Barresi MJF, Hutson LD, Chien C-B, Karlstrom RO (2005) Hedgehog regulated Slit expression determines commissure and glial cell position in the zebrafish forebrain. Development 132:3643–3656. doi:10.1242/dev.01929
Becker TS, Lenhard B (2007) The random versus fragile breakage models of chromosome evolution: a matter of resolution. Mol Genet Genomics 278:487–491. doi:10.1007/s00438-007-0287-0
Beguin S, Crépel V, Aniksztejn L et al (2013) An epilepsy-related ARX polyalanine expansion modifies glutamatergic neurons excitability and morphology without affecting GABAergic neurons development. Cereb Cortex 23:1484–1494. doi:10.1093/cercor/bhs138
Berman P, Zhang Z, Wolf YI et al (2000) Winnowing sequences from a database search. J Comput Biol 7:293–302. doi:10.1089/10665270050081531
Bienvenu T, Poirier K, Friocourt G et al (2002) ARX, a novel Prd-class-homeobox gene highly expressed in the telencephalon, is mutated in X-linked mental retardation. Hum Mol Genet 11:981–991
Biressi S, Messina G, Collombat P et al (2008) The homeobox gene Arx is a novel positive regulator of embryonic myogenesis. Cell Death Differ 15:94–104. doi:10.1038/sj.cdd.4402230
Cholvin T, Loureiro M, Cassel R et al (2013) The ventral midline thalamus contributes to strategy shifting in a memory task requiring both prefrontal cortical and hippocampal functions. J Neurosci 33:8772–8783. doi:10.1523/JNEUROSCI.0771-13.2013
Colasante G, Collombat P, Raimondi V et al (2008) Arx is a direct target of Dlx2 and thereby contributes to the tangential migration of GABAergic interneurons. J Neurosci 28:10674–10686. doi:10.1523/JNEUROSCI.1283-08.2008
Colasante G, Sessa A, Crispi S et al (2009) Arx acts as a regional key selector gene in the ventral telencephalon mainly through its transcriptional repression activity. Dev Biol 334:59–71. doi:10.1016/j.ydbio.2009.07.014
Colasante G, Simonet JC, Calogero R et al (2013) ARX regulates cortical intermediate progenitor cell expansion and upper layer neuron formation through repression of Cdkn1c. Cereb Cortex. doi:10.1093/cercor/bht222
Collombat P, Mansouri A, Hecksher-Sorensen J et al (2003) Opposing actions of Arx and Pax4 in endocrine pancreas development. Genes Dev 17:2591–2603. doi:10.1101/gad.269003
Collombat P, Xu X, Ravassard P et al (2009) The ectopic expression of Pax4 in the mouse pancreas converts progenitor cells into alpha and subsequently beta cells. Cell 138:449–462. doi:10.1016/j.cell.2009.05.035
Colombo E, Galli R, Cossu G et al (2004) Mouse orthologue of ARX, a gene mutated in several X-linked forms of mental retardation and epilepsy, is a marker of adult neural stem cells and forebrain GABAergic neurons. Dev Dyn 231:631–639. doi:10.1002/dvdy.20164
Colombo E, Collombat P, Colasante G et al (2007) Inactivation of Arx, the murine ortholog of the X-linked lissencephaly with ambiguous genitalia gene, leads to severe disorganization of the ventral telencephalon with impaired neuronal migration and differentiation. J Neurosci 27:4786–4798. doi:10.1523/JNEUROSCI.0417-07.2007
Distel M, Wullimann MF, Koster RW (2009) Optimized Gal4 genetics for permanent gene expression mapping in zebrafish. Proc Natl Acad Sci USA 106:13365–13370. doi:10.1073/pnas.0903060106
Djiotsa J, Verbruggen V, Giacomotto J et al (2012) Pax4 is not essential for beta-cell differentiation in zebrafish embryos but modulates alpha-cell generation by repressing arx gene expression. BMC Dev Biol 12:37. doi:10.1186/1471-213X-12-37
Dong X, Fredman D, Lenhard B (2009) Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol 10:R86. doi:10.1186/gb-2009-10-8-r86
Engstrom PG, Fredman D, Lenhard B (2008) Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol 9:R34. doi:10.1186/gb-2008-9-2-r34
Filippi A, Mueller T, Driever W (2014) vglut2 and gad expression reveal distinct patterns of dual GABAergic versus glutamatergic cotransmitter phenotypes of dopaminergic and noradrenergic neurons in the zebrafish brain. J Comp Neurol 522:2019–2037. doi:10.1002/cne.23524
Folgueira M, Bayley P, Navratilova P et al (2012) Morphogenesis underlying the development of the everted teleost telencephalon. Neural Dev 7:32. doi:10.1186/1749-8104-7-32
Forlano PM, Bass AH (2011) Neural and hormonal mechanisms of reproductive-related arousal in fishes. Horm Behav 59:616–629. doi:10.1016/j.yhbeh.2010.10.006
Frankel N, Davis GK, Vargas D et al (2010) Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466:490–493
Fredman D, Engstrom PG, Lenhard B (2009) Web-based tools and approaches to study long-range gene regulation in Metazoa. Brief Funct Genomic Proteomic 8:231–242. doi:10.1093/bfgp/elp023
Friocourt G, Poirier K, Rakić S et al (2006) The role of ARX in cortical development. Eur J Neurosci 23:869–876. doi:10.1111/j.1460-9568.2006.04629.x
Friocourt G, Kanatani S, Tabata H et al (2008) Cell-autonomous roles of ARX in cell proliferation and neuronal migration during corticogenesis. J Neurosci 28:5794–5805. doi:10.1523/JNEUROSCI.1067-08.2008
Fullston T, Finnis M, Hackett A et al (2011) Screening and cell-based assessment of mutations in the Aristaless-related homeobox (ARX) gene. Clin Genet 80:510–522. doi:10.1111/j.1399-0004.2011.01685.x
Fulp CT, Cho G, Marsh ED et al (2008) Identification of Arx transcriptional targets in the developing basal forebrain. Hum Mol Genet 17:3740–3760. doi:10.1093/hmg/ddn271
Gecz J, Cloosterman D, Partington M (2006) ARX: a gene for all seasons. Curr Opin Genet Dev 16:308–316. doi:10.1016/j.gde.2006.04.003
Hong JW, Hendrix DA, Levine MS (2008) Shadow enhancers as a source of evolutionary novelty. Science 321:1314
Ishibashi M, Mechaly AS, Becker TS, Rinkwitz S (2013) Using zebrafish transgenesis to test human genomic sequences for specific enhancer activity. Methods 62:216–225. doi:10.1016/j.ymeth.2013.03.018
Jackman WR, Stock DW (2006) Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss. Proc Natl Acad Sci USA 103:19390–19395
Kikuta H, Fredman D, Rinkwitz S et al (2007a) Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks—a fundamental feature of vertebrate genomes. Genome Biol 8(Suppl 1):S4. doi:10.1186/gb-2007-8-s1-s4
Kikuta H, Laplante M, Navratilova P et al (2007b) Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 17:545–555. doi:10.1101/gr.6086307
Kimmel CB, Ballard WW, Kimmel SR et al (1995) Stages of embryonic development of the zebrafish. Dev Dyn 203:253–310. doi:10.1002/aja.1002030302
Kitamura K, Yanazawa M, Sugiyama N et al (2002) Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans. Nat Genet 32:359–369. doi:10.1038/ng1009
Kitamura K, Itou Y, Yanazawa M et al (2009) Three human ARX mutations cause the lissencephaly-like and mental retardation with epilepsy-like pleiotropic phenotypes in mice. Hum Mol Genet 18:3708–3724. doi:10.1093/hmg/ddp318
Komisarczuk AZ, Kawakami K, Becker TS (2009) Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split. Dev Biol 336:301–312. doi:10.1016/j.ydbio.2009.09.029
Machluf Y, Levkowitz G (2011) Visualization of mRNA expression in the zebrafish embryo. Methods Mol Biol 714:83–102. doi:10.1007/978-1-61779-005-8_6
McBride DJ, Buckle A, van Heyningen V, Kleinjan DA (2011) DNaseI hypersensitivity and ultraconservation reveal novel, interdependent long-range enhancers at the complex Pax6 cis-regulatory region. PLoS One 6:e28616. doi:10.1371/journal.pone.0028616
Miura H, Yanazawa M, Kato K, Kitamura K (1997) Expression of a novel aristaless related homeobox gene “Arx” in the vertebrate telencephalon, diencephalon and floor plate. Mech Dev 65:99–109
Mueller T (2012) What is the thalamus in zebrafish? Front Neurosci 6:64. doi:10.3389/fnins.2012.00064
Mueller T, Wullimann MF (2002) BrdU-, neuroD (nrd)- and Hu-studies reveal unusual non-ventricular neurogenesis in the postembryonic zebrafish forebrain. Mech Dev 117:123–135
Mueller T, Wullimann MF (2005) Atlas of early zebrafish brain development: a tool for molecular neurogenetics. Elsevier, Amsterdam
Mueller T, Dong Z, Berberoglu MA, Guo S (2011) The dorsal pallium in zebrafish, Danio rerio (Cyprinidae, Teleostei). Brain Res 1381:95–105. doi:10.1016/j.brainres.2010.12.089
Navratilova P, Fredman D, Hawkins TA et al (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol 327:526–540. doi:10.1016/j.ydbio.2008.10.044
Navratilova P, Fredman D, Lenhard B, Becker TS (2010) Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol Genet Genomics 283:171–184. doi:10.1007/s00438-009-0503-1
Norton WH, Mangoli M, Lele Z et al (2005) Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphé neurones and cranial motoneurones. Development 132:645–658. doi:10.1242/dev.01611
Osório J, Mueller T, Rétaux S et al (2010) Phylotypic expression of the bHLH genes Neurogenin2, Neurod, and Mash1 in the mouse embryonic forebrain. J Comp Neurol 518:851–871. doi:10.1002/cne.22247
Oxtoby E, Jowett T (1993) Cloning of the zebrafish krox-20 gene (krx-20) and its expression during hindbrain development. Nucleic Acids Res 21:1087–1095
Partington MW, Turner G, Boyle J, Gecz J (2004) Three new families with X-linked mental retardation caused by the 428-451dup(24 bp) mutation in ARX. Clin Genet 66:39–45. doi:10.1111/j.0009-9163.2004.00268.x
Perry MW, Boettiger AN, Bothma JP, Levine M (2010) Shadow enhancers foster robustness of drosophila gastrulation. Curr Biol. doi:10.1016/j.cub.2010.07.043
Popovici C, Busa T, Boute O, Thuresson AC, Perret O, Sigaudy S, Södergren T, Andrieux J, Moncla A, Philip N (2014) Whole ARX gene duplication is compatible with normal intellectual development. Am J Med Genet A 164A(9):2324–2327
Price MG, Yoo JW, Burgess DL et al (2009) A triplet repeat expansion genetic mouse model of infantile spasms syndrome, Arx(GCG)10 + 7, with interneuronopathy, spasms in infancy, persistent seizures, and adult cognitive and behavioral impairment. J Neurosci 29:8752–8763. doi:10.1523/JNEUROSCI.0915-09.2009
Punnamoottil B, Kikuta H, Pezeron G et al (2008) Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs. Dev Dyn 237:2195–2208. doi:10.1002/dvdy.21618
Quillé M-L, Carat S, Quéméner-Redon S et al (2011) High-throughput analysis of promoter occupancy reveals new targets for Arx, a gene mutated in mental retardation and interneuronopathies. PLoS One 6:e25181. doi:10.1371/journal.pone.0025181
Rada-Iglesias A, Bajpai R, Swigut T et al (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470:279–283. doi:10.1038/nature09692
Rink E, Wullimann MF (2001) The teleostean (zebrafish) dopaminergic system ascending to the subpallium (striatum) is located in the basal diencephalon (posterior tuberculum). Brain Res 889:316–330
Rink E, Wullimann MF (2004) Connections of the ventral telencephalon (subpallium) in the zebrafish (Danio rerio). Brain Res 1011:206–220. doi:10.1016/j.brainres.2004.03.027
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B (2004a) JASPAR: an open-access database for eukaryotic transcription factor binding pro- files. Nucleic Acids Res 32D:91–94
Sandelin A, Wasserman WW, Lenhard B (2004b) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 32:W249–W252
Seufert DW, Prescott NL, El-Hodiri HM (2005) Xenopus aristaless-related homeobox (xARX) gene product functions as both a transcriptional activator and repressor in forebrain development. Dev Dyn 232:313–324. doi:10.1002/dvdy.20234
Shoubridge C, Fullston T, Gecz J (2010) ARX spectrum disorders: making inroads into the molecular pathology. Hum Mutat 31:889–900. doi:10.1002/humu.21288
Sohn J, Natale J, Chew LJ, Belachew S, Cheng Y, Aguirre A, Lytle J, Nait-Oumesmar B, Kerninon C, Kanai-Azuma M, Kanai Y, Gallo V (2006) Identification of Sox17 as a transcription factor that regulates oligodendrocyte development. J Neurosci 26:9722–9735
Stromme P, Mangelsdorf ME, Shaw MA et al (2002) Mutations in the human ortholog of Aristaless cause X-linked mental retardation and epilepsy. Nat Genet 30:441–445. doi:10.1038/ng862
Turner KJ, Bracewell TG, Hawkins TA (2014) Anatomical dissection of zebrafish brain development. Methods Mol Biol 1082:197–214. doi:10.1007/978-1-62703-655-9_14
Visel A, Blow MJ, Li Z et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854–858
Visel A, Taher L, Girgis H et al (2013) A high-resolution enhancer atlas of the developing telencephalon. Cell 152:895–908. doi:10.1016/j.cell.2012.12.041
Whibley AC, Plagnol V, Tarpey PS et al (2010) Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability. Am J Hum Genet 87:173–188. doi:10.1016/j.ajhg.2010.06.017
Wilson SW, Ross LS, Parrett T, Easter SS (1990) The development of a simple scaffold of axon tracts in the brain of the embryonic zebrafish, Brachydanio rerio. Development 108:121–145
Wullimann MF, Mueller T (2004) Identification and morphogenesis of the eminentia thalami in the zebrafish. J Comp Neurol 471:37–48. doi:10.1002/cne.20011
Wullimann MF, Rupp B, Reichert H (1996) Neuroanatomy of the zebrafish brain. A topological atlas. Birkhäuser, Basel