Genomes and Genes
Summary: Proteins obtained from the ZEBRAFISH. Many of the proteins in this species have been the subject of studies involving basic embryological development (EMBRYOLOGY).
- Kettleborough R, Busch Nentwich E, Harvey S, Dooley C, de Bruijn E, van Eeden F, et al. A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature. 2013;496:494-7 pubmed publisher..All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis. ..
- Wang L, Fu C, Fan H, Du T, Dong M, Chen Y, et al. miR-34b regulates multiciliogenesis during organ formation in zebrafish. Development. 2013;140:2755-64 pubmed publisher..Thus, miR-34b serves as a guardian to maintain the proper level of cmyb expression. In summary, our studies have uncovered an essential role for miR-34b-Cmyb signaling during multiciliogenesis and kidney morphogenesis. ..
- van der Vaart M, van Soest J, Spaink H, Meijer A. Functional analysis of a zebrafish myd88 mutant identifies key transcriptional components of the innate immune system. Dis Model Mech. 2013;6:841-54 pubmed publisher..This zebrafish myd88 mutant will be a valuable tool for further study of the role of IL1R and TLR signaling in the innate immunity processes underlying infectious diseases, inflammatory disorders and cancer...
- Laranjeiro R, Tamai T, Peyric E, Krusche P, Ott S, Whitmore D. Cyclin-dependent kinase inhibitor p20 controls circadian cell-cycle timing. Proc Natl Acad Sci U S A. 2013;110:6835-40 pubmed publisher..Such differences provide a unique mechanism whereby S phase is set to different times of day in a tissue-specific manner, depending on the balance of these two inhibitors...
- Nguyen Chi M, Bryson Richardson R, Sonntag C, Hall T, Gibson A, Sztal T, et al. Morphogenesis and cell fate determination within the adaxial cell equivalence group of the zebrafish myotome. PLoS Genet. 2012;8:e1003014 pubmed publisher..Thus our results reveal that the synergistic actions of HH, FGF, and BMP signaling independently create a three-dimensional (3D) signaling milieu that coordinates cell fate within the adaxial cell equivalence group. ..
- Lin F, Xu S, Ma D, Xiao Z, Zhao C, Xiao Y, et al. Germ line specific expression of a vasa homologue gene in turbot (Scophthalmus maximus): evidence for vasa localization at cleavage furrows in euteleostei. Mol Reprod Dev. 2012;79:803-13 pubmed publisher..The results not only facilitate the germ cell manipulation of the turbot, but also improve our understanding of germline development and evolution of vasa localization in teleost. ..
- zhan G, Sezgin E, Wehner D, Pfister A, K hl S, Kagermeier Schenk B, et al. Lypd6 enhances Wnt/?-catenin signaling by promoting Lrp6 phosphorylation in raft plasma membrane domains. Dev Cell. 2013;26:331-45 pubmed publisher..Thus, Lypd6 appears to control Lrp6 activation specifically in membrane rafts, which is essential for downstream signaling...
- Wang Y, Luo Y, Hong Y, Peng J, Lo L. Ribosome biogenesis factor Bms1-like is essential for liver development in zebrafish. J Genet Genomics. 2012;39:451-62 pubmed publisher..Therefore, our findings demonstrate that Bms1l is necessary for zebrafish liver development...
- Kruse Bend R, Rosenthal J, Quist T, Veien E, Fuhrmann S, Dorsky R, et al. Extraocular ectoderm triggers dorsal retinal fate during optic vesicle evagination in zebrafish. Dev Biol. 2012;371:57-65 pubmed publisher..We find that bmp2b is involved in dorsal retina initiation, acting upstream of gdf6a. Together, this work has identified the nature and source of extraocular signals required to pattern the dorsal retina. ..
- Kamel G, Hoyos T, Rochard L, Dougherty M, Kong Y, Tse W, et al. Requirement for frzb and fzd7a in cranial neural crest convergence and extension mechanisms during zebrafish palate and jaw morphogenesis. Dev Biol. 2013;381:423-33 pubmed publisher..lower jaw structures, and integration of wnt-frizzled with endothelin signaling to coordinate shaping of the facial form. ..
- Le X, Pugach E, Hettmer S, Storer N, Liu J, Wills A, et al. A novel chemical screening strategy in zebrafish identifies common pathways in embryogenesis and rhabdomyosarcoma development. Development. 2013;140:2354-64 pubmed publisher..Our work demonstrates that the activated pathways in RAS induction during embryogenesis are also important in oncogenesis and that inhibition of these pathways suppresses tumor growth. ..
- Fior R, Maxwell A, Ma T, Vezzaro A, Moens C, Amacher S, et al. The differentiation and movement of presomitic mesoderm progenitor cells are controlled by Mesogenin 1. Development. 2012;139:4656-65 pubmed publisher..Through its combined effects on gene expression and cell movement, Msgn1 (with Spt) plays a key role both in genesis of the paraxial mesoderm and in maintenance of the progenitor population from which it derives...
- Wong T, Collodi P. Effects of specific and prolonged expression of zebrafish growth factors, Fgf2 and Lif in primordial germ cells in vivo. Biochem Biophys Res Commun. 2013;430:347-51 pubmed publisher..Understanding this mechanism may make it possible to achieve prolonged RNA expression in other cell types. ..
- Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, et al. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res. 2013;23:465-72 pubmed publisher..Together with other genome-engineering technologies, the Cas9 system is promising for applications in biology, agriculture, environmental studies and medicine. ..
- Song S, Eckerle S, Onichtchouk D, Marrs J, Nitschke R, Driever W. Pou5f1-dependent EGF expression controls E-cadherin endocytosis, cell adhesion, and zebrafish epiboly movements. Dev Cell. 2013;24:486-501 pubmed publisher..We hypothesize that dynamic control of E-cad trafficking is essential to effectively generate new adhesion sites when cells move relative to each other. ..
- Hochgreb Hägele T, Bronner M. A novel FoxD3 gene trap line reveals neural crest precursor movement and a role for FoxD3 in their specification. Dev Biol. 2013;374:1-11 pubmed publisher..These novel lines provide new insights and useful new tools for studying specification, migration and differentiation of neural crest cells...
- Tovin A, Alon S, Ben Moshe Z, Mracek P, Vatine G, Foulkes N, et al. Systematic identification of rhythmic genes reveals camk1gb as a new element in the circadian clockwork. PLoS Genet. 2012;8:e1003116 pubmed publisher..Therefore, it appears that camk1gb plays a role in linking the pineal master clock with the periphery...
- Yabe T, Takada S. Mesogenin causes embryonic mesoderm progenitors to differentiate during development of zebrafish tail somites. Dev Biol. 2012;370:213-22 pubmed publisher..Based on these results, we speculate that msgn1 expression in association with that of ntl may allow the differentiation of progenitor cells to proceed during development of somites in the tail...
- Glenn T, Talbot W. Analysis of Gpr126 function defines distinct mechanisms controlling the initiation and maturation of myelin. Development. 2013;140:3167-75 pubmed publisher..These results indicate that the mechanisms regulating the initiation of myelination are distinct from those mediating the maturation and maintenance of myelin...
- Neugebauer J, Cadwallader A, Amack J, Bisgrove B, Yost H. Differential roles for 3-OSTs in the regulation of cilia length and motility. Development. 2013;140:3892-902 pubmed publisher..We propose that individual 3-OST isozymes create distinct modified domains or 'glycocodes' on cell surface proteoglycans, which in turn regulate the response to diverse cell signaling pathways. ..
- Fernandes A, Fero K, Arrenberg A, Bergeron S, Driever W, Burgess H. Deep brain photoreceptors control light-seeking behavior in zebrafish larvae. Curr Biol. 2012;22:2042-7 pubmed publisher..Our findings shed light on the identity and function of deep brain photoreceptors and suggest that otpa specifies an ancient population of sensory neurons that mediate behavioral responses to light. ..
- Wang X, He H, Tang W, Zhang X, Hua X, Yan J. Two origins of blastemal progenitors define blastemal regeneration of zebrafish lower jaw. PLoS ONE. 2012;7:e45380 pubmed publisher..Meanwhile, the positional identity of blastema reformation is implicated in mesenchymal segmentation and characteristic expression pattern of Hox genes. ..
- Buckley C, Ren X, Ward L, Girdler G, Araya C, Green M, et al. Mirror-symmetric microtubule assembly and cell interactions drive lumen formation in the zebrafish neural rod. EMBO J. 2013;32:30-44 pubmed publisher..Although the midline division is not necessary for apical polarisation, it confers a morphogenetic advantage by efficiently eliminating cellular processes that would otherwise bridge the developing lumen. ..
- Bohnsack B, Kahana A. Thyroid hormone and retinoic acid interact to regulate zebrafish craniofacial neural crest development. Dev Biol. 2013;373:300-9 pubmed publisher..We conclude that TH regulates both rostral and caudal cranial neural crest. Further, coordinated interactions of TH and RA are required for proper craniofacial and ocular development...
- Boglev Y, Badrock A, Trotter A, Du Q, Richardson E, Parslow A, et al. Autophagy induction is a Tor- and Tp53-independent cell survival response in a zebrafish model of disrupted ribosome biogenesis. PLoS Genet. 2013;9:e1003279 pubmed publisher..This response may be of relevance to therapeutic strategies aimed at killing cancer cells by targeting ribosome biogenesis. In certain contexts, these treatments may promote autophagy and contribute to cancer cells evading cell death. ..
- Eom D, Inoue S, Patterson L, Gordon T, Slingwine R, Kondo S, et al. Melanophore migration and survival during zebrafish adult pigment stripe development require the immunoglobulin superfamily adhesion molecule Igsf11. PLoS Genet. 2012;8:e1002899 pubmed publisher..Our results provide new insights into adult pigment pattern morphogenesis and how cellular interactions mediate pattern formation...
- Wu S, Shin J, Sepich D, Solnica Krezel L. Chemokine GPCR signaling inhibits ?-catenin during zebrafish axis formation. PLoS Biol. 2012;10:e1001403 pubmed publisher..Our study delineates a novel negative, Gsk3?-independent control mechanism of ?-catenin and implicates Ccr7 as a long-hypothesized GPCR regulating vertebrate axis formation. ..
- Luo J, Uribe R, Hayton S, Calinescu A, Gross J, Hitchcock P. Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina. Neural Dev. 2012;7:33 pubmed publisher..This is the first study to demonstrate the function of Midkine during retinal development and adds Midkine to the list of growth factors that transcriptionally regulate Id proteins. ..
- Guner Ataman B, Paffett Lugassy N, Adams M, Nevis K, Jahangiri L, Obregon P, et al. Zebrafish second heart field development relies on progenitor specification in anterior lateral plate mesoderm and nkx2.5 function. Development. 2013;140:1353-63 pubmed publisher..Taken together, our data highlight two conserved features of zebrafish SHF development, reveal a novel genetic relationship between nkx2.5 and ltbp3, and underscore the utility of this model organism for deciphering SHF biology...
- Wang L, Liu T, Xu L, Gao Y, Wei Y, Duan C, et al. Fev regulates hematopoietic stem cell development via ERK signaling. Blood. 2013;122:367-75 pubmed publisher..Our data indicate that Fev-ERK signaling is essential for hemogenic endothelium-based HSC development. ..
- Einhorn Z, Trapani J, Liu Q, Nicolson T. Rabconnectin3? promotes stable activity of the H+ pump on synaptic vesicles in hair cells. J Neurosci. 2012;32:11144-56 pubmed publisher..Collectively, our data suggest that Rbc3? modulates synaptic transmission in hair cells by promoting V-ATPase activity in synaptic vesicles. ..
- Alunni A, Krecsmarik M, Bosco A, Galant S, Pan L, Moens C, et al. Notch3 signaling gates cell cycle entry and limits neural stem cell amplification in the adult pallium. Development. 2013;140:3335-47 pubmed publisher..They implicate Notch3 at the top of this hierarchy to gate NSC activation and amplification, protecting the homeostasis of adult NSC reservoirs under physiological conditions. ..
- Hüsken U, Carl M. The Wnt/beta-catenin signaling pathway establishes neuroanatomical asymmetries and their laterality. Mech Dev. 2013;130:330-5 pubmed publisher..The Wnt/beta-catenin pathway has turned out to play a pivotal role in the regulation of brain laterality and asymmetry and acts reiteratively during embryonic development. ..
- Kanwal Z, Zakrzewska A, den Hertog J, Spaink H, Schaaf M, Meijer A. Deficiency in hematopoietic phosphatase ptpn6/Shp1 hyperactivates the innate immune system and impairs control of bacterial infections in zebrafish embryos. J Immunol. 2013;190:1631-45 pubmed publisher..These results support that ptpn6 has a crucial regulatory function in preventing host-detrimental effects of inflammation and is essential for a successful defense mechanism against invading microbes. ..
- Manousaki T, Feiner N, Begemann G, Meyer A, Kuraku S. Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses. Evol Dev. 2011;13:448-59 pubmed publisher..In this context, evolution of transcriptional regulation associated with the Pax4-Pax6 split is also discussed in light of the zebrafish pax4 expression pattern that is analyzed here for the first time. ..
- Ramachandran R, Zhao X, Goldman D. Insm1a-mediated gene repression is essential for the formation and differentiation of Müller glia-derived progenitors in the injured retina. Nat Cell Biol. 2012;14:1013-23 pubmed publisher..Our studies identify Insm1a as a key regulator of retina regeneration and provide a mechanistic understanding of how it contributes to multiple phases of this process. ..
- Tsetskhladze Z, Canfield V, Ang K, Wentzel S, Reid K, Berg A, et al. Functional assessment of human coding mutations affecting skin pigmentation using zebrafish. PLoS ONE. 2012;7:e47398 pubmed publisher..The developed approach may be extended to other model systems and may potentially contribute to our understanding the functional relationships between DNA sequence variation, human biology, and disease. ..
- Nelson C, Gorsuch R, Bailey T, Ackerman K, Kassen S, Hyde D. Stat3 defines three populations of Müller glia and is required for initiating maximal müller glia proliferation in the regenerating zebrafish retina. J Comp Neurol. 2012;520:4294-311 pubmed publisher..Whereas Ascl1a and Lin28a are required for Müller glia proliferation, Stat3 is necessary for the maximal number of Müller glia to proliferate during regeneration of the damaged zebrafish retina. ..
- Sheehan Rooney K, Swartz M, Lovely C, Dixon M, Eberhart J. Bmp and Shh signaling mediate the expression of satb2 in the pharyngeal arches. PLoS ONE. 2013;8:e59533 pubmed publisher..We propose that Bmp signaling establishes competence for the neural crest to respond to Hh signaling, thus inducing satb2 expression...
- Jönsson M, Kubota A, Timme Laragy A, Woodin B, Stegeman J. Ahr2-dependence of PCB126 effects on the swim bladder in relation to expression of CYP1 and cox-2 genes in developing zebrafish. Toxicol Appl Pharmacol. 2012;265:166-74 pubmed publisher..Our results indicate that PCB126 blocks swim bladder inflation via an Ahr2-mediated mechanism. This mechanism seems independent of CYP1 or cox-2 mRNA induction but may involve abnormal development of swim bladder cells. ..
- Guh Y, Tseng Y, Yang C, Hwang P. Endothelin-1 regulates H?-ATPase-dependent transepithelial H? secretion in zebrafish. Endocrinology. 2014;155:1728-37 pubmed publisher..These findings provide evidence that EDN1 signaling is involved in acid-base regulation in zebrafish and enhance our understanding of EDN1 regulation of transepithelial H? secretion in vertebrates. ..
- Dickover M, Hegarty J, Ly K, Lopez D, Yang H, Zhang R, et al. The atypical Rho GTPase, RhoU, regulates cell-adhesion molecules during cardiac morphogenesis. Dev Biol. 2014;389:182-91 pubmed publisher..Failure to properly form these cell adhesions during cardiac development may lead to structural heart defects and mechanistically account for the cellular events that occur in certain human congenital heart diseases. ..
- Liu H, Chu T, Chen L, Gui W, Zhu G. In vivo cardiovascular toxicity induced by acetochlor in zebrafish larvae. Chemosphere. 2017;181:600-608 pubmed publisher..Our data generated here might provide novel insights into cardiovascular disease risk following acetochlor exposure to human, especially to pesticide suicides population, occupational population and special population. ..
- Zheng S, Liu C, Huang Y, Bao M, Huang Y, Wu K. Effects of 2,2',4,4'-tetrabromodiphenyl ether on neurobehavior and memory change and bcl-2, c-fos, grin1b and lingo1b gene expression in male zebrafish (Danio rerio). Toxicol Appl Pharmacol. 2017;333:10-16 pubmed publisher..The PBDE BDE-47 had a negative impact on the neurobehaviors of zebrafish and affected the expression of c-fos, bcl-2, lingo1b and grin1b in zebrafish brain tissue. ..
- Shu Y, Lou Q, Dai Z, Dai X, He J, Hu W, et al. The basal function of teleost prolactin as a key regulator on ion uptake identified with zebrafish knockout models. Sci Rep. 2016;6:18597 pubmed publisher..Our study provides valuable evidence to understand the mechanisms of PRL function better through both phylogenetic and physiological perspectives. ..