ZFIN

ZFIN ID: ZDB-GENE-980526-333

ZFIN ID: ZDB-GENE-980526-333

CITATIONS (164 total)

Gene Name:	SRY-box transcription factor 3
Gene Symbol:	sox3

Alsakran, A.A., Gibson, B., Wong, H.Y., Heaton, C., Boreham, R., Minhas, R., Ball, J., Kudoh, T. (2025) Ethanol down-regulates gastrula gene expression and cell movement, causing symptoms of foetal alcohol spectrum disorders. Biology Open. :

Dicipulo, R., Selland, L.G., Carpenter, R.G., Waskiewicz, A.J. (2025) Functional role for Taz during hindbrain ventricle morphogenesis. PLoS One. 20:e0313262e0313262

Mai, J., Yang, L., Wang, M., Deng, J.M., Min, M., Xie, H.J., Jiang, Y.M., Sun, H.Q., Liu, X.J. (2025) Elevated Serum Homocysteine Levels Impair Embryonic Neurodevelopment by Dysregulating the Heat Shock Proteins. Developmental Neurobiology. 85:e22958e22958

Xu, W., Liu, X., Li, J., Sun, C., Chen, L., Zhou, J., Li, K., Li, Q., Meng, A., Sun, Q. (2024) ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. Cell insight. 3:100179100179

Yang, X., Zhou, W., Zhou, J., Li, A., Zhang, C., Fang, Z., Wang, C., Liu, S., Hao, A., Zhang, M. (2024) Pcgf5: An important regulatory factor in early embryonic neural induction. Heliyon. 10:e27634e27634

He, T., Sun, H., Xu, B., Qu, H., Cai, X., Zhou, H., Liu, Y., Lin, Z., Zhang, X. (2023) Novel bi-allelic variants of CHMP1A contribute to pontocerebellar hypoplasia type 8: additional clinical and genetic evidence. Frontiers in neurology. 14:12282181228218

Shih, H.Y., Chang, C.W., Chen, Y.C., Cheng, Y.C. (2023) Identification of the Time Period during Which BMP Signaling Regulates Proliferation of Neural Progenitor Cells in Zebrafish. International Journal of Molecular Sciences. 24(2):

Silva, N., Campinho, M.A. (2023) In a zebrafish biomedical model of human Allan-Herndon-Dudley syndrome impaired MTH signaling leads to decreased neural cell diversity. Frontiers in endocrinology. 14:11576851157685

Yuikawa, T., Sato, T., Ikeda, M., Tsuruoka, M., Yasuda, K., Sato, Y., Nasu, K., Yamasu, K. (2023) Elongation of the developing spinal cord is driven by Oct4-type transcription factor-mediated regulation of retinoic acid signaling in zebrafish embryos. Developmental Dynamics : an official publication of the American Association of Anatomists. 253(4):404-422

Baek, S., Tran, N.T.T., Diaz, D.C., Tsai, Y.Y., Acedo, J.N., Lush, M.E., Piotrowski, T. (2022) Single-cell transcriptome analysis reveals three sequential phases of gene expression during zebrafish sensory hair cell regeneration. Developmental Cell. 57(6):799-819.e6

Gao, M., Veil, M., Rosenblatt, M., Riesle, A.J., Gebhard, A., Hass, H., Buryanova, L., Yampolsky, L.Y., Grüning, B., Ulianov, S.V., Timmer, J., Onichtchouk, D. (2022) Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nature communications. 13:788

Liu, Y., Lin, Z., Peng, Y., Jiang, Y., Zhang, X., Zhu, H., Zhang, L., Chen, J., Shu, X., Luo, M., Xie, D., Chen, Y., Liao, H., Liu, M., Zhang, X., Liu, S., Wang, H., Zhou, B., Sun, H. (2022) Embryonic organizer formation disorder leads to multiorgan dysplasia in Down syndrome. Cell Death & Disease. 13:10541054

Lo, Y.H., Huang, Y.S., Chang, Y.C., Hung, P.Y., Wang, W.D., Liu, W., Urade, R., Wen, Z.H., Wu, C.Y. (2022) GTP-Binding Protein 1-Like (GTPBP1l) Regulates Vascular Patterning during Zebrafish Development. Biomedicines. 10(12):

Michel, L., Palma, K., Cerda, M., Lagadec, R., Mayeur, H., Fuentès, M., Besseau, L., Martin, P., Magnanou, E., Blader, P., Concha, M.L., Mazan, S. (2022) Diversification of habenular organization and asymmetries in teleosts: Insights from the Atlantic salmon and European eel. Frontiers in cell and developmental biology. 10:1015074

Okada, K., Aoki, K., Tabei, T., Sugio, K., Imai, K., Bonkohara, Y., Kamachi, Y. (2022) Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9. Nucleic acids research. 50(5):2854-2871

Westphal, M., Panza, P., Kastenhuber, E., Wehrle, J., Driever, W. (2022) Wnt/β-catenin signaling promotes neurogenesis in the diencephalospinal dopaminergic system of embryonic zebrafish. Scientific Reports. 12:1030

Yang, M., Liu, Y., Lin, Z., Sun, H., Hu, T. (2022) A novel de novo missense mutation in EFTUD2 identified by whole-exome sequencing in mandibulofacial dysostosis with microcephaly. Journal of clinical laboratory analysis. 36(5):e24440

Yao, S., Zhou, X., Vona, B., Fan, L., Zhang, C., Li, D., Yuan, H., Du, Y., Ma, L., Pan, Y. (2022) Skeletal Class III Malocclusion Is Associated with ADAMTS2 Variants and Reduced Expression in a Familial Case. International Journal of Molecular Sciences. 23(18)

Zou, T.T., Sun, H.Q., Zhu, Y., He, T.T., Ling, W.W., Zhu, H.M., Lin, Z.Y., Liu, Y.Y., Liu, S.L., Wang, H., Zhang, X.M. (2022) Compound heterozygous variations in IARS1 cause recurrent liver failure and growth retardation in a Chinese patient: a case report. BMC pediatrics. 22:329

Blanc, M., Antczak, P., Cousin, X., Grunau, C., Scherbak, N., Rüegg, J., Keiter, S.H. (2021) The insecticide permethrin induces transgenerational behavioral changes linked to transcriptomic and epigenetic alterations in zebrafish (Danio rerio). The Science of the total environment. 779:146404

Li, X., Ji, G., Zhou, J., Du, J., Li, X., Shi, W., Hu, Y., Zhou, W., Hao, A. (2021) Pcgf1 Regulates Early Neural Tube Development Through Histone Methylation in Zebrafish. Frontiers in cell and developmental biology. 8:581636

Metikala, S., Casie Chetty, S., Sumanas, S. (2021) Single-cell transcriptome analysis of the zebrafish embryonic trunk. PLoS One. 16:e0254024

Mukaigasa, K., Sakuma, C., Yaginuma, H. (2021) The developmental hourglass model is applicable to the spinal cord based on single-cell transcriptomes and non-conserved cis-regulatory elements. Development, growth & differentiation. 63(7):372-391

Ogita, Y., Tamura, K., Mawaribuchi, S., Takamatsu, N., Ito, M. (2021) Independent pseudogenizations and losses of sox15 during amniote diversification following asymmetric ohnolog evolution. BMC ecology and evolution. 21:134

Ranawakage, D.C., Okada, K., Sugio, K., Kawaguchi, Y., Kuninobu-Bonkohara, Y., Takada, T., Kamachi, Y. (2021) Efficient CRISPR-Cas9-Mediated Knock-In of Composite Tags in Zebrafish Using Long ssDNA as a Donor. Frontiers in cell and developmental biology. 8:598634

Yuikawa, T., Ikeda, M., Tsuda, S., Saito, S., Yamasu, K. (2021) Involvement of Oct4-type transcription factor Pou5f3 in posterior spinal cord formation in zebrafish embryos. Development, growth & differentiation. 63(6):306-322

Zafar, I., Iftikhar, R., Ahmad, S.U., Rather, M.A. (2021) Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio). Biotechnology reports (Amsterdam, Netherlands). 30:e00607

Hawkey-Noble, A., Umali, J., Fowler, G., French, C.R. (2020) Expression of three P4- phospholipid Flippases-atp11a, atp11b, and atp11c in zebrafish (Danio rerio). Gene expression patterns : GEP. 36:119115

Huang, X., Wu, C., Gong, K., Chen, Q., Gu, Q., Qin, H., Zhao, C., Yu, T., Yang, L., Fu, W., Wang, Y., Qin, Q., Liu, S. (2020) Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus. Frontiers in genetics. 11:804

Liu, Y., Lin, Z., Sun, H. (2020) Cystic fibrosis transmembrane conductance regulator (CFTR) regulates embryonic organizer formation during zebrafish early embryogenesis. The International journal of developmental biology. 64:409-413

Pak, B., Schmitt, C.E., Choi, W., Kim, J.D., Han, O., Alsiö, J., Jung, D.W., Williams, D.R., Coppieters, W., Stainier, D.Y.R., Jin, S.W. (2020) Analyses of Avascular Mutants Reveal Unique Transcriptomic Signature of Non-conventional Endothelial Cells. Frontiers in cell and developmental biology. 8:589717

Tambalo, M., Mitter, R., Wilkinson, D.G. (2020) A single cell transcriptome atlas of the developing zebrafish hindbrain. Development (Cambridge, England). 147(6):

Wang, B., Dong, J., Xiao, H., Li, Y., Jin, Y., Cui, M., Zhang, S.Q., Fan, S.J. (2020) Metformin fights against radiation-induced early developmental toxicity. The Science of the total environment. 732:139274

Weger, M., Weger, B.D., Schink, A., Takamiya, M., Stegmaier, J., Gobet, C., Parisi, A., Kobitski, A.Y., Mertes, J., Krone, N., Strähle, U., Nienhaus, G.U., Mikut, R., Gachon, F., Gut, P., Dickmeis, T. (2020) MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly. eLIFE. 9:

Inomata, C., Yuikawa, T., Nakayama-Sadakiyo, Y., Kobayashi, K., Ikeda, M., Chiba, M., Konishi, C., Ishioka, A., Tsuda, S., Yamasu, K. (2019) Involvement of an Oct4-related PouV gene, pou5f3/pou2, in neurogenesis in the early neural plate of zebrafish embryos. Developmental Biology. 457(1):30-42

Li, X., Zhou, W., Li, X., Gao, M., Ji, S., Tian, W., Ji, G., Du, J., Hao, A. (2019) SOX19b regulates the premature neuronal differentiation of neural stem cells through EZH2-mediated histone methylation in neural tube development of zebrafish. Stem Cell Research & Therapy. 10:389

Sun, Y., Zhang, B., Luo, L., Shi, D.L., Wang, H., Cui, Z., Huang, H., Cao, Y., Shu, X., Zhang, W., Zhou, J., Li, Y., Du, J., Zhao, Q., Chen, J., Zhong, H., Zhong, T.P., Li, L., Xiong, J.W., Peng, J., Xiao, W., Zhang, J., Yao, J., Yin, Z., Mo, X., Peng, G., Zhu, J., Chen, Y., Zhou, Y., Liu, D., Pan, W., Zhang, Y., Ruan, H., Liu, F., Zhu, Z., Meng, A., ZAKOC Consortium (2019) Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9. Genome research. 30(1):118-26

Yan, Y., Ning, G., Li, L., Liu, J., Yang, S., Cao, Y., Wang, Q. (2019) The BMP ligand Pinhead together with Admp supports the robustness of embryonic patterning. Science advances. 5:eaau6455

Almuedo-Castillo, M., Bläßle, A., Mörsdorf, D., Marcon, L., Soh, G.H., Rogers, K.W., Schier, A.F., Müller, P. (2018) Scale-invariant patterning by size-dependent inhibition of Nodal signalling. Nature cell biology. 20(9):1032-1042

Gou, Y., Guo, J., Maulding, K., Riley, B.B. (2018) sox2 and sox3 cooperate to regulate otic/epibranchial placode induction in zebrafish. Developmental Biology. 435(1):84-95

Gou, Y., Vemaraju, S., Sweet, E.M., Kwon, H.J., Riley, B.B. (2018) sox2 and sox3 play unique roles in development of hair cells and neurons in the zebrafish inner ear. Developmental Biology. 435(1):73-83

Hong, Q., Li, C., Ying, R., Lin, H., Li, J., Zhao, Y., Cheng, H., Zhou, R. (2018) Loss-of-function of sox3 causes follicle development retardation and reduces fecundity in zebrafish. Protein & cell. 10(5):347-364

Kobayashi, K., Khan, A., Ikeda, M., Nakamoto, A., Maekawa, M., Yamasu, K. (2018) In vitro analysis of the transcriptional regulatory mechanism of zebrafish pou5f3. Experimental cell research. 364(1):28-41

Lagadec, R., Lanoizelet, M., Sánchez-Farías, N., Hérard, F., Menuet, A., Mayeur, H., Billoud, B., Rodriguez-Moldes, I., Candal, E., Mazan, S. (2018) Neurogenetic asymmetries in the catshark developing habenulae: mechanistic and evolutionary implications. Scientific Reports. 8:4616

Vopalensky, P., Pralow, S., Vastenhouw, N.L. (2018) Reduced expression of the Nodal coreceptor Oep causes loss of mesendodermal competence in zebrafish. Development (Cambridge, England). 145(5)

Yan, L., Chen, J., Zhu, X., Sun, J., Wu, X., Shen, W., Zhang, W., Tao, Q., Meng, A. (2018) Maternal Huluwa dictates the embryonic body axis through β-catenin in vertebrates. Science (New York, N.Y.). 362(6417)

Chang, H.W., Wang, W.D., Chiu, C.C., Chen, C.H., Wang, Y.S., Chen, Z.Y., Liu, W., Tai, M.H., Wen, Z.H., Wu, C.Y. (2017) Ftr82 Is Critical for Vascular Patterning during Zebrafish Development. International Journal of Molecular Sciences. 18(1)

Ciarlo, C., Kaufman, C.K., Kinikoglu, B., Michael, J., Yang, S., D Amato, C., Blokzijl-Franke, S., den Hertog, J., Schlaeger, T.M., Zhou, Y., Liao, E., Zon, L.I. (2017) A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development. eLIFE. 6

Gross-Thebing, T., Yigit, S., Pfeiffer, J., Reichman-Fried, M., Bandemer, J., Ruckert, C., Rathmer, C., Goudarzi, M., Stehling, M., Tarbashevich, K., Seggewiss, J., Raz, E. (2017) The Vertebrate Protein Dead End Maintains Primordial Germ Cell Fate by Inhibiting Somatic Differentiation. Developmental Cell. 43:704-715.e5

Nakayama, Y., Inomata, C., Yuikawa, T., Tsuda, S., Yamasu, K. (2017) Comprehensive analysis of target genes in zebrafish embryos reveals gbx2 involvement in neurogenesis. Developmental Biology. 430(1):237-248

Song, Y.C., Wu, B.J., Chiu, C.C., Chen, C.L., Zhou, J.Q., Liang, S.R., Duh, C.Y., Sung, P.J., Wen, Z.H., Wu, C.Y. (2017) Coral-Derived Natural Marine Compound GB9 Impairs Vascular Development in Zebrafish. International Journal of Molecular Sciences. 18(8)

Veil, M., Schaechtle, M.A., Gao, M., Kirner, V., Buryanova, L., Grethen, R., Onichtchouk, D. (2017) Maternal Nanog is critical for the zebrafish embryo architecture and for cell viability during gastrulation. Development (Cambridge, England). 145(1)

Wei, S., Dai, M., Liu, Z., Ma, Y., Shang, H., Cao, Y., Wang, Q. (2017) The guanine nucleotide exchange factor Net1 facilitates the specification of dorsal cell fates in zebrafish embryos by promoting maternal β-catenin activation. Cell Research. 27(2):202-225

Wu, T.Y., Wang, Y.S., Song, Y.C., Chen, Z.Y., Chen, Y.T., Chiu, C.C., Wu, C.Y. (2017) Fine-tune regulation of carboxypeptidase N1 controls vascular patterning during zebrafish development. Scientific Reports. 7:1852

Gore, A.V., Athans, B., Iben, J.R., Johnson, K., Russanova, V., Castranova, D., Pham, V.N., Butler, M.G., Williams-Simons, L., Nichols, J.T., Bresciani, E., Feldman, B., Kimmel, C.B., Liu, P.P., Weinstein, B.M. (2016) Epigenetic regulation of hematopoiesis by DNA methylation. eLIFE. 5:e11813

Hagey, D.W., Zaouter, C., Combeau, G., Andersson Lendahl, M., Andersson, O., Huss, M., Muhr, J. (2016) Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells. Genome research. 26(7):908-17

Hrubik, J., Glisic, B., Samardzija, D., Stanic, B., Pogrmic-Majkic, K., Fa, S., Andric, N. (2016) Effect of PMA-induced protein kinase C activation on development and apoptosis in early zebrafish embryos. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 190:24-31

Muthu, V., Eachus, H., Ellis, P., Brown, S., Placzek, M. (2016) Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus. Development (Cambridge, England). 143(14):2651-63

Shi, W., Chen, X., Wang, F., Gao, M., Yang, Y., Du, Z., Wang, C., Yao, Y., He, K., Hao, A. (2016) ZDHHC16 Modulates FGF/ERK Dependent Proliferation of Neural Stem/Progenitor Cells in the Zebrafish Telencephalon. Developmental Neurobiology. 76(9):1014-28

Cheng, Y.C., Chiang, M.C., Shih, H.Y., Ma, T.L., Yeh, T.H., Huang, Y.C., Lin, C.Y., Lin, S.J. (2015) The transcription factor hairy/E(spl)-related 2 induces proliferation of neural progenitors and regulates neurogenesis and gliogenesis. Developmental Biology. 397(1):116-28

Deng, C., Chen, H., Yang, N., Feng, Y., Hsueh, A.J. (2015) Apela regulates fluid homeostasis by binding to the APJ receptor to activate Gi signaling. The Journal of biological chemistry. 290(30):18261-8

Diotel, N., Viales, R.R., Armant, O., März, M., Ferg, M., Rastegar, S., Strähle, U. (2015) Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. The Journal of comparative neurology. 523(8):1202-21

Elkon, R., Milon, B., Morrison, L., Shah, M., Vijayakumar, S., Racherla, M., Leitch, C.C., Silipino, L., Hadi, S., Weiss-Gayet, M., Barras, E., Schmid, C.D., Ait-Lounis, A., Barnes, A., Song, Y., Eisenman, D.J., Eliyahu, E., Frolenkov, G.I., Strome, S.E., Durand, B., Zaghloul, N.A., Jones, S.M., Reith, W., Hertzano, R. (2015) RFX transcription factors are essential for hearing in mice. Nature communications. 6:8549

Ma, Y., Liu, X., Liu, Z., Wei, S., Shang, H., Xue, Y., Cao, Y., Meng, A., Wang, Q. (2015) The Chromatin Remodeling Protein Bptf Promotes Posterior Neuroectodermal Fate by Enhancing Smad2-Activated wnt8a Expression. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35:8493-506

Satija, R., Farrell, J.A., Gennert, D., Schier, A.F., Regev, A. (2015) Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol.. 33(5):495-502

Takamiya, M., Weger, B.D., Schindler, S., Beil, T., Yang, L., Armant, O., Ferg, M., Schlunck, G., Reinhard, T., Dickmeis, T., Rastegar, S., Strähle, U. (2015) Molecular Description of Eye Defects in the Zebrafish Pax6b Mutant, sunrise, Reveals a Pax6b-Dependent Genetic Network in the Developing Anterior Chamber. PLoS One. 10:e0117645

van Boxtel, A.L., Chesebro, J.E., Heliot, C., Ramel, M.C., Stone, R.K., Hill, C.S. (2015) A Temporal Window for Signal Activation Dictates the Dimensions of a Nodal Signaling Domain. Developmental Cell. 35:175-185

Wang, C., Chen, X., Shi, W., Wang, F., Du, Z., Li, X., Yao, Y., Liu, T., Shao, T., Li, G., Hao, A. (2015) 2-bromopalmitate impairs neural stem/progenitor cell proliferation, promotes cell apoptosis and induces malformation in zebrafish embryonic brain. Neurotoxicology and teratology. 50:53-63

Wang, Y., Lu, Y., Zhang, Y., Ning, Z., Li, Y., Zhao, Q., Lu, H., Huang, R., Xia, X., Feng, Q., Liang, X., Liu, K., Zhang, L., Lu, T., Huang, T., Fan, D., Weng, Q., Zhu, C., Lu, Y., Li, W., Wen, Z., Zhou, C., Tian, Q., Kang, X., Shi, M., Zhang, W., Jang, S., Du, F., He, S., Liao, L., Li, Y., Gui, B., He, H., Ning, Z., Yang, C., He, L., Luo, L., Yang, R., Luo, Q., Liu, X., Li, S., Huang, W., Xiao, L., Lin, H., Han, B., Zhu, Z. (2015) The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. Nature Genetics. 47(6):625-31

Yue, H., Li, C., Du, H., Zhang, S., Wei, Q. (2015) Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis). PLoS One. 10:e0127332

Chen, X., Shi, W., Wang, F., Du, Z., Yang, Y., Gao, M., Yao, Y., He, K., Wang, C., Hao, A. (2014) Zinc finger DHHC-type containing 13 regulates fate specification of ectoderm and mesoderm cell lineages by modulating Smad6 activity. Stem cells and development. 23(16):1899-909

Corrales, J., Fang, X., Thornton, C., Mei, W., Barbazuk, W.B., Duke, M., Scheffler, B.E., Willett, K.L. (2014) Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 163:37-46

Han, X., Gui, B., Xiong, C., Zhao, L., Liang, J., Sun, L., Yang, X., Yu, W., Si, W., Yan, R., Yi, X., Zhang, D., Li, W., Li, L., Yang, J., Wang, Y., Sun, Y.E., Zhang, D., Meng, A., Shang, Y. (2014) Destabilizing LSD1 by Jade-2 promotes neurogenesis: an antibraking system in neural development. Molecular Cell. 55:482-94

Maulding, K., Padanad, M.S., Dong, J., Riley, B.B. (2014) Mesodermal Fgf10b cooperates with other Fgfs during induction of otic and epibranchial placodes in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 243(10):1275-85

Pavlou, S., Astell, K., Kasioulis, I., Gakovic, M., Baldock, R., van Heyningen, V., and Coutinho, P. (2014) Pleiotropic effects of Sox2 during the development of the zebrafish epithalamus. PLoS One. 9(1):e87546

Yao, D., Zhao, F., Wu, Y., Wang, J., Wei, D., Zhao, J., Zhu, Z., Liu, D. (2014) Dissecting the differentiation process of the pre-placodal ectoderm in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 243(10):1338-51

Konzer, A., Ruhs, A., Braun, H., Jungblut, B., Braun, T., and Krueger, M. (2013) Stable Isotope Labeling in Zebrafish Allows in Vivo Monitoring of Cardiac Morphogenesis. Molecular & cellular proteomics : MCP. 12(6):1502-12

Kuo, C.L., Lam, C.M., Hewitt, J.E., and Scotting, P.J. (2013) Formation of the Embryonic Organizer Is Restricted by the Competitive Influences of Fgf Signaling and the SoxB1 Transcription Factors. PLoS One. 8(2):e57698

Lee, M.T., Bonneau, A.R., Takacs, C.M., Bazzini, A.A., Divito, K.R., Fleming, E.S., and Giraldez, A.J. (2013) Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature. 503(7476):360-4

Leichsenring, M., Maes, J., Mössner, R., Driever, W., and Onichtchouk, D. (2013) Pou5f1 transcription factor controls zygotic gene activation in vertebrates. Science (New York, N.Y.). 341(6149):1005-1009

McCarroll, M.N., and Nechiporuk, A.V. (2013) Fgf3 and Fgf10a work in concert to promote maturation of the epibranchial placodes in zebrafish. PLoS One. 8(12):e85087

Riesco, M.F., and Robles, V. (2013) Cryopreservation Causes Genetic and Epigenetic Changes in Zebrafish Genital Ridges. PLoS One. 8(6):e67614

Sarras, M.P., Leontovich, A.A., Olsen, A.S., and Intine, R.V. (2013) Impaired tissue regeneration corresponds with altered expression of developmental genes that persists in the metabolic memory state of diabetic zebrafish. Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society. 21(2):320-328

Garnett, A.T., Square, T.A., and Medeiros, D.M. (2012) BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border. Development (Cambridge, England). 39(22):4220-4231

Martin, B.L., and Kimelman, D. (2012) Canonical Wnt Signaling Dynamically Controls Multiple Stem Cell Fate Decisions during Vertebrate Body Formation. Developmental Cell. 22(1):223-232

Padanad, M.S., Bhat, N., Guo, B., and Riley, B.B. (2012) Conditions that influence the response to Fgf during otic placode induction. Developmental Biology. 364(1):1-10

Takesono, A., Moger, J., Faroq, S., Cartwright, E., Dawid, I.B., Wilson, S.W., and Kudoh, T. (2012) Solute carrier family 3 member 2 (Slc3a2) controls yolk syncytial layer (YSL) formation by regulating microtubule networks in the zebrafish embryo. Proceedings of the National Academy of Sciences of the United States of America. 109(9):3371-3376

Wang, X., Kopinke, D., Lin, J., McPherson, A.D., Duncan, R.N., Otsuna, H., Moro, E., Hoshijima, K., Grunwald, D.J., Argenton, F., Chien, C.B., Murtaugh, L.C., and Dorsky, R.I. (2012) Wnt signaling regulates postembryonic hypothalamic progenitor differentiation. Developmental Cell. 23(3):624-636

Bhat, N., and Riley, B.B. (2011) Integrin-α5 Coordinates Assembly of Posterior Cranial Placodes in Zebrafish and Enhances Fgf-Dependent Regulation of Otic/Epibranchial Cells. PLoS One. 6(12):e27778

Chung, P.C., Lin, W.S., Scotting, P.J., Hsieh, F.Y., Wu, H.L., and Cheng, Y.C. (2011) Zebrafish her8a is activated by Su(H)-dependent Notch signaling and is essential for the inhibition of neurogenesis. PLoS One. 6(4):e19394

Ko, C.Y., Tsai, M.Y., Tseng, W.F., Cheng, C.H., Huang, C.R., Wu, J.S., Chung, H.Y., Hsieh, C.S., Sun, C.K., Hwang, S.P., Yuh, C.H., Huang, C.J., Pai, T.W., Tzou, W.S., and Hu, C.H. (2011) Integration of CNS survival and differentiation by HIF2α. Cell death and differentiation. 18(11):1757-70

Padanad, M.S., and Riley, B.B. (2011) Pax2/8 proteins coordinate sequential induction of otic and epibranchial placodes through differential regulation of foxi1, sox3 and fgf24. Developmental Biology. 351(1):90-98

Takano, A., Zochi, R., Hibi, M., Terashima, T., and Katsuyama, Y. (2011) Function of strawberry notch Family Genes in the Zebrafish Brain Development. The Kobe journal of medical sciences. 56(5):E220-E230

Webb, K.J., Coolen, M., Gloeckner, C.J., Stigloher, C., Bahn, B., Topp, S., Ueffing, M., and Bally-Cuif, L. (2011) The Enhancer of split transcription factor Her8a is a novel dimerisation partner for Her3 that controls anterior hindbrain neurogenesis in zebrafish. BMC Developmental Biology. 11(1):27

Wu, S.F., Zhang, H., and Cairns, B.R. (2011) Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome research. 21(4):578-89

Ahn, H.J., Park, Y., Kim, S., Park, H.C., Seo, S.K., Yeo, S.Y., and Geum, D. (2010) The expression profile and function of Satb2 in zebrafish embryonic development. Molecules and cells. 30(4):377-382

Cruz, C., Maegawa, S., Weinberg, E.S., Wilson, S.W., Dawid, I.B., and Kudoh, T. (2010) Induction and patterning of trunk and tail neural ectoderm by the homeobox gene eve1 in zebrafish embryos. Proceedings of the National Academy of Sciences of the United States of America. 107(8):3564-3569

Gonzalez-Quevedo, R., Lee, Y., Poss, K.D., and Wilkinson, D.G. (2010) Neuronal Regulation of the Spatial Patterning of Neurogenesis. Developmental Cell. 18(1):136-147

Harrington, M.J., Chalasani, K., and Brewster, R. (2010) Cellular mechanisms of posterior neural tube morphogenesis in the zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 239(3):747-762

Kwon, H.J., Bhat, N., Sweet, E.M., Cornell, R.A., and Riley, B.B. (2010) Identification of early requirements for preplacodal ectoderm and sensory organ development. PLoS Genetics. 6(9):pii: e1001133

Lindeman, L.C., Reiner, A.H., Mathavan, S., Aleström, P., and Collas, P. (2010) Tiling histone h3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. PLoS One. 5(12):e15651

Lindeman, L.C., Winata, C.L., Aanes, H., Mathavan, S., Alestrom, P., and Collas, P. (2010) Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos. The International journal of developmental biology. 54(5):803-813

Okuda, Y., Ogura, E., Kondoh, H., and Kamachi, Y. (2010) B1 SOX coordinate cell specification with patterning and morphogenesis in the early zebrafish embryo. PLoS Genetics. 6:e1000936

Shih, Y.H., Kuo, C.L., Hirst, C.S., Dee, C.T., Liu, Y.R., Laghari, Z.A., and Scotting, P.J. (2010) SoxB1 transcription factors restrict organizer gene expression by repressing multiple events downstream of Wnt signalling. Development (Cambridge, England). 137(16):2671-2681

Gribble, S.L., Kim, H.S., Bonner, J., Wang, X., and Dorsky, R.I. (2009) Tcf3 inhibits spinal cord neurogenesis by regulating sox4a expression. Development (Cambridge, England). 136(5):781-789

Jia, S., Wu, D., Xing, C., and Meng, A. (2009) Smad2/3 activities are required for induction and patterning of the neuroectoderm in zebrafish. Developmental Biology. 333(2):273-284

Navratilova, P., Fredman, D., Hawkins, T.A., Turner, K., Lenhard, B., and Becker, T.S. (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Developmental Biology. 327(2):526-540

Nikolaou, N., Watanabe-Asaka, T., Gerety, S., Distel, M., Köster, R.W., and Wilkinson, D.G. (2009) Lunatic fringe promotes the lateral inhibition of neurogenesis. Development (Cambridge, England). 136(15):2523-2533

Rossi, C.C., Kaji, T., and Artinger, K.B. (2009) Transcriptional control of Rohon-Beard sensory neuron development at the neural plate border. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(4):931-943

Bonner, J., Gribble, S.L., Veien, E.S., Nikolaus, O.B., Weidinger, G., and Dorsky, R.I. (2008) Proliferation and patterning are mediated independently in the dorsal spinal cord downstream of canonical Wnt signaling. Developmental Biology. 313(1):398-407

Dee, C.T., Hirst, C.S., Shih, Y.H., Tripathi, V.B., Patient, R.K., and Scotting, P.J. (2008) Sox3 regulates both neural fate and differentiation in the zebrafish ectoderm. Developmental Biology. 320(1):289-301

Kamachi, Y., Okuda, Y., and Kondoh, H. (2008) Quantitative assessment of the knockdown efficiency of morpholino antisense oligonucleotides in zebrafish embryos using a luciferase assay. Genesis (New York, N.Y. : 2000). 46(1):1-7

Lemeer, S., Jopling, C., Gouw, J.W., Mohammed, S., Heck, A.J., Slijper, M., and den Hertog, J. (2008) Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos. Molecular & cellular proteomics : MCP. 7(11):2176-2187

Dee, C.T., Gibson, A., Rengifo, A., Sun, S.K., Patient, R.K., and Scotting, P.J. (2007) A change in response to Bmp signalling precedes ectodermal fate choice. The International journal of developmental biology. 51(1):79-84

Harrington, M.J., Hong, E., Fasanmi, O., and Brewster, R. (2007) Cadherin-mediated adhesion regulates posterior body formation. BMC Developmental Biology. 7(1):130

Londin, E.R., Mentzer, L., and Sirotkin, H.I. (2007) Churchill regulates cell movement and mesoderm specification by repressing Nodal signaling. BMC Developmental Biology. 7(1):120

Loucks, E.J., Schwend, T., and Ahlgren, S.C. (2007) Molecular changes associated with teratogen-induced cyclopia. Birth defects research. Part A, Clinical and molecular teratology. 79(9):642-651

Nikaido, M., Doi, K., Shimizu, T., Hibi, M., Kikuchi, Y., and Yamasu, K. (2007) Initial specification of the epibranchial placode in zebrafish embryos depends on the fibroblast growth factor signal. Developmental Dynamics : an official publication of the American Association of Anatomists. 236(2):564-571

O'Boyle, S., Bree, R.T., McLoughlin, S., Grealy, M., and Byrnes, L. (2007) Identification of zygotic genes expressed at the midblastula transition in zebrafish. Biochemical and Biophysical Research Communications. 358(2):462-468

Sun, S.K., Dee, C.T., Tripathi, V.B., Rengifo, A., Hirst, C.S., and Scotting, P.J. (2007) Epibranchial and otic placodes are induced by a common Fgf signal, but their subsequent development is independent. Developmental Biology. 303(2):675-686

Diks, S.H., Bink, R.J., van de Water, S., Joore, J., van Rooijen, C., Verbeek, F.J., den Hertog, J., Peppelenbosch, M.P., and Zivkovic, D. (2006) The novel gene asb11: a regulator of the size of the neural progenitor compartment. The Journal of cell biology. 174(4):581-592

Gulati-Leekha, A., and Goldman, D. (2006) A reporter-assisted mutagenesis screen using α1-tubulin-GFP transgenic zebrafish uncovers missteps during neuronal development and axonogenesis. Developmental Biology. 296(1):29-47

Lee, J.E., Wu, S.F., Goering, L.M., and Dorsky, R.I. (2006) Canonical Wnt signaling through Lef1 is required for hypothalamic neurogenesis. Development (Cambridge, England). 133(22):4451-4461

Okuda, Y., Yoda, H., Uchikawa, M., Furutani-Seiki, M., Takeda, H., Kondoh, H., Kamachi, Y. (2006) Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(3):811-825

Zhong, L., Yu, X., and Tong, J. (2006) Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution. Genetics, selection, evolution : GSE. 38(6):673-687

Cavodeassi, F., Carreira-Barbosa, F., Young, R., Concha, M., Allende, M.L., Houart, C., Tada, M., and Wilson, S. (2005) Early Stages of Zebrafish Eye Formation Require the Coordinated Activity of Wnt11, Fz5, and the Wnt/Catenin Pathway. Neuron. 47(1):43-56

Formstone, C.J., and Mason, I. (2005) Combinatorial activity of Flamingo proteins directs convergence and extension within the early zebrafish embryo via the planar cell polarity pathway. Developmental Biology. 282(2):320-335

Gestri, G., Carl, M., Appolloni, I., Wilson, S.W., Barsacchi, G., and Andreazzoli, M. (2005) Six3 functions in anterior neural plate specification by promoting cell proliferation and inhibiting Bmp4 expression. Development (Cambridge, England). 132(10):2401-2413

Katoh, Y., and Katoh, M. (2005) Comparative genomics on SOX2 orthologs. Oncology reports. 14(3):797-800

Kudoh, T., Concha, M.L., Houart, C., Dawid, I.B., and Wilson, S.W. (2004) Combinatorial Fgf and Bmp signalling patterns the gastrula ectoderm into prospective neural and epidermal domains. Development (Cambridge, England). 131(15):3581-3592

Rentzsch, F., Bakkers, J., Kramer, C., and Hammerschmidt, M. (2004) Fgf signaling induces posterior neuroectoderm independently of Bmp signaling inhibition. Developmental Dynamics : an official publication of the American Association of Anatomists. 231(4):750-757

Zhang, C., Basta, T., Hernandez-Lagunas, L., Simpson, P., Stemple, D.L., Artinger, K.B., and Klymkowsky, M.W. (2004) Repression of nodal expression by maternal B1-type SOXs regulates germ layer formation in Xenopus and zebrafish. Developmental Biology. 273(1):23-37

Nanda, I., Haaf, T., Schartl, M., Schmid, M., and Burt, D.W. (2002) Comparative mapping of Z-orthologous genes in vertebrates: implications for the evolution of avian sex chromosomes. Cytogenetic and genome research. 99(1-4):178-184

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

Tsang, M., Kim, R., De Caestecker, M.P., Kudoh, T., Roberts, A.B., and Dawid, I.B. (2000) Zebrafish nma is involved in TGFb family signaling. Genesis (New York, N.Y. : 2000). 28(2):47-57

Additional Citations (29):

Zebrafish Nomenclature Committee (2025) Nomenclature Data Curation (2025). Nomenclature Committee Submission.

ZFIN Staff (2023) Automated Curation of UniProt Database Links. Automated Data Submission.

Zebrafish Nomenclature Committee (2020) Nomenclature Data Curation (2020). Nomenclature Committee Submission.

ZFIN Staff (2020) Addition of links from ZFIN to Expression Atlas. Semi-automated Curation.

ZFIN Staff (2017) Curation of PANTHER Gene IDs. Automated Data Submission.

ZFIN Staff (2017) Curation of Alliance of Genome Resources Database Links. Automated Data Submission.

ZFIN Staff (2015) Data Model Change: Sequence Targeting Reagents Removed from Environment. ZFIN Historical Data.

ZFIN Staff (2013) Semi-automated association of ENSDARG identifiers with ZFIN genes for the ZMP project. Semi-automated Curation.

UniProt-GOA (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries. Manually curated data.

UniProt-GOA (2011) Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries. Manually curated data.

Gaudet, P., Livstone, M., Thomas, P., The Reference Genome Project (2010) Annotation inferences using phylogenetic trees. Automated Data Submission.

Moens, C.B. and ZFIN Staff (2009) Curation of TILLING Database Links. ZFIN Direct Data Submission.

ZIRC and ZFIN Staff (2008) Mutant and Transgenic Line Submissions 2008. ZFIN Direct Data Submission.

GOA curators, UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping. Manually curated data.

ZFIN Staff (2007) Microarray Expression to Gene Association in ZFIN. Semi-automated Curation.

ZFIN Staff (2006) Curation of Ensembl Database Links. Automated Data Submission.

ZFIN Staff (2004) ZGC Data Curation and Association in ZFIN by ZFIN Staff. Semi-automated Curation.

Rauch, G.J., Lyons, D.A., Middendorf, I., Friedlander, B., Arana, N., Reyes, T., and Talbot, W.S. (2003) Submission and Curation of Gene Expression Data. ZFIN Direct Data Submission.

Zebrafish Nomenclature Committee (2003) Nomenclature Data Curation (2003-2010). Nomenclature Committee Submission.

ZFIN Staff (2003) Curation of VEGA Database Links. Automated Data Submission.

ZFIN Staff (2003) Curation of orthology data. Manually curated data.

ZFIN Staff (2003) Curation of unpublished nucleotide sequence accession numbers. Manually curated data.

ZFIN Staff (2002) Gene Ontology Annotation Through Association of UniProt Keywords with GO Terms. Automated Data Submission.

ZFIN Staff (2002) Curation of NCBI Gene Data Via Shared RNA Sequence IDs. Automated Data Submission.

ZFIN Staff (2002) Scientific Curation. Manually curated data.

ZFIN Staff (2002) Gene Ontology Annotation Through Association of InterPro Records with GO Terms. Automated Data Submission.

ZFIN Staff (2002) Curation of EMBL records. Automated Data Submission.

Kudoh, T., Tsang, M., Hukriede, N.A., Chen, X., Dedekian, M., Clarke, C.J., Kiang, A., Schultz, S., Epstein, J.A., Toyama, R., and Dawid, I.B. (2001) A gene expression screen in zebrafish embryogenesis. ZFIN Direct Data Submission.

Thisse, B., Pflumio, S., Fürthauer, M., Loppin, B., Heyer, V., Degrave, A., Woehl, R., Lux, A., Steffan, T., Charbonnier, X.Q. and Thisse, C. (2001) Expression of the zebrafish genome during embryogenesis (NIH R01 RR15402). ZFIN Direct Data Submission.