845
    • Bhatia, S.1    Kleinjan, D.A.2
  • 4
    • 84865249952 scopus 로고    scopus 로고
    • Transcription factors: from enhancer binding to developmental control
    • Spitz F, Furlong EEM, Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13: 613–626. doi: 10.1038/nrg3207 22868264
    • (2012) Nat Rev Genet , vol.13 , pp. 613-626
    • Spitz, F.1    Furlong, E.E.M.2
  • 5
    • 84903993789 scopus 로고    scopus 로고
    • Zebrafish models in translational research: tipping the scales toward advancements in human health
    • Phillips JB, Westerfield M, Zebrafish models in translational research: tipping the scales toward advancements in human health. Dis Model Mech. 2014;7: 739–743. doi: 10.1242/dmm.015545 24973743
    • (2014) Dis Model Mech , vol.7 , pp. 739-743
    • Phillips, J.B.1    Westerfield, M.2
  • 6
    • 78650607495 scopus 로고    scopus 로고
    • Zebrafish: an integrative system for neurogenomics and neurosciences
    • Rinkwitz S1, Mourrain P, Becker TS, Zebrafish: an integrative system for neurogenomics and neurosciences. Progress in Neurobiology. 2011;93(2): 231–43. doi: 10.1016/j.pneurobio.2010.11.003 21130139
    • (2011) Progress in Neurobiology , vol.93 , Issue.2 , pp. 231-243
    • Rinkwitz, S.1    Mourrain, P.2    Becker, T.S.3
  • 7
    • 84904405924 scopus 로고    scopus 로고
    • Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence
    • Gordon CT, Attanasio C, Bhatia S, Benko S, Ansari M, et al. Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence. Hum Mutat. 2014;35: 1011–1020. doi: 10.1002/humu.22606 24934569
    • (2014) Hum Mutat , vol.35 , pp. 1011-1020
    • Gordon, C.T.1    Attanasio, C.2    Bhatia, S.3    Benko, S.4    Ansari, M.5
  • 8
    • 16644391315 scopus 로고    scopus 로고
    • Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element
    • Kawakami K., Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element. Methods Cell Biol. 2004;77: 201–222. 15602913
    • (2004) Methods Cell Biol , vol.77 , pp. 201-222
    • Kawakami, K.1
  • 9
    • 55049108856 scopus 로고    scopus 로고
    • Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein
    • Jeong Y, Leskow FC, El-Jaick K, Roessler E, Muenke M, et al. Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nat Genet. 2008; 40: 1348–1353. doi: 10.1038/ng.230 18836447
    • (2008) Nat Genet , vol.40 , pp. 1348-1353
    • Jeong, Y.1    Leskow, F.C.2    El-Jaick, K.3    Roessler, E.4    Muenke, M.5
  • 10
    • 48549091913 scopus 로고    scopus 로고
    • Haploinsufficiency of Six3 fails to activate Sonic hedgehog expression in the ventral forebrain and causes holoprosencephaly
    • Geng X, Speirs C, Lagutin O, Inbal A, Liu W, et al. Haploinsufficiency of Six3 fails to activate Sonic hedgehog expression in the ventral forebrain and causes holoprosencephaly. Dev Cell. 2009;15(2): 236–47.
    • (2009) Dev Cell , vol.15 , Issue.2 , pp. 236-247
    • Geng, X.1    Speirs, C.2    Lagutin, O.3    Inbal, A.4    Liu, W.5
  • 11
    • 27744483787 scopus 로고    scopus 로고
    • Lhx2 mediates the activity of Six3 in zebrafish forebrain growth
    • Ando H, Kobayashi M, Tsubokawa T, Uyemura K, Furuta T, et al. Lhx2 mediates the activity of Six3 in zebrafish forebrain growth. Dev Biol.2005; 287: 456–468. 16226737
    • (2005) Dev Biol , vol.287 , pp. 456-468
    • Ando, H.1    Kobayashi, M.2    Tsubokawa, T.3    Uyemura, K.4    Furuta, T.5
  • 12
    • 84863869789 scopus 로고    scopus 로고
    • Human limb abnormalities caused by disruption of hedgehog signaling
    • Anderson E, Peluso S, Lettice LA, Hill RE, Human limb abnormalities caused by disruption of hedgehog signaling. Trends Genet. 2012;28: 364–373. doi: 10.1016/j.tig.2012.03.012 22534646
    • (2012) Trends Genet , vol.28 , pp. 364-373
    • Anderson, E.1    Peluso, S.2    Lettice, L.A.3    Hill, R.E.4
  • 13
    • 41149157070 scopus 로고    scopus 로고
    • Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly
    • Lettice LA, Hill AE, Devenney PS, Hill RE, Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly. Hum Mol Genet. 2008;17: 978–985. 18156157
    • (2008) Hum Mol Genet , vol.17 , pp. 978-985
    • Lettice, L.A.1    Hill, A.E.2    Devenney, P.S.3    Hill, R.E.4
  • 14
    • 84890314164 scopus 로고    scopus 로고
    • Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia
    • Bhatia S, Bengani H, Fish M, Brown A, Divizia MT, et al. Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia. Am J Hum Genet. 2013;93: 1126–1134. doi: 10.1016/j.ajhg.2013.10.028 24290376
    • (2013) Am J Hum Genet , vol.93 , pp. 1126-1134
    • Bhatia, S.1    Bengani, H.2    Fish, M.3    Brown, A.4    Divizia, M.T.5
  • 15
    • 55049105999 scopus 로고    scopus 로고
    • Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip
    • Rahimov F, Marazita ML, Visel A, Cooper ME, Hitchler MJ, et al. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet. 2008;40: 1341–1347. doi: 10.1038/ng.242 18836445
    • (2008) Nat Genet , vol.40 , pp. 1341-1347
    • Rahimov, F.1    Marazita, M.L.2    Visel, A.3    Cooper, M.E.4    Hitchler, M.J.5
  • 16
    • 84870716409 scopus 로고    scopus 로고
    • Distinct requirements for wnt9a and irf6 in extension and integration mechanisms during zebrafish palate morphogenesis
    • Dougherty M, Kamel G, Grimaldi M, Gfrerer L, Shubinets V, et al. Distinct requirements for wnt9a and irf6 in extension and integration mechanisms during zebrafish palate morphogenesis. Development. 2013;140: 76–81. doi: 10.1242/dev.080473 23154410
    • (2013) Development , vol.140 , pp. 76-81
    • Dougherty, M.1    Kamel, G.2    Grimaldi, M.3    Gfrerer, L.4    Shubinets, V.5
  • 17
    • 70349705754 scopus 로고    scopus 로고
    • Long-range regulation at the SOX9 locus in development and disease
    • Gordon CT, Tan TY, Benko S, Fitzpatrick D, Lyonnet S, et al. Long-range regulation at the SOX9 locus in development and disease. J Med Genet. 2009;46: 649–656. doi: 10.1136/jmg.2009.068361 19473998
    • (2009) J Med Genet , vol.46 , pp. 649-656
    • Gordon, C.T.1    Tan, T.Y.2    Benko, S.3    Fitzpatrick, D.4    Lyonnet, S.5
  • 18
    • 61349104285 scopus 로고    scopus 로고
    • Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence
    • Benko S, Fantes JA, Amiel J, Kleinjan DJ, Thomas S, et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet. 2009;41: 359–364. doi: 10.1038/ng.329 19234473
    • (2009) Nat Genet , vol.41 , pp. 359-364
    • Benko, S.1    Fantes, J.A.2    Amiel, J.3    Kleinjan, D.J.4    Thomas, S.5
  • 19
    • 84886257610 scopus 로고    scopus 로고
    • Fine tuning of craniofacial morphology by distant-acting enhancers
    • Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, et al. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013;342: 1241006. doi: 10.1126/science.1241006 24159046
    • (2013) Science , vol.342 , pp. 1241006
    • Attanasio, C.1    Nord, A.S.2    Zhu, Y.3    Blow, M.J.4    Li, Z.5
  • 20
    • 84891347416 scopus 로고    scopus 로고
    • Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis
    • Weedon MN, Cebola I, Patch AM, Flanagan SE, De Franco E, et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet. 2014;46: 61–64. doi: 10.1038/ng.2826 24212882
    • (2014) Nat Genet , vol.46 , pp. 61-64
    • Weedon, M.N.1    Cebola, I.2    Patch, A.M.3    Flanagan, S.E.4    De Franco, E.5
  • 21
    • 84863230316 scopus 로고    scopus 로고
    • Massively parallel functional dissection of mammalian enhancers in vivo
    • Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol. 2012;30: 265–270. doi: 10.1038/nbt.2136 22371081
    • (2012) Nat Biotechnol , vol.30 , pp. 265-270
    • Patwardhan, R.P.1    Hiatt, J.B.2    Witten, D.M.3    Kim, M.J.4    Smith, R.P.5
  • 22
    • 84869853147 scopus 로고    scopus 로고
    • Complex effects of nucleotide variants in a mammalian cis-regulatory element
    • Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA, Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A. 2012;109(47):19498–503. doi: 10.1073/pnas.1210678109 23129659
    • (2012) Proc Natl Acad Sci U S A , vol.109 , Issue.47 , pp. 19498-19503
    • Kwasnieski, J.C.1    Mogno, I.2    Myers, C.A.3    Corbo, J.C.4    Cohen, B.A.5
  • 23
    • 84880362638 scopus 로고    scopus 로고
    • Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
    • White MA, Myers CA, Corbo JC, Cohen BA, Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc Natl Acad Sci U S A. 2013;110(29):11952–7. doi: 10.1073/pnas.1307449110 23818646
    • (2013) Proc Natl Acad Sci U S A , vol.110 , Issue.29 , pp. 11952-11957
    • White, M.A.1    Myers, C.A.2    Corbo, J.C.3    Cohen, B.A.4
  • 24
    • 84892730257 scopus 로고    scopus 로고
    • Targeted transgene integration overcomes variability of position effects in zebrafish
    • Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, et al. Targeted transgene integration overcomes variability of position effects in zebrafish. Development. 2014;141: 715–724. doi: 10.1242/dev.100347 24449846
    • (2014) Development , vol.141 , pp. 715-724
    • Roberts, J.A.1    Miguel-Escalada, I.2    Slovik, K.J.3    Walsh, K.T.4    Hadzhiev, Y.5
  • 25
    • 3042525132 scopus 로고    scopus 로고
    • Synapsis and DNA cleavage in phiC31 integrase-mediated site-specific recombination
    • Smith MCA, Till R, Brady K, Soultanas P, Thorpe H, et al. Synapsis and DNA cleavage in phiC31 integrase-mediated site-specific recombination. Nucleic Acids Res. 2004;32: 2607–2617. 15141031
    • (2004) Nucleic Acids Res , vol.32 , pp. 2607-2617
    • Smith, M.C.A.1    Till, R.2    Brady, K.3    Soultanas, P.4    Thorpe, H.5
  • 26
    • 84874617789 scopus 로고    scopus 로고
    • Efficient genome editing in zebrafish using a CRISPR-Cas system
    • Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013;31: 227–229. doi: 10.1038/nbt.2501 23360964
    • (2013) Nat Biotechnol , vol.31 , pp. 227-229
    • Hwang, W.Y.1    Fu, Y.2    Reyon, D.3    Maeder, M.L.4    Tsai, S.Q.5
  • 27
    • 84882788354 scopus 로고    scopus 로고
    • Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system
    • Jao LE, Wente SR, Chen W, Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci U S A. 2013; 110: 13904–13909. doi: 10.1073/pnas.1308335110 23918387
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 13904-13909
    • Jao, L.E.1    Wente, S.R.2    Chen, W.3
  • 28
    • 84884934419 scopus 로고    scopus 로고
    • Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase
    • Kirchmaier S, Höckendorf B, Möller EK, Bornhorst D, Spitz F, et al. Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase. Development. 2013;140: 4287–4295. doi: 10.1242/dev.096081 24048591
    • (2013) Development , vol.140 , pp. 4287-4295
    • Kirchmaier, S.1    Höckendorf, B.2    Möller, E.K.3    Bornhorst, D.4    Spitz, F.5
  • 29
    • 0347914540 scopus 로고    scopus 로고
    • Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription
    • Kleinjan DA, Seawright A, Childs AJ, van Heyningen V, Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription. Dev Biol. 2004;265: 462–477. 14732405
    • (2004) Dev Biol , vol.265 , pp. 462-477
    • Kleinjan, D.A.1    Seawright, A.2    Childs, A.J.3    van Heyningen, V.4
  • 30
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: emerging mechanisms and disruption in disease
    • Kleinjan DA, van Heyningen V, Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet. 2005; 76: 8–32. 15549674
    • (2005) Am J Hum Genet , vol.76 , pp. 8-32
    • Kleinjan, D.A.1    van Heyningen, V.2
  • 31
    • 70349611559 scopus 로고    scopus 로고
    • Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease
    • Kleinjan DJ, Coutinho P, Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease. Brief Funct Genomic Proteomic. 2009;8: 317–332. doi: 10.1093/bfgp/elp022 19596743
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 317-332
    • Kleinjan, D.J.1    Coutinho, P.2
  • 32
    • 41949113742 scopus 로고    scopus 로고
    • The enhanceosome
    • Panne D, The enhanceosome. Curr Opin Struct Biol. 2008;18: 236–242. doi: 10.1016/j.sbi.2007.12.002 18206362
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 236-242
    • Panne, D.1
  • 33
    • 84901834984 scopus 로고    scopus 로고
    • The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains
    • Schwarzer W, Spitz F, The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains. Curr Opin Genet Dev. 2014;27C: 74–82.
    • (2014) Curr Opin Genet Dev , vol.27C , pp. 74-82
    • Schwarzer, W.1    Spitz, F.2
  • 34
    • 75149143994 scopus 로고    scopus 로고
    • Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
    • Weirauch MT, Hughes TR, Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet. 2010;26: 66–74. doi: 10.1016/j.tig.2009.12.002 20083321
    • (2010) Trends Genet , vol.26 , pp. 66-74
    • Weirauch, M.T.1    Hughes, T.R.2
  • 35
    • 79952163548 scopus 로고    scopus 로고
    • Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
    • Lee AP, Kerk SY, Tan YY, Brenner S, Venkatesh B, Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol Biol Evol. 2011;28: 1205–1215. doi: 10.1093/molbev/msq304 21081479
    • (2011) Mol Biol Evol , vol.28 , pp. 1205-1215
    • Lee, A.P.1    Kerk, S.Y.2    Tan, Y.Y.3    Brenner, S.4    Venkatesh, B.5
  • 36
    • 0037351989 scopus 로고    scopus 로고
    • Genome duplication, a trait shared by 22000 species of ray-finned fish
    • Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y, Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res. 2003;13: 382–390. 12618368
    • (2003) Genome Res , vol.13 , pp. 382-390
    • Taylor, J.S.1    Braasch, I.2    Frickey, T.3    Meyer, A.4    Van de Peer, Y.5
  • 37
    • 34347244234 scopus 로고    scopus 로고
    • Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish
    • Fisher S, et al. Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nature Protocols. 2006b;1(3):1297–1305. 17406414
    • (2006) Nature Protocols , vol.1 , Issue.3 , pp. 1297-1305
    • Fisher, S.1
  • 38
    • 3242891068 scopus 로고    scopus 로고
    • VISTA: computational tools for comparative genomics
    • Frazer KA, et al. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32 (Web Server issue):W273–9
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server issue , pp. 273-279
    • Frazer, K.A.1
  • 39
    • 3242878193 scopus 로고    scopus 로고
    • ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    • Ovcharenko I, et al. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Research 32(Web Server Issue). 2004: W280–W286. 15215395
    • (2004) Nucleic Acids Research , vol.32 , Issue.Web Server Issue , pp. W280-W286
    • Ovcharenko, I.1
  • 41
    • 0029045033 scopus 로고
    • Stages of embryonic development of the zebrafish
    • Kimmel CB, et al. Stages of embryonic development of the zebrafish. Dev Dyn. 1995;203: 253–310. 8589427
    • (1995) Dev Dyn , vol.203 , pp. 253-310
    • Kimmel, C.B.1
  • 42
    • 84883244450 scopus 로고    scopus 로고
    • Using zebrafish transgenesis to test human genomic sequences for specific enhancer activity
    • Ishibashi M, Mechaly AS, Becker TS, Rinkwitz S, Using zebrafish transgenesis to test human genomic sequences for specific enhancer activity. Methods. 2013;62: 216–225. doi: 10.1016/j.ymeth.2013.03.018 23542551
    • (2013) Methods , vol.62 , pp. 216-225
    • Ishibashi, M.1    Mechaly, A.S.2    Becker, T.S.3    Rinkwitz, S.4
  • 43
    • 38149126474 scopus 로고    scopus 로고
    • High-resolution in situ hybridization to whole-mount zebrafish embryos
    • Thisse C, Thisse B, High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat Protoc. 2008;3: 59–69. doi: 10.1038/nprot.2007.514 18193022
    • (2008) Nat Protoc , vol.3 , pp. 59-69
    • Thisse, C.1    Thisse, B.2


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