1. WareSM, HarutyunyanKG, BelmontJW (2006) Zic3 is critical for early embryonic patterning during gastrulation. Dev Dyn 235: 776–785.
2. ArugaJ (2004) The role of Zic genes in neural development. Mol Cell Neurosci 26: 205–221.
3. GrinblatY, SiveH (2001) zic Gene expression marks anteroposterior pattern in the presumptive neurectoderm of the zebrafish gastrula. Dev Dyn 222: 688–693.
4. NagaiT, ArugaJ, TakadaS, GuntherT, SporleR, et al. (1997) The expression of the mouse Zic1, Zic2, and Zic3 gene suggests an essential role for Zic genes in body pattern formation. Dev Biol 182: 299–313.
5. ArugaJ, NagaiT, TokuyamaT, HayashizakiY, OkazakiY, et al. (1996) The mouse zic gene family. Homologues of the Drosophila pair-rule gene odd-paired. J Biol Chem 271: 1043–1047.
6. BenedykMJ, MullenJR, DiNardoS (1994) odd-paired: a zinc finger pair-rule protein required for the timely activation of engrailed and wingless in Drosophila embryos. Genes Dev 8: 105–117.
7. MerzdorfCS (2007) Emerging roles for zic genes in early development. Dev Dyn 236: 922–940.
8. GrinbergI, MillenKJ (2005) The ZIC gene family in development and disease. Clin Genet 67: 290–296.
9. GebbiaM, FerreroGB, PiliaG, BassiMT, AylsworthA, et al. (1997) X-linked situs abnormalities result from mutations in ZIC3. Nat Genet 17: 305–308.
10. CastAE, GaoC, AmackJD, WareSM (2012) An essential and highly conserved role for Zic3 in left-right patterning, gastrulation and convergent extension morphogenesis. Dev Biol 364: 22–31.
11. KitaguchiT, MizugishiK, HatayamaM, ArugaJ, MikoshibaK (2002) Xenopus Brachyury regulates mesodermal expression of Zic3, a gene controlling left-right asymmetry. Dev Growth Differ 44: 55–61.
12. KitaguchiT, NagaiT, NakataK, ArugaJ, MikoshibaK (2000) Zic3 is involved in the left-right specification of the Xenopus embryo. Development 127: 4787–4795.
13. CampioneM, SteinbeisserH, SchweickertA, DeisslerK, van BebberF, et al. (1999) The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. Development 126: 1225–1234.
14. RyanAK, BlumbergB, Rodriguez-EstebanC, Yonei-TamuraS, TamuraK, et al. (1998) Pitx2 determines left-right asymmetry of internal organs in vertebrates. Nature 394: 545–551.
15. SampathK, RubinsteinAL, ChengAM, LiangJO, FekanyK, et al. (1998) Induction of the zebrafish ventral brain and floorplate requires cyclops/nodal signalling. Nature 395: 185–189.
16. FujimiTJ, HatayamaM, ArugaJ (2012) Xenopus Zic3 controls notochord and organizer development through suppression of the Wnt/beta-catenin signaling pathway. Dev Biol 361: 220–231.
17. PurandareSM, WareSM, KwanKM, GebbiaM, BassiMT, et al. (2002) A complex syndrome of left-right axis, central nervous system and axial skeleton defects in Zic3 mutant mice. Development 129: 2293–2302.
18. NakataK, NagaiT, ArugaJ, MikoshibaK (1997) Xenopus Zic3, a primary regulator both in neural and neural crest development. Proc Natl Acad Sci U S A 94: 11980–11985.
19. MarchalL, LuxardiG, ThomeV, KodjabachianL (2009) BMP inhibition initiates neural induction via FGF signaling and Zic genes. Proc Natl Acad Sci U S A 106: 17437–17442.
20. WeberJR, SokolSY (2003) Identification of a phylogenetically conserved activin-responsive enhancer in the Zic3 gene. Mech Dev 120: 955–964.
21. ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636–640.
22. SanyalA, LajoieBR, JainG, DekkerJ (2012) The long-range interaction landscape of gene promoters. Nature 489: 109–113.
23. FarnhamPJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10: 605–616.
24. SpitzF, FurlongEE (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13: 613–626.
25. WederellED, BilenkyM, CullumR, ThiessenN, DagpinarM, et al. (2008) Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res 36: 4549–4564.
26. ChenX, XuH, YuanP, FangF, HussM, et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106–1117.
27. CarrollJS, LiuXS, BrodskyAS, LiW, MeyerCA, et al. (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122: 33–43.
28. ParinovS, KondrichinI, KorzhV, EmelyanovA (2004) Tol2 transposon-mediated enhancer trap to identify developmentally regulated zebrafish genes in vivo. Dev Dyn 231: 449–459.
29. AanesH, WinataCL, LinCH, ChenJP, SrinivasanKG, et al. (2011) Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res 21: 1328–1338.
30. SchmitzB, PapanC, Campos-OrtegaJA (1993) Neurulation in the anterior trunk region of the zebrafish Brachydanio rerio. Roux's Arch Dev Biol 202: 250–259.
31. WooK, FraserSE (1995) Order and coherence in the fate map of the zebrafish nervous system. Development 121: 2595–2609.
32. GrinblatY, GamseJ, PatelM, SiveH (1998) Determination of the zebrafish forebrain: induction and patterning. Development 125: 4403–4416.
33. SagerstromCG, GrinbaltY, SiveH (1996) Anteroposterior patterning in the zebrafish, Danio rerio: an explant assay reveals inductive and suppressive cell interactions. Development 122: 1873–1883.
34. KondrychynI, Garcia-LeceaM, EmelyanovA, ParinovS, KorzhV (2009) Genome-wide analysis of Tol2 transposon reintegration in zebrafish. BMC Genomics 10: 418.
35. McLeanCY, BristorD, HillerM, ClarkeSL, SchaarBT, et al. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28: 495–501.
36. ArugaJ, MikoshibaK (2011) Role of BMP, FGF, calcium signaling, and Zic proteins in vertebrate neuroectodermal differentiation. Neurochem Res 36: 1286–1292.
37. AppelB (2000) Zebrafish neural induction and patterning. Dev Dyn 219: 155–168.
38. LimLS, HongFH, KunarsoG, StantonLW (2010) The pluripotency regulator Zic3 is a direct activator of the Nanog promoter in ESCs. Stem Cells 28: 1961–1969.
39. NewburgerDE, BulykML (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37: D77–82.
40. MizugishiK, ArugaJ, NakataK, MikoshibaK (2001) Molecular properties of Zic proteins as transcriptional regulators and their relationship to GLI proteins. J Biol Chem 276: 2180–2188.
41. KoyabuY, NakataK, MizugishiK, ArugaJ, MikoshibaK (2001) Physical and functional interactions between Zic and Gli proteins. J Biol Chem 276: 6889–6892.
42. ThisseC, ThisseB (1999) Antivin, a novel and divergent member of the TGFbeta superfamily, negatively regulates mesoderm induction. Development 126: 229–240.
43. FaucourtM, HoulistonE, BesnardeauL, KimelmanD, LepageT (2001) The pitx2 homeobox protein is required early for endoderm formation and nodal signaling. Dev Biol 229: 287–306.
44. FeldmanB, DouganST, SchierAF, TalbotWS (2000) Nodal-related signals establish mesendodermal fate and trunk neural identity in zebrafish. Curr Biol 10: 531–534.
45. FeldmanB, GatesMA, EganES, DouganST, RennebeckG, et al. (1998) Zebrafish organizer development and germ-layer formation require nodal-related signals. Nature 395: 181–185.
46. BisgroveBW, EssnerJJ, YostHJ (1999) Regulation of midline development by antagonism of lefty and nodal signaling. Development 126: 3253–3262.
47. EkkerM, AkimenkoMA, AllendeML, SmithR, DrouinG, et al. (1997) Relationships among msx gene structure and function in zebrafish and other vertebrates. Mol Biol Evol 14: 1008–1022.
48. WodaJM, PastagiaJ, MercolaM, ArtingerKB (2003) Dlx proteins position the neural plate border and determine adjacent cell fates. Development 130: 331–342.
49. de la Calle-MustienesE, GlavicA, ModolellJ, Gomez-SkarmetaJL (2002) Xiro homeoproteins coordinate cell cycle exit and primary neuron formation by upregulating neuronal-fate repressors and downregulating the cell-cycle inhibitor XGadd45-gamma. Mech Dev 119: 69–80.
50. LecaudeyV, AnselmeI, DildropR, RutherU, Schneider-MaunouryS (2005) Expression of the zebrafish Iroquois genes during early nervous system formation and patterning. J Comp Neurol 492: 289–302.
51. KorzhV, SleptsovaI, LiaoJ, HeJ, GongZ (1998) Expression of zebrafish bHLH genes ngn1 and nrd defines distinct stages of neural differentiation. Dev Dyn 213: 92–104.
52. WallingfordJB, HarlandRM (2002) Neural tube closure requires Dishevelled-dependent convergent extension of the midline. Development 129: 5815–5825.
53. SongH, HuJ, ChenW, ElliottG, AndreP, et al. (2010) Planar cell polarity breaks bilateral symmetry by controlling ciliary positioning. Nature 466: 378–382.
54. ThirietN, AgasseF, NicoleauC, GueganC, ValletteF, et al. (2011) NPY promotes chemokinesis and neurogenesis in the rat subventricular zone. J Neurochem 116: 1018–1027.
55. YehCM, LiuYC, ChangCJ, LaiSL, HsiaoCD, et al. (2011) Ptenb mediates gastrulation cell movements via Cdc42/AKT1 in zebrafish. PLoS One 6: e18702.
56. GhignaC, GiordanoS, ShenH, BenvenutoF, CastiglioniF, et al. (2005) Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol Cell 20: 881–890.
57. SeuxM, PeugetS, MonteroMP, SiretC, RigotV, et al. (2011) TP53INP1 decreases pancreatic cancer cell migration by regulating SPARC expression. Oncogene 30: 3049–3061.
58. GilbertMM, RobinsonBS, MobergKH (2009) Functional interactions between the erupted/tsg101 growth suppressor gene and the DaPKC and rbf1 genes in Drosophila imaginal disc tumors. PLoS One 4: e7039.
59. WangY, KanekoN, AsaiN, EnomotoA, Isotani-SakakibaraM, et al. (2011) Girdin is an intrinsic regulator of neuroblast chain migration in the rostral migratory stream of the postnatal brain. J Neurosci 31: 8109–8122.
60. OharaK, EnomotoA, KatoT, HashimotoT, Isotani-SakakibaraM, et al. (2012) Involvement of Girdin in the determination of cell polarity during cell migration. PLoS One 7: e36681.
61. FisherS, GriceEA, VintonRM, BesslingSL, UrasakiA, et al. (2006) Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nat Protoc 1: 1297–1305.
62. LiG, RuanX, AuerbachRK, SandhuKS, ZhengM, et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148: 84–98.
63. TenaJJ, AlonsoME, de la Calle-MustienesE, SplinterE, de LaatW, et al. (2011) An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nat Commun 2: 310.
64. EngstromPG, FredmanD, LenhardB (2008) Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol 9: R34.
65. CawleyS, BekiranovS, NgHH, KapranovP, SekingerEA, et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499–509.
66. SandelinA, BaileyP, BruceS, EngstromPG, KlosJM, et al. (2004) Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 99.
67. WoolfeA, GoodsonM, GoodeDK, SnellP, McEwenGK, et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7.
68. VenkateshB, KirknessEF, LohYH, HalpernAL, LeeAP, et al. (2006) Ancient noncoding elements conserved in the human genome. Science 314: 1892.
69. BejeranoG, PheasantM, MakuninI, StephenS, KentWJ, et al. (2004) Ultraconserved elements in the human genome. Science 304: 1321–1325.
70. BlowMJ, McCulleyDJ, LiZ, ZhangT, AkiyamaJA, et al. (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42: 806–810.
71. SchmidtD, WilsonMD, BallesterB, SchwaliePC, BrownGD, et al. (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: 1036–1040.
72. LeeAP, KerkSY, TanYY, BrennerS, VenkateshB (2011) Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol Biol Evol 28: 1205–1215.
73. ChristoffelsA, KohEG, ChiaJM, BrennerS, AparicioS, et al. (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21: 1146–1151.
74. HoeggS, BrinkmannH, TaylorJS, MeyerA (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59: 190–203.
75. CrowKD, StadlerPF, LynchVJ, AmemiyaC, WagnerGP (2006) The “fish-specific” Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 23: 121–136.
76. LaneyJD, BigginMD (1997) Zeste-mediated activation by an enhancer is independent of cooperative DNA binding in vivo. Proc Natl Acad Sci U S A 94: 3602–3604.
77. CookPR (1999) The organization of replication and transcription. Science 284: 1790–1795.
78. OuyangZ, ZhouQ, WongWH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A 106: 21521–21526.
79. MullenAC, OrlandoDA, NewmanJJ, LovenJ, KumarRM, et al. (2011) Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell 147: 565–576.
80. LimLS, LohYH, ZhangW, LiY, ChenX, et al. (2007) Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol Biol Cell 18: 1348–1358.
81. OrianA, van SteenselB, DelrowJ, BussemakerHJ, LiL, et al. (2003) Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev 17: 1101–1114.
82. FernandezPC, FrankSR, WangL, SchroederM, LiuS, et al. (2003) Genomic targets of the human c-Myc protein. Genes Dev 17: 1115–1129.
83. ZeitlingerJ, ZinzenRP, StarkA, KellisM, ZhangH, et al. (2007) Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 21: 385–390.
84. SandmannT, GirardotC, BrehmeM, TongprasitW, StolcV, et al. (2007) A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev 21: 436–449.
85. RobertsonG, HirstM, BainbridgeM, BilenkyM, ZhaoY, et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651–657.
86. CaoY, YaoZ, SarkarD, LawrenceM, SanchezGJ, et al. (2010) Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell 18: 662–674.
87. MacQuarrieKL, FongAP, MorseRH, TapscottSJ (2011) Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 27: 141–148.
88. LiXY, ThomasS, SaboPJ, EisenMB, StamatoyannopoulosJA, et al. (2011) The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol 12: R34.
89. FujiokaM, WuX, JaynesJB (2009) A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication. Development 136: 3077–3087.
90. ChepelevI, WeiG, WangsaD, TangQ, ZhaoK (2012) Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res 22: 490–503.
91. Carmany-RampeyA, SchierAF (2001) Single-cell internalization during zebrafish gastrulation. Curr Biol 11: 1261–1265.
92. MyersDC, SepichDS, Solnica-KrezelL (2002) Convergence and extension in vertebrate gastrulae: cell movements according to or in search of identity? Trends Genet 18: 447–455.
93. Solnica-KrezelL (2006) Gastrulation in zebrafish – all just about adhesion? Curr Opin Genet Dev 16: 433–441.
94. RohdeLA, HeisenbergCP (2007) Zebrafish gastrulation: cell movements, signals, and mechanisms. Int Rev Cytol 261: 159–192.
95. BisgroveBW, EssnerJJ, YostHJ (2000) Multiple pathways in the midline regulate concordant brain, heart and gut left-right asymmetry. Development 127: 3567–3579.
96. DanosMC, YostHJ (1996) Role of notochord in specification of cardiac left-right orientation in zebrafish and Xenopus. Dev Biol 177: 96–103.
97. MorganD, TurnpennyL, GoodshipJ, DaiW, MajumderK, et al. (1998) Inversin, a novel gene in the vertebrate left-right axis pathway, is partially deleted in the inv mouse. Nat Genet 20: 149–156.
98. OttoEA, SchermerB, ObaraT, O'TooleJF, HillerKS, et al. (2003) Mutations in INVS encoding inversin cause nephronophthisis type 2, linking renal cystic disease to the function of primary cilia and left-right axis determination. Nat Genet 34: 413–420.
99. OkadaY, TakedaS, TanakaY, Izpisua BelmonteJC, HirokawaN (2005) Mechanism of nodal flow: a conserved symmetry breaking event in left-right axis determination. Cell 121: 633–644.
100. HashimotoM, ShinoharaK, WangJ, IkeuchiS, YoshibaS, et al. (2010) Planar polarization of node cells determines the rotational axis of node cilia. Nat Cell Biol 12: 170–176.
101. WangG, CadwalladerAB, JangDS, TsangM, YostHJ, et al. (2011) The Rho kinase Rock2b establishes anteroposterior asymmetry of the ciliated Kupffer's vesicle in zebrafish. Development 138: 45–54.
102. WatanabeD, SaijohY, NonakaS, SasakiG, IkawaY, et al. (2003) The left-right determinant Inversin is a component of node monocilia and other 9+0 cilia. Development 130: 1725–1734.
103. May-SimeraHL, KaiM, HernandezV, OsbornDP, TadaM, et al. (2010) Bbs8, together with the planar cell polarity protein Vangl2, is required to establish left-right asymmetry in zebrafish. Dev Biol 345: 215–225.
104. RossAJ, May-SimeraH, EichersER, KaiM, HillJ, et al. (2005) Disruption of Bardet-Biedl syndrome ciliary proteins perturbs planar cell polarity in vertebrates. Nat Genet 37: 1135–1140.
105. HeisenbergCP, TadaM (2002) Wnt signalling: a moving picture emerges from van gogh. Curr Biol 12: R126–128.
106. YenHJ, TayehMK, MullinsRF, StoneEM, SheffieldVC, et al. (2006) Bardet-Biedl syndrome genes are important in retrograde intracellular trafficking and Kupffer's vesicle cilia function. Hum Mol Genet 15: 667–677.
107. ArugaJ, TohmondaT, HommaS, MikoshibaK (2002) Zic1 promotes the expansion of dorsal neural progenitors in spinal cord by inhibiting neuronal differentiation. Dev Biol 244: 329–341.
108. Westerfield M (2000) The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th edition. Eugene: Univ. of Oregon Press.
109. KimmelCB, BallardWW, KimmelSR, UllmannB, SchillingTF (1995) Stages of embryonic development of the zebrafish. Dev Dyn 203: 253–310.
110. ValouevA, JohnsonDS, SundquistA, MedinaC, AntonE, et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5: 829–834.
111. Huang daW, ShermanBT, LempickiRA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44–57.
112. Huang daW, ShermanBT, LempickiRA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1–13.
113. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36.
114. TusherVG, TibshiraniR, ChuG (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116–5121.
115. DorskyRI, SheldahlLC, MoonRT (2002) A transgenic Lef1/beta-catenin-dependent reporter is expressed in spatially restricted domains throughout zebrafish development. Dev Biol 241: 229–237.