Albadri, S., Naso, F., Thauvin, M., Gauron, C., Parolin, C., Duroure, K., Vougny, J., Fiori, J., Boga, C., Vriz, S., Calonghi, N., Del Bene, F. (2019) Redox Signaling via Lipid Peroxidation Regulates Retinal Progenitor Cell Differentiation. Developmental Cell. 50(1):73-89.e6
|
Amsterdam, A., Nissen, R.M., Sun, Z., Swindell, E., Farrington, S., and Hopkins, N. (2004) Identification of 315 genes essential for early zebrafish development. Proceedings of the National Academy of Sciences of the United States of America. 101(35):12792-12797
|
Anderson, N.M., Li, D., Peng, H.L., Laroche, F.J., Mansour, M.R., Gjini, E., Aioub, M., Helman, D.J., Roderick, J.E., Cheng, T., Harrold, I., Samaha, Y., Meng, L., Amsterdam, A., Neuberg, D.S., Denton, T.T., Sanda, T., Kelliher, M.A., Singh, A., Look, A.T., Feng, H. (2016) The TCA cycle transferase DLST is important for MYC-mediated leukemogenesis. Leukemia. 30(6):1365-74
|
Bayés, À., Collins, M.O., Reig-Viader, R., Gou, G., Goulding, D., Izquierdo, A., Choudhary, J.S., Emes, R.D., Grant, S.G. (2017) Evolution of complexity in the zebrafish synapse proteome. Nature communications. 8:14613
|
Bertrand, S., Thisse, B., Tavares, R., Sachs, L., Chaumot, A., Bardet, P.L., Escrivà, H., Duffraisse, M., Marchand, O., Safi, R., Thisse, C., and Laudet, V. (2007) Unexpected Novel Relational Links Uncovered by Extensive Developmental Profiling of Nuclear Receptor Expression. PLoS Genetics. 3(11):e188
|
|
|
|
Bu, H., Ding, Y., Li, J., Zhu, P., Shih, Y.H., Wang, M., Zhang, Y., Lin, X., Xu, X. (2021) Inhibition of mTOR or MAPK ameliorates vmhcl/myh7 cardiomyopathy in zebrafish. JCI insight. 6(24):
|
Burns, C.E., Galloway, J.L., Smith, A.C., Keefe, M.D., Cashman, T.J., Paik, E.J., Mayhall, E.A., Amsterdam, A.H., and Zon, L.I. (2009) A genetic screen in zebrafish defines a hierarchical network of pathways required for hematopoietic stem cell emergence. Blood. 113(23):5776-5782
|
Bühler, A., Gahr, B.M., Park, D.D., Bertozzi, A., Boos, A., Dalvoy, M., Pott, A., Oswald, F., Kovall, R.A., Kühn, B., Weidinger, G., Rottbauer, W., Just, S. (2021) Histone deacetylase 1 controls cardiomyocyte proliferation during embryonic heart development and cardiac regeneration in zebrafish. PLoS Genetics. 17:e1009890
|
|
Cao, Y., Semanchik, N., Lee, S.H., Somlo, S., Barbano, P.E., Coifman, R., and Sun, Z. (2009) Chemical modifier screen identifies HDAC inhibitors as suppressors of PKD models. Proceedings of the National Academy of Sciences of the United States of America. 106(51):21819-21824
|
Cavone, L., McCann, T., Drake, L.K., Aguzzi, E.A., Oprişoreanu, A.M., Pedersen, E., Sandi, S., Selvarajah, J., Tsarouchas, T.M., Wehner, D., Keatinge, M., Mysiak, K.S., Henderson, B.E.P., Dobie, R., Henderson, N.C., Becker, T., Becker, C.G. (2021) A unique macrophage subpopulation signals directly to progenitor cells to promote regenerative neurogenesis in the zebrafish spinal cord. Developmental Cell. 56(11):1617-1630.e6
|
Cerveny, K.L., Bronstein, H., Hagen, O., Lamb, D.B., Martin, G., Tower, I., Van Duzer, A., Welch, E., Varga, M. (2021) Mutations linked to loss of cell cycle control can render cells responsive to local differentiation cues. microPublication. Biology. 2021:
|
|
|
DeMoya, R.A., Forman-Rubinsky, R.E., Fontaine, D., Shin, J., Watkins, S.C., Lo, C.W., Tsang, M. (2023) Sin3a associated protein 130 kDa, sap130, plays an evolutionary conserved role in zebrafish heart development. Frontiers in cell and developmental biology. 11:11971091197109
|
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
|
Farooq, M., Sulochana, K.N., Pan, X., To, J., Sheng, D., Gong, Z., and Ge, R. (2008) Histone deacetylase 3 (hdac3) is specifically required for liver development in zebrafish. Developmental Biology. 317(1):336-353
|
Fazio, M., van Rooijen, E., Dang, M., van de Hoek, G., Ablain, J., Mito, J.K., Yang, S., Thomas, A., Michael, J., Fabo, T., Modhurima, R., Pessina, P., Kaufman, C.K., Zhou, Y., White, R.M., Zon, L.I. (2021) SATB2 induction of a neural crest mesenchyme-like program drives melanoma invasion and drug resistance. eLIFE. 10:
|
|
Fischer, S., Prykhozhij, S., Rau, M.J., and Neumann, C.J. (2007) Mutation of Zebrafish caf-1b Results in S Phase Arrest, Defective Differentiation, and p53-Mediated Apoptosis During Organogenesis. Cell cycle (Georgetown, Tex.). 6(23):2962-2969
|
Golling, G., Amsterdam, A., Sun, Z., Antonelli, M., Maldonado, E., Chen, W., Burgess, S., Haldi, M., Artzt, K., Farrington, S., Lin, S.Y., Nissen, R.M., and Hopkins, N. (2002) Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nature Genetics. 31(2):135-140
|
|
|
Henion, P.D., Raible, D.W., Beattie, C.E., Stoesser, K.L., Weston, J.A., and Eisen, J.S. (1996) Screen for mutations affecting development of zebrafish neural crest. Developmental genetics. 18:11-17
|
|
Huang, H.T., Kathrein, K.L., Barton, A., Gitlin, Z., Huang, Y.H., Ward, T.P., Hofmann, O., Dibiase, A., Song, A., Tyekucheva, S., Hide, W., Zhou, Y., and Zon, L.I. (2013) A network of epigenetic regulators guides developmental haematopoiesis in vivo. Nature cell biology. 15(12):1516-1525
|
|
Ignatius, M.S., Unal Eroglu, A., Malireddy, S., Gallagher, G., Nambiar, R.M., and Henion, P.D. (2013) Distinct Functional and Temporal Requirements for Zebrafish Hdac1 during Neural Crest-Derived Craniofacial and Peripheral Neuron Development. PLoS One. 8(5):e63218
|
Jacob, J., Ribes, V., Moore, S., Constable, S.C., Sasai, N., Gerety, S.S., Martin, D.J., Sergeant, C.P., Wilkinson, D.G., and Briscoe, J. (2014) Valproic Acid silencing of ascl1b/ascl1 results in the failure of serotonergic differentiation in a zebrafish model of Fetal Valproate Syndrome. Disease models & mechanisms. 7(1):107-17
|
Jia, S., Dai, F., Wu, D., Lin, X., Xing, C., Xue, Y., Wang, Y., Xiao, M., Wu, W., Feng, X.H., and Meng, A. (2012) Protein Phosphatase 4 Cooperates with Smads to Promote BMP Signaling in Dorsoventral Patterning of Zebrafish Embryos. Developmental Cell. 22(5):1065-1078
|
|
Ko, S., Russell, J.O., Tian, J., Gao, C., Kobayashi, M., Feng, R., Yuan, X., Shao, C., Ding, H., Poddar, M., Singh, S., Locker, J., Weng, H.L., Monga, S.P., Shin, D. (2018) Hdac1 Regulates Differentiation of Bipotent Liver Progenitor Cells During Regeneration via Sox9b and Cdk8. Gastroenterology. 156(1):187-202.e14
|
Koltowska, K., Apitz, H., Stamataki, D., Hirst, E.M., Verkade, H., Salecker, I., and Ober, E.A. (2013) Ssrp1a controls organogenesis by promoting cell cycle progression and RNA synthesis. Development (Cambridge, England). 140(9):1912-8
|
Laing, L.V., Viana, J., Dempster, E., Uren Webster, T.M., van Aerle, R., Mill, J., Santos, E.M. (2018) Sex-specific transcription and DNA methylation profiles of reproductive and epigenetic associated genes in the gonads and livers of breeding zebrafish. Comparative biochemistry and physiology. Part A, Molecular & integrative physiology. 222:16-25
|
Laing, L.V., Viana, J., Dempster, E.L., Trznadel, M., Trunkfield, L.A., Webster, T.M., van Aerle, R., Paull, G.C., Wilson, R.J., Mill, J., Santos, E.M. (2016) Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio). Epigenetics. 11(7):526-38
|
|
Lemeer, S., Pinkse, M.W., Mohammed, S., van Breukelen, B., den Hertog, J., Slijper, M., and Heck, A.J. (2008) Online Automated in Vivo Zebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo. Journal of Proteome Research. 7(4):1555-1564
|
|
|
Liu, C., Wang, Y., Deng, J., Lin, J., Hu, C., Li, Q., Xu, X. (2021) Social Deficits and Repetitive Behaviors Are Improved by Early Postnatal Low-Dose VPA Intervention in a Novel shank3-Deficient Zebrafish Model. Frontiers in neuroscience. 15:682054
|
Loponte, S., Segré, C.V., Senese, S., Miccolo, C., Santaguida, S., Deflorian, G., Citro, S., Mattoscio, D., Pisati, F., Moser, M.A., Visintin, R., Seiser, C., Chiocca, S. (2016) Dynamic phosphorylation of Histone Deacetylase 1 by Aurora kinases during mitosis regulates zebrafish embryos development. Scientific Reports. 6:30213
|
|
Matrone, G., Jung, S.Y., Choi, J.M., Jain, A., Leung, H.E., Rajapakshe, K., Coarfa, C., Rodor, J., Denvir, M.A., Baker, A.H., Cooke, J.P. (2021) Nuclear S-nitrosylation impacts tissue regeneration in zebrafish. Nature communications. 12:6282
|
Mitra, S., Sharma, P., Kaur, S., Khursheed, M.A., Gupta, S., Ahuja, R., Kurup, A.J., Chaudhary, M., Ramachandran, R. (2018) Histone Deacetylase-Mediated Müller Glia Reprogramming through Her4.1-Lin28a Axis Is Essential for Retina Regeneration in Zebrafish. iScience. 7:68-84
|
Mitra, S., Sharma, P., Kaur, S., Khursheed, M.A., Gupta, S., Chaudhary, M., Kurup, A.J., Ramachandran, R. (2019) Dual regulation of lin28a by Myc is necessary during zebrafish retina regeneration. The Journal of cell biology. 218(2):489-507
|
|
|
Noël, E.S., Casal-Sueiro, A., Busch-Nentwich, E., Verkade, H., Dong, P.D., Stemple, D.L., and Ober, E.A. (2008) Organ-specific requirements for Hdac1 in liver and pancreas formation. Developmental Biology. 322(2):237-250
|
|
Ota, S., Ishitani, S., Shimizu, N., Matsumoto, K., Itoh, M., and Ishitani, T. (2012) NLK positively regulates Wnt/beta-catenin signalling by phosphorylating LEF1 in neural progenitor cells. The EMBO journal. 31(8):1904-1915
|
Pei, W., Xu, L., Huang, S.C., Pettie, K., Idol, J., Rissone, A., Jimenez, E., Sinclair, J.W., Slevin, C., Varshney, G.K., Jones, M., Carrington, B., Bishop, K., Huang, H., Sood, R., Lin, S., Burgess, S.M. (2018) Guided genetic screen to identify genes essential in the regeneration of hair cells and other tissues. NPJ Regenerative medicine. 3:11
|
|
|
Pinho, B.R., Reis, S.D., Guedes-Dias, P., Leitão-Rocha, A., Quintas, C., Valentão, P., Andrade, P.B., Santos, M.M., Oliveira, J.M. (2016) Pharmacological modulation of HDAC1 and HDAC6 in vivo in a zebrafish model: therapeutic implications for Parkinson's disease. Pharmacological research. 103:328-39
|
|
|
|
Román, A.C., Vicente-Page, J., Pérez-Escudero, A., Carvajal-González, J.M., Fernández-Salguero, P.M., de Polavieja, G.G. (2018) Histone H4 acetylation regulates behavioral inter-individual variability in zebrafish. Genome biology. 19:55
|
Ryan, S., Willer, J., Marjoram, L., Bagwell, J., Mankiewicz, J., Leshchiner, I., Goessling, W., Bagnat, M., and Katsanis, N. (2013) Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish. Development (Cambridge, England). 140(21):4445-4451
|
Sant, K.E., Moreau, H.M., Williams, L.M., Jacobs, H.M., Bowsher, A.M., Boisvert, J.D., Smolowitz, R.M., Pantazis, J., Annunziato, K., Nguyen, M., Timme-Laragy, A. (2020) Embryonic exposures to mono-2-ethylhexyl phthalate induce larval steatosis in zebrafish independent of Nrf2a signaling. Journal of developmental origins of health and disease. 12(1):132-140
|
Schultz, L.E., Haltom, J.A., Almeida, M.P., Wierson, W.A., Solin, S.L., Weiss, T.J., Helmer, J.A., Sandquist, E.J., Shive, H.R., McGrail, M. (2018) Epigenetic regulators Rbbp4 and Hdac1 are overexpressed in a zebrafish model of RB1 embryonal brain tumor, and are required for neural progenitor survival and proliferation. Disease models & mechanisms. 11(6)
|
Sharma, P., Gupta, S., Chaudhary, M., Mitra, S., Chawla, B., Khursheed, M.A., Ramachandran, R. (2019) Oct4 mediates Müller glia reprogramming and cell cycle exit during retina regeneration in zebrafish. Life science alliance. 2(5):
|
Sharma, P., Gupta, S., Chaudhary, M., Mitra, S., Chawla, B., Khursheed, M.A., Saran, N.K., Ramachandran, R. (2020) Biphasic Role of Tgf-β Signaling during Müller Glia Reprogramming and Retinal Regeneration in Zebrafish. iScience. 23:100817
|
So, J.H., Chun, H.S., Bae, Y.K., Kim, H.S., Park, Y.M., Huh, T.L., Chitnis, A.B., Kim, C.H., and Yeo, S.Y. (2009) Her4 is necessary for establishing peripheral projections of the trigeminal ganglia in zebrafish. Biochemical and Biophysical Research Communications. 379(1):22-26
|
|
Stadler, J.A., Shkumatava, A., Norton, W.H., Rau, M.J., Geisler, R., Fischer, S., and Neumann, C.J. (2005) Histone deacetylase 1 is required for cell cycle exit and differentiation in the zebrafish retina. Developmental Dynamics : an official publication of the American Association of Anatomists. 233(3):883-889
|
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
|
Tsai, T.C., Shih, C.C., Chien, H.P., Yang, A.H., Lu, J.K., Lu, J.H. (2018) Anti-apoptotic effects of IGF-I on mortality and dysmorphogenesis in tbx5-deficient zebrafish embryos. BMC Developmental Biology. 18:5
|
Tu, J., Liu, X., Jia, H., Reilly, J., Yu, S., Cai, C., Liu, F., Lv, Y., Huang, Y., Lu, Z., Han, S., Jiang, T., Shu, X., Wu, X., Tang, Z., Lu, Q., Liu, M. (2020) The chromatin remodeler Brg1 is required for formation and maintenance of hematopoietic stem cells. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 34(9):11997-12008
|
Turner, K.J., Hoyle, J., Valdivia, L.E., Cerveny, K.L., Hart, W., Mangoli, M., Geisler, R., Rees, M., Houart, C., Poole, R.J., Wilson, S.W., Gestri, G. (2019) Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits. PLoS One. 14:e0211073
|
Varshney, G.K., Lu, J., Gildea, D., Huang, H., Pei, W., Yang, Z., Huang, S.C., Schoenfeld, D.S., Pho, N., Casero, D., Hirase, T., Mosbrook-Davis, D.M., Zhang, S., Jao, L.E., Zhang, B., Woods, I.G., Zimmerman, S., Schier, A.F., Wolfsberg, T., Pellegrini, M., Burgess, S.M., and Lin, S. (2013) A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome research. 23(4):727-735
|
Wang, D., Jao, L.E., Zheng, N., Dolan, K., Ivey, J., Zonies, S., Wu, X., Wu, K., Yang, H., Meng, Q., Zhu, Z., Zhang, B., Lin, S., and Burgess, S.M. (2007) Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proceedings of the National Academy of Sciences of the United States of America. 104(30):12428-12433
|
Wang, S., Yang, Q., Wang, Z., Feng, S., Li, H., Ji, D., Zhang, S. (2018) Evolutionary and Expression Analyses Show Co-option of khdrbs Genes for Origin of Vertebrate Brain.. Frontiers in genetics. 8:225
|
|
Woods, I.G., Wilson, C., Friedlander, B., Chang, P., Reyes, D.K., Nix, R., Kelly, P.D., Chu, F., Postlethwait, J.H., and Talbot, W.S. (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome research. 15(9):1307-1314
|
Xiong, G., Zou, L., Deng, Y., Meng, Y., Liao, X., Lu, H. (2018) Clethodim exposure induces developmental immunotoxicity and neurobehavioral dysfunction in zebrafish embryos. Fish & shellfish immunology. 86:549-558
|
|
Yamaguchi, M., Tonou-Fujimori, N., Komori, A., Maeda, R., Nojima, Y., Li, H., Okamoto, H., and Masai, I. (2005) Histone deacetylase 1 regulates retinal neurogenesis in zebrafish by suppressing Wnt and Notch signaling pathways. Development (Cambridge, England). 32(13):3027-3043
|
Zhang, X., Zhou, Q., Li, X., Zou, W., Hu, X. (2020) Integrating omics and traditional analyses to profile the synergistic toxicity of graphene oxide and triphenyl phosphate. Environmental pollution (Barking, Essex : 1987). 263:114473
|
|
Zou, J., Li, W.Q., Li, Q., Li, X.Q., Zhang, J.T., Liu, G.Q., Chen, J., Qiu, X.X., Tian, F.J., Wang, Z.Z., Zhu, N., Qin, Y.W., Shen, B., Liu, T.X., and Jing, Q. (2011) Two Functional MicroRNA-126s Repress a Novel Target Gene p21-Activated Kinase 1 to Regulate Vascular Integrity in Zebrafish. Circulation research. 108(2):201-209
|