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Molnar N, Capik A, Ishak A, Maglakelidze N, Pasick LJ, Reneker B, Volino A, O'Connell ML. The temporal control and activity of maternal zsquildlike-A/ hnrnpaba during zebrafish embryogenesis indicate a role in early pattern formation. ZYGOTE 2025; 33:45-55. [PMID: 39995299 DOI: 10.1017/s0967199425000024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
Abstract
During embryogenesis in Danio rerio (zebrafish), the earliest morphological patterning events are dependent on the precise temporal translation and/or localization of specific maternal mRNAs/proteins. Dorsoventral patterning in particular requires the translocation of maternal factors that are present in the Balbiani Body from the vegetal region of the unfertilized egg to the future dorsal side of the embryo (Fuentes et al., 2020), leading to the localized activation of the β-catenin pathway in the cells in that region. Since zebrafish are chordates, this dorsoventral patterning then leads to the formation of neural tissue on the dorsal side of the embryo. What is not yet clear is the identity of all maternal and zygotic factors that first establish dorsoventral patterning, and which factors lead to the establishment of neural versus non-neural tissue. Taking an evolutionary approach to this question, we investigated a gene in zebrafish, zsquidlike-A (hnrnpaba), that is homologous to a key dorsoventral patterning gene in fruit flies (Drosophila melanogaster) called squid (Kelley, 1993). While dorsoventral patterning in flies and fish looks quite different both morphologically and at the molecular level, we demonstrate that not only has a key dorsoventral patterning gene in flies been conserved in fish, maternal fish zsquidlike-A protein is synthesized precisely as dorsoventral patterning is unfolding in fish embryos, and in its absence, dorsoventral patterning is severely disrupted.
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Affiliation(s)
- Nicole Molnar
- The Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Allie Capik
- The Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Amgad Ishak
- The Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | | | - Luke J Pasick
- The Department of Biology, The College of New Jersey, Ewing, NJ, USA
| | - Billie Reneker
- The Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alyse Volino
- The Department of Biology, The College of New Jersey, Ewing, NJ, USA
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Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience 2024; 27:110083. [PMID: 38872974 PMCID: PMC11170199 DOI: 10.1016/j.isci.2024.110083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Ochocka
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Richard Ho
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
- The Njord Centre, Department of Physics, University of Oslo, Oslo, Norway
| | - Bożena Kamińska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
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Leggieri A, Palladino A, Attanasio C, Avallone L, de Girolamo P, D'Angelo L, Lucini C. Id(entifying) the inhibitor of DNA binding 3 in the brain of Nothobranchius furzeri upon aging. J Anat 2020; 238:1106-1115. [PMID: 33314133 PMCID: PMC8053586 DOI: 10.1111/joa.13367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 01/02/2023] Open
Abstract
Inhibitors of DNA (Id) are key transcription factors (TFs) regulating neurogenic processes. They belong to the helix-loop-helix (HLH) TF family and are dominant negative regulators of basic HLH proteins (bHLHs). Specifically, they inhibit cell differentiation and enhance cell proliferation and motility. The Id family includes four members, Id1, Id2, Id3, and Id4, which have been identified in nearly all vertebrates. The transcript catalog of the African turquoise killifish, Nothobranchius furzeri, contains all four TFs and has evolved showing positive selection for Id3. N. furzeri, a teleost, is the short-lived vertebrate and is gaining increasing scientific interest as a new model organism in aging research. It is characterized by embryonic diapause, explosive sexual maturation, and rapid aging. In this study, we investigated both the expression and the role of Id3 in the brain of this model organism. Interestingly, Id3 was upregulated age-dependently along with a distribution pattern resembling that of other vertebrates. Additionally, the gene has undergone positive selection during evolution and shows a high degree of conservation relative to that of other vertebrates. These features make N. furzeri a valid tool for aging studies and a potential model in translational research.
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Affiliation(s)
- Adele Leggieri
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Antonio Palladino
- CESMA-Centro Servizi Metrologici e Tecnologici Avanzati, University of Naples Federico II, Naples, Italy
| | - Chiara Attanasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy.,Center for Advanced Biomaterials for Health Care, IIT@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | - Luigi Avallone
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Paolo de Girolamo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Livia D'Angelo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Carla Lucini
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
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Yu R, Wang P, Chen XW. The role of gfi1.2 in the development of zebrafish inner ear. Hear Res 2020; 396:108055. [DOI: 10.1016/j.heares.2020.108055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 06/30/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
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5
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Diotel N, Beil T, Strähle U, Rastegar S. Differential expression of id genes and their potential regulator znf238 in zebrafish adult neural progenitor cells and neurons suggests distinct functions in adult neurogenesis. Gene Expr Patterns 2015; 19:1-13. [PMID: 26107416 DOI: 10.1016/j.gep.2015.05.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
Abstract
Teleost fish display a remarkable ability to generate new neurons and to repair brain lesions during adulthood. They are, therefore, a very popular model to investigate the molecular mechanisms of constitutive and induced neurogenesis in adult vertebrates. In this study, we investigated the expression patterns of inhibitor of DNA binding (id) genes and of their potential transcriptional repressor, znf238, in the whole brain of adult zebrafish. We show that while id1 is exclusively expressed in ventricular cells in the whole brain, id2a, id3 and id4 genes are expressed in broader areas. Interestingly, znf238 was also detected in these regions, its expression overlapping with id2a, id3 and id4 expression. Further detailed characterization of the id-expressing cells demonstrated that (a) id1 is expressed in type 1 and type 2 neural progenitors as previously published, (b) id2a in type 1, 2 and 3 neural progenitors, (c) id3 in type 3 neural progenitors and (d) id4 in postmitotic neurons. Our data provide a detailed map of id and znf238 expression in the brain of adult zebrafish, supplying a framework for studies of id genes function during adult neurogenesis and brain regeneration in the zebrafish.
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Affiliation(s)
- Nicolas Diotel
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany; Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Plateforme CYROI, Sainte-Clotilde, F-97490, France; Université de La Réunion, UMR 1188, Sainte-Clotilde, F-97490, France.
| | - Tanja Beil
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Uwe Strähle
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Sepand Rastegar
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany.
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6
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Li H, Cai Y, Xie P, Chen J, Hao L, Li G, Xiong Q. Identification and expression profile of Id1 in bighead carp in response to microcystin-LR. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2012; 34:324-333. [PMID: 22683524 DOI: 10.1016/j.etap.2012.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 04/21/2012] [Accepted: 04/25/2012] [Indexed: 06/01/2023]
Abstract
Microcystin-LR (MCLR) is a widespread cyanotoxin produced in algal blooms, and has potent hepatotoxicity and tumor-promoting activity. We cloned the full-length cDNA of Id1 in bighead carp. The full-length Id1 cDNA was 954bp and contained a 387bp ORF. Bighead carp Id1 shared high identity with zebrafish Id1 amino acid sequence, and phylogenetic analysis showed that teleost Id1 evolved closely. Bighead carp Id1 constitutively expressed in all tested tissues in normal. When tested at two different time points post exposure and at 3 different MCLR doses, Id1 expression increased in a time-dependent pattern, and Id1 expression in brain was very sensitive to MCLR exposure. The present study will help us to understand more about the evolution of Id1 molecule and its role in the MCLR induced cell differentiation and cancer promoting in bighead carp.
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Affiliation(s)
- Huiying Li
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Yan Cai
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Le Hao
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Guangyu Li
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Qian Xiong
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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Chong SW, Korzh V, Jiang YJ. Myogenesis and molecules - insights from zebrafish Danio rerio. JOURNAL OF FISH BIOLOGY 2009; 74:1693-1755. [PMID: 20735668 DOI: 10.1111/j.1095-8649.2009.02174.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Myogenesis is a fundamental process governing the formation of muscle in multicellular organisms. Recent studies in zebrafish Danio rerio have described the molecular events occurring during embryonic morphogenesis and have thus greatly clarified this process, helping to distinguish between the events that give rise to fast v. slow muscle. Coupled with the well-known Hedgehog signalling cascade and a wide variety of cellular processes during early development, the continual research on D. rerio slow muscle precursors has provided novel insights into their cellular behaviours in this organism. Similarly, analyses on fast muscle precursors have provided knowledge of the behaviour of a sub-set of epitheloid cells residing in the anterior domain of somites. Additionally, the findings by various groups on the roles of several molecules in somitic myogenesis have been clarified in the past year. In this study, the authors briefly review the current trends in the field of research of D. rerio trunk myogenesis.
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Affiliation(s)
- S-W Chong
- Laboratory of Developmental Signalling and Patterning, Genes and Development Division, A STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
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8
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The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev Biol 2008; 318:366-77. [PMID: 18455719 DOI: 10.1016/j.ydbio.2008.03.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 01/29/2023]
Abstract
The cis-regulatory regions of many developmental regulators and transcription factors are believed to be highly conserved in the genomes of vertebrate species, suggesting specific regulatory mechanisms for these gene classes. We functionally characterized five notochord enhancers, whose sequence is highly conserved, and systematically mutated two of them. Two subregions were identified to be essential for expression in the notochord of the zebrafish embryo. Synthetic enhancers containing the two essential regions in front of a TATA-box drive expression in the notochord while concatemerization of the subregions alone is not sufficient, indicating that the combination of the two sequence elements is required for notochord expression. Both regions are present in the five functionally characterized notochord enhancers. However, the position, the distance and relative orientation of the two sequence motifs can vary substantially within the enhancer sequences. This suggests that the regulatory grammar itself does not dictate the high evolutionary conservation between these orthologous cis-regulatory sequences. Rather, it represents a less well-conserved layer of sequence organization within these sequences.
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9
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Hillegass JM, Villano CM, Cooper KR, White LA. Matrix metalloproteinase-13 is required for zebra fish (Danio rerio) development and is a target for glucocorticoids. Toxicol Sci 2007; 100:168-79. [PMID: 17728286 DOI: 10.1093/toxsci/kfm192] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are endopeptidases that degrade the proteins of the extracellular matrix (ECM). Expression and activity of the MMPs are essential for embryogenesis, where MMPs participate in the normal ECM remodeling that occurs during tissue morphogenesis and development. Studies have demonstrated that MMP gene expression is inhibited by glucocorticoids in mammalian cell culture systems and that exposure to glucocorticoids causes developmental abnormalities in several species. Therefore, we proposed that glucocorticoids impede normal development through alteration of MMP expression. Zebra fish (Danio rerio) were used as a model to study MMP-13 expression both during normal embryogenesis and following acute exposure to two glucocorticoids, dexamethasone, and hydrocortisone. MMP-13 is one of three collagenases identified in vertebrates that catalyzes the degradation of type I collagens at neutral pH. MMP-13 expression varied during zebra fish development, with peak expression at 48 h post-fertilization (hpf). Morpholino knockdown studies showed that MMP-13 expression is necessary for normal zebra fish embryogenesis. Acute exposure to dexamethasone and hydrocortisone resulted in abnormal zebra fish development including craniofacial abnormalities, altered somitogenesis, blood pooling and pericardial and yolk sac edema as well as increased MMP-13 mRNA and activity at 72 hpf. In situ hybridization experiments were used to confirm the increase in MMP-13 expression following glucocorticoid treatment and showed elevated MMP-13 expression in the rostral trunk, brain, eye, heart, and anterior kidney of treated embryos. These data demonstrate that normal zebra fish embryogenesis requires MMP-13 and that dexamethasone and hydrocortisone modulate the expression of this gene, leading to increased activity and potentially contributing to subsequent dysmorphogenesis.
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Affiliation(s)
- Jedd Michael Hillegass
- Joint Graduate Program in Toxicology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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10
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Chong SW, Nguyen TTH, Chu LT, Jiang YJ, Korzh V. Zebrafish id2 developmental expression pattern contains evolutionary conserved and species-specific characteristics. Dev Dyn 2006; 234:1055-63. [PMID: 16252281 DOI: 10.1002/dvdy.20625] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The inhibitor of differentiation or inhibitor of DNA binding (Id) family are members of the helix-loop-helix (HLH) group of transcription factors that play important roles in cell proliferation, differentiation, cell cycle control, and apoptosis. They modulate the formation of active class A-class B basic HLH (bHLH) complexes. Ids lack the amino-terminal associated basic region necessary for DNA binding, thus sequestering the class A factors, inhibiting the formation of active class A-class B heterodimers and, therefore, are considered to act as dominant-negative regulators of differentiation pathways. We isolated zebrafish id2, and its expression during development was characterized. id2, in addition to regions of expression detected in Xenopus and mice, is also expressed in the tegmentum; midbrain-hindbrain boundary; cerebellum; rhombomeres 2,3,4,6; notochord; and corpuscles of Stannius. Furthermore, we show that expression of id2 is repressed in mind bomb mutants, suggesting a role of Notch upstream of Id2.
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Affiliation(s)
- Shang-Wei Chong
- Laboratory of Fish Developmental Biology, Institute of Molecular and Cell Biology, National University of Singapore
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Gahr SA, Rodriguez MF, Rexroad CE. Identification and expression profile of the ID gene family in the rainbow trout (Oncorhynchus mykiss). ACTA ACUST UNITED AC 2005; 1729:64-73. [PMID: 15866514 DOI: 10.1016/j.bbaexp.2005.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 02/23/2005] [Accepted: 03/26/2005] [Indexed: 11/17/2022]
Abstract
ID proteins are negative regulators of basic helix-loop-helix transcription factors governing growth and development in mammals. However, little is known about the ID gene function and expression in fish. We report the identification and characterization of two new rainbow trout ID genes (ID1D and ID2B) and extend our expression analyses of two previously identified ID genes (ID1A and ID2A). Phylogenetic analyses indicate an evolutionary relationship between ID1A and ID1D and between ID1B and ID1C, suggesting a mechanism of divergence throughout salmonid evolution. To access the expression of these genes in adult and developing fish, we measured the relative transcript abundance of four ID1 and two ID2 genes by real-time PCR. ID1 transcripts were expressed in a variety of tissues and the ID1 paralogues showed similar patterns of expression, whereas the ID2 paralogues were differentially expressed. To access the role of the ID genes during embryonic development, gene expression was measured at early (day 0 and day 2), mid (day 9 and day 18) and late (day 30 and day 50) embryonic development. ID1A and ID1D expression remained unchanged throughout embryonic development, while ID1B and ID1C were lowest during early, highest at mid, and decreased during late embryonic development. The ID2 transcripts revealed the highest expression in unfertilized eggs and day 2 embryos, and remained low throughout the remainder of embryonic development. The sequence analyses and gene expression patterns implicate gene and genome duplication in rainbow trout ID gene evolution and suggest an extensive role for the IDs in rainbow trout growth and development.
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Affiliation(s)
- Scott A Gahr
- United States Department of Agriculture, Agriculture Research Service, National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
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Gahr SA, Palti Y, Rexroad CE. Genomic characterization of a novel pair of ID genes in the rainbow trout (Oncorhynchus mykiss). Anim Genet 2004; 35:317-20. [PMID: 15265072 DOI: 10.1111/j.1365-2052.2004.01142.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ID (inhibitors of DNA binding/differentiation) proteins represent a family of dominant negative regulators of the basic helix-loop-helix transcription factors whose activities result in delayed cell differentiation and prolonged proliferation. A pair of expressed sequence tag clones with homologies to the ID proteins were identified and used to screen a rainbow trout bacterial artificial chromosome (BAC) library to identify clones containing homologues sequences. Phylogenetic analysis of the predicted amino acid sequences revealed close similarities to the rainbow trout ID1 protein, the genes were therefore classified as rainbow trout ID1B and ID1C. Genome characterization based on BAC sequencing showed each gene to have two exons separated by a small intron. The genes are 83% similar in their transcribed regions, yet they are only 64 and 65% similar in the upstream and downstream sequences, respectively. Using reverse transcription polymerase chain reaction, we found both genes to be expressed in a variety of tissues in the adult rainbow trout.
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Affiliation(s)
- S A Gahr
- United Stated Department of Agriculture, Agriculture Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
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Rallière C, Chauvigné F, Rescan PY. The genes for the helix-loop-helix proteins Id6a, Id6b, Id1 and Id2 are specifically expressed in the ventral and dorsal domains of the fish developing somites. J Exp Biol 2004; 207:2679-84. [PMID: 15201300 DOI: 10.1242/jeb.01088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SUMMARY
Muscle differentiation is inhibited by members of the Id family that block the transcriptional effect of myogenic bHLH regulators by forming inactive heterodimers with them. Also, Id proteins promote cell proliferation by interacting with key regulators of the cell cycle. In order to determine the role of Id-encoding genes during fish development and especially in early myogenesis, we examined the expression patterns of Id1, Id2 and two nonallelic Id6 (Id6a and Id6b)-encoding genes in developing trout embryos. These four Id paralogs were found to exhibit discrete expression in the developing nervous system and in the eye rudiment. During the segmentation process, Id6a, Id6b and Id1 were expressed in the tail bud, the paraxial mesoderm and the ventral and dorsal domains of neoformed somites. As the somite matured in a rostrocaudal progression, the labelling for Id1 transcripts rapidly faded whereas labelling for Id6 transcripts was found to persist until at least the completion of segmentation. By contrast, Id2 transcripts were visualised transiently only in dorsal domains of neoformed somites and strongly accumulated in the pronephros. The preferential localisation of Id6a, Id6b, Id1 and Id2 transcripts within ventral and/or dorsal extremes of the developing somites, suggests that these areas, which were the last ones to express muscle-specific genes, contain dividing cells involved in somite expansion.
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Del Bene F, Tessmar-Raible K, Wittbrodt J. Direct interaction of geminin and Six3 in eye development. Nature 2004; 427:745-9. [PMID: 14973488 DOI: 10.1038/nature02292] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2003] [Accepted: 12/11/2003] [Indexed: 01/19/2023]
Abstract
Organogenesis in vertebrates requires the tight control of cell proliferation and differentiation. The homeobox-containing transcription factor Six3 plays a pivotal role in the proliferation of retinal precursor cells. In a yeast two-hybrid screen, we identified the DNA replication-inhibitor geminin as a partner of Six3. Geminin inhibits cell-cycle progression by sequestering Cdt1 (refs 4, 5), the key component for the assembly of the pre-replication complex. Here, we show that Six3 efficiently competes with Cdt1 directly to bind to geminin, which reveals how Six3 can promote cell proliferation without transcription. In common with Six3 inactivation, overexpression of the geminin gene (Gem; also known as Gmn) in medaka (Oryzias latipes) induces specific forebrain and eye defects that are rescued by Six3. Conversely, loss of Gem (in common with gain of Six3 (ref. 1)) promotes retinal precursor-cell proliferation and results in expanded optic vesicles, markedly potentiating Six3 gain-of-function phenotypes. Our data indicate that the transcription factor Six3 and the replication-initiation inhibitor geminin act antagonistically to control the balance between proliferation and differentiation during early vertebrate eye development.
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Affiliation(s)
- Filippo Del Bene
- Developmental Biology Programme, EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
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15
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Abstract
We have identified Xenopus Id4, a member of the Id (inhibitor of differentiation/DNA binding) class of helix-loop-helix proteins. Id factors dimerize with general bHLH factors, preventing their interaction with tissue-specific bHLH factors, to inhibit premature differentiation. The presence of several Id proteins could reflect simple redundancy in function, or more interestingly, might suggest different activities for these proteins. During embryonic development, Xenopus Id4 is expressed in a number of neural tissues, including Rohon-Beard neurons, olfactory placode, eye primordia, and the trigeminal ganglia. It is also expressed in other organs, such as the pronephros and liver primordium. As embryogenesis progresses, it is expressed in the migrating melanocytes and lateral line structures. We compare the expression of Id4 mRNA with that of Id2 and Id3 and find that the Id genes are expressed in complementary patterns during neurogenesis, myogenesis, kidney development, in the tailbud, and in the migrating neural crest. To examine the regulation of Id gene expression during Xenopus neural development, we show that expression of Id3 and Id4 can be induced by overexpression of BMP4 in the whole embryo and in ectodermal explants. Expression of Id2, Id3, and Id4 in these explants is unaffected by the expression of FGF-8 or a dominant-negative Ras (N17ras), suggesting that Id genes are not regulated by the FGF signaling pathway in naive ectoderm. We also show that Notch signaling can activate Id2 and Id3 expression in the whole embryo. In contrast, Id4 expression in the Rohon-Beard cells is inhibited by activated Notch and increased by a dominant-negative Delta. This may reflect an increase in Rohon-Beard cells in response to inhibition of Notch signaling rather than transcriptional regulation of Id4. Finally, to compare the activities of Id2, Id3, and Id4, we use animal cap explants and in vivo overexpression to show that Id proteins can differentially inhibit the activities of neurogenin and neuroD, both neurogenic bHLH molecules and MyoD, a myogenic bHLH protein. Id4 is able to inhibit the activity all these bHLH molecules, Id2 inhibits MyoD and neuroD, while Id3 blocks only neuroD activity in our assays.
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Affiliation(s)
- Karen J Liu
- Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
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Wang X, Emelyanov A, Korzh V, Gong Z. Zebrafish atonal homologue zath3 is expressed during neurogenesis in embryonic development. Dev Dyn 2003; 227:587-92. [PMID: 12889068 DOI: 10.1002/dvdy.10331] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Basic helix-loop-helix (bHLH) transcriptional activators function in development of various cell lineages, including the central nervous system. One of the bHLH proteins, Math3/Xath3/NeuroM, was suggested to act as a late proneural gene in the mouse, Xenopus, and chick. Here, we isolated a zebrafish homologue, named zath3, and analyzed its expression pattern in zebrafish embryos. In the neural plate, zath3 is expressed first in the primordia of the tegmentum and trigeminal ganglia and three classes of primary neurons: sensory neurons, interneurons, and motor neurons. During later development, zath3 transcripts were localized along the boundaries of the optic tectum in the midbrain and rhombomeres of the hindbrain. Analyses of zath3 expression in three mid-hindbrain boundary mutants, acerebellar, no isthmus, and spiel-ohne-grensen, indicated that distribution of zath3 mRNAs in the midbrain and hindbrain was dramatically disturbed. In addition, these mutants also affect expression of zath3 in the neuroretina.
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Affiliation(s)
- Xukun Wang
- Department of Biological Sciences, National University of Singapore, Singapore
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17
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Desprez PY, Sumida T, Coppé JP. Helix-loop-helix proteins in mammary gland development and breast cancer. J Mammary Gland Biol Neoplasia 2003; 8:225-39. [PMID: 14635797 DOI: 10.1023/a:1025957025773] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The basic helix-loop-helix (bHLH) family of transcription factors functions in the coordinated regulation of gene expression, cell lineage commitment, and cell differentiation in most mammalian tissues. Helix-loop-helix Id (Inhibitor of DNA binding) proteins are distinct from bHLH transcription factors in that they lack the basic domain necessary for DNA binding. Id proteins thus function as dominant negative regulators of bHLH transcription factors. The inhibition of bHLH factor activity by forced constitutive expression of Id proteins is closely associated with the inhibition of differentiation in a number of different cell types, including mammary epithelial cells. Moreover, recent literature suggests important roles of HLH proteins in many normal and transformed tissues, including mammary gland. Therefore, future directions for prognosis or therapeutic treatments of breast cancer may be able to exploit bHLH and Id genes as useful molecular targets. The purpose of this review is to summarize the evidence implicating HLH proteins in the regulation of normal and transformed mammary epithelial cell phenotypes.
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Affiliation(s)
- Pierre-Yves Desprez
- California Pacific Medical Center, Cancer Research Institute, San Francisco, California 94115, USA.
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18
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Kee Y, Bronner-Fraser M. Temporally and spatially restricted expression of the helix-loop-helix transcriptional regulator Id1 during avian embryogenesis. Mech Dev 2001; 109:331-5. [PMID: 11731245 DOI: 10.1016/s0925-4773(01)00574-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We isolated the chick orthologue of the Id1 helix-loop-helix gene and analyzed its expression pattern during early chick embryo development by whole-mount in situ hybridization. The Id1 expression pattern is dynamic and confined to discrete locations including the neural plate border, prospective olfactory placode, hindbrain, mesenchyme of distal branchial arches and adjacent to placodes, and the distal mesoderm of the limb buds.
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Affiliation(s)
- Y Kee
- Division of Biology, 139-74 California Institute of Technology, Pasadena, CA 91125, USA
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19
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Rescan PY. Regulation and functions of myogenic regulatory factors in lower vertebrates. Comp Biochem Physiol B Biochem Mol Biol 2001; 130:1-12. [PMID: 11470439 DOI: 10.1016/s1096-4959(01)00412-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The transcription factors of the MyoD family have essential functions in myogenic lineage determination and muscle differentiation. These myogenic regulatory factors (MRFs) activate muscle-specific transcription through binding to a DNA consensus sequence known as the E-box present in the promoter of numerous muscle genes. Four members, MyoD, myogenin, myf5 and MRF4/herculin/myf6, have been identified in higher vertebrates and have been shown to exhibit distinct but overlapping functions. Homologues of these four MRFs have also been isolated in a variety of lower vertebrates, including amphibians and fish. Differences have been observed, however, in both the expression patterns of MRFs during muscle development and the function of individual MRFs between lower and higher vertebrates. These differences reflect the variety of body muscle formation patterns among vertebrates. Furthermore, as a result of an additional polyploidy that occurred during the evolution of some amphibians and fish, MyoD, myogenin, myf5 and MRF4 may exist in lower vertebrates in two distinct copies that have evolved separately, acquiring specific roles and resulting in increased complexity of the myogenic regulatory network. Evidence is now accumulating that many of the co-factors (E12, Id, MEF2 and CRP proteins) that regulate MRF activity in mammals are also present in lower vertebrates. The inductive signals controlling the initial expression of MRFs within the developing somite of lower vertebrate proteins are currently being elucidated.
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Affiliation(s)
- P Y Rescan
- Scribe-INRA, Campus de Beaulieu, 35042, Rennes, France.
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20
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Woo PL, Cercek A, Desprez PY, Firestone GL. Involvement of the helix-loop-helix protein Id-1 in the glucocorticoid regulation of tight junctions in mammary epithelial cells. J Biol Chem 2000; 275:28649-58. [PMID: 10878025 DOI: 10.1074/jbc.m910373199] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammary epithelial cell-cell junctions undergo morphological and structural differentiation during pregnancy and lactation, but little is known about the transcriptional regulators that are involved in this process. In Con8 mammary epithelial tumor cells, we have previously documented that the synthetic glucocorticoid, dexamethasone, induces the reorganization of the tight junction and adherens junction and stimulates the monolayer transepithelial electrical resistance (TER), a reliable in vitro measurement of tight junction sealing. Western blots demonstrated that dexamethasone treatment rapidly and strongly stimulated the level of the Id-1 protein, which is a serum-inducible helix-loop-helix transcriptional repressor. The steroid induction of Id-1 was robust by 4 h of treatment and maintained over a 24-h period. Isopropyl-1-thio-beta-d-galactopyranoside-inducible expression of exogenous Id-1 in Con8 cells was shown to strongly facilitate the dexamethasone induction of TER in the absence of serum without altering the dexamethasone-dependent reorganization of ZO-1, beta-catenin, or F-actin. Ectopic overexpression of Id-1 in the SCp2 nontumorigenic mammary epithelial cells, which does not undergo complete dexamethasone-dependent tight junction reorganization, enhanced the dexamethasone-induced ZO-1 tight junction localization and stimulated the monolayer TER. Moreover, antisense reduction of Id-1 protein in SCp2 cells prevented the apical junction reorganization and dexamethasone-stimulated TER. Our results implicate Id-1 as acting as a critical regulator of mammary epithelial cell-cell interactions at an early step in the glucocorticoid-dependent signaling pathway that controls tight junction integrity.
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Affiliation(s)
- P L Woo
- Department of Molecular and Cell Biology and the Cancer Research Laboratory, University of California at Berkeley, Berkeley, California 94720-3200, USA
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21
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Takke C, Dornseifer P, v Weizsäcker E, Campos-Ortega JA. her4, a zebrafish homologue of the Drosophila neurogenic gene E(spl), is a target of NOTCH signalling. Development 1999; 126:1811-21. [PMID: 10101116 DOI: 10.1242/dev.126.9.1811] [Citation(s) in RCA: 124] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
her4 encodes a zebrafish bHLH protein of the hairy-E(spl) family. The gene is transcribed in a complex pattern in the developing nervous system and in the hypoblast. During early neurogenesis, her4 expression domains include the regions of the neural plate from which primary neurons arise, suggesting that the gene is involved in directing their development. Indeed, misexpression of specific her4 variants leads to a reduction in the number of primary neurons formed. The amino-terminal region of her4, including the basic domain, and the region between the putative helix IV and the carboxy-terminal tetrapeptide wrpw are essential for this effect, since her4 variants lacking either of these regions are non-functional. However, the carboxy-terminal wrpw itself is dispensable. We have examined the interrelationships between deltaD, deltaA, notch1, her4 and neurogenin1 by means of RNA injections. her4 is involved in a regulatory feedback loop which modulates the activity of the proneural gene neurogenin, and as a consequence, of deltaA and deltaD. Activation of notch1 leads to strong activation of her4, to suppression of neurogenin transcription and, ultimately, to a reduction in the number of primary neurons. These results suggest that her4 acts as a target of notch-mediated signals that regulate primary neurogenesis.
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Affiliation(s)
- C Takke
- Institut für Entwicklungsbiologie, Universität zu Köln, Germany
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22
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van Crüchten I, Cinato E, Fox M, King ER, Newton JS, Riechmann V, Sablitzky F. Structure, chromosomal localisation and expression of the murine dominant negative helix-loop-helix Id4 gene. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1443:55-64. [PMID: 9838043 DOI: 10.1016/s0167-4781(98)00196-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Id proteins antagonise the functional properties of DNA-binding, basic helix-loop-helix transcription factors. Id proteins inhibited cell differentiation in various model systems, both in vitro and in vivo. They are transcriptionally and post-transcriptionally regulated during cell cycle progression and promote cell proliferation. In order to establish the molecular and functional properties of Id4, we analysed structure, chromosomal localisation and expression of the murine Id4 gene. Sequence analysis indicated that the Id4 gene consists of three exons. Multiple transcription start sites map about 300 bp upstream of the ATG translational start codon within a 30-bp region of the Id4 promoter, which lacks a classic TATA box. Expression of the Id4 gene results in four major transcripts, most likely generated by differential use of polyadenylation sites. Abundance of the four transcripts varies across tissues, suggesting tissue-specific regulation of polyadenylation and/or post-transcriptional regulation of Id4 expression. However, the Id4 gene seems to be expressed as a single protein. Id4 expression is switched on during embryogenesis between day 7.5 and 9.5 of gestation and is most abundant in adult brain, kidney and testis. Id4 maps to chromosome 13 of the mouse.
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Affiliation(s)
- I van Crüchten
- University College London, Department of Medicine, The Windeyer Institute of Medical Sciences, 46 Cleveland Street, London W1P 6DB, UK
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Abstract
Vertebrate neural crest cells, derived from the neural folds, generate a variety of tissues, such as cartilage, ganglia, and cranial (intramembranous) bone. The chick homolog of the helix-loop-helix transcriptional regulator Id2 is expressed in cranial but not trunk neural folds and subsequently in some migrating cranial neural crest cells. Ectopic expression of Id2 with recombinant retroviruses converted ectodermal cells to a neural crest fate, demonstrating that proper regulation of Id2 is important for sustaining epidermal traits. In addition, overexpression of Id2 resulted in overgrowth and premature neurogenesis of the dorsal neural tube. These results suggest that Id2 may allocate ectodermal precursors into neural rather than epidermal lineages.
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Affiliation(s)
- B J Martinsen
- B. J. Martinsen, Division of Biology, Beckman Institute 139-74, California Institute of Technology, Pasadena, CA 91125, USA
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Norton JD, Deed RW, Craggs G, Sablitzky F. Id helix—loop—helix proteins in cell growth and differentiation. Trends Cell Biol 1998. [DOI: 10.1016/s0962-8924(98)80013-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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