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Baldera D, Baxendale S, van Hateren NJ, Marzo M, Glendenning E, Geng F, Yokoya K, Knight RD, Whitfield TT. Enhancer trap lines with GFP driven by smad6b and frizzled1 regulatory sequences for the study of epithelial morphogenesis in the developing zebrafish inner ear. J Anat 2023; 243:78-89. [PMID: 36748120 PMCID: PMC10273346 DOI: 10.1111/joa.13845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
Live imaging in the zebrafish embryo using tissue-specific expression of fluorescent proteins can yield important insights into the mechanisms that drive sensory organ morphogenesis and cell differentiation. Morphogenesis of the semicircular canal ducts of the vertebrate inner ear requires a complex rearrangement of epithelial cells, including outgrowth, adhesion, fusion and perforation of epithelial projections to generate pillars of tissue that form the hubs of each canal. We report the insertion sites and expression patterns of two enhancer trap lines in the developing zebrafish embryo, each of which highlight different aspects of epithelial cell morphogenesis in the inner ear. A membrane-linked EGFP driven by smad6b regulatory sequences is expressed throughout the otic epithelium, most strongly on the lateral side of the ear and in the sensory cristae. A second enhancer trap line, with cytoplasmic EGFP driven by frizzled1 (fzd1) regulatory sequences, specifically marks cells of the ventral projection and pillar in the developing ear, and marginal cells in the sensory cristae, together with variable expression in the retina and epiphysis, and neurons elsewhere in the developing central nervous system. We have used a combination of methods to identify the insertion sites of these two transgenes, which were generated through random insertion, and show that Targeted Locus Amplification is a rapid and reliable method for the identification of insertion sites of randomly inserted transgenes.
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Affiliation(s)
- Davide Baldera
- School of BiosciencesUniversity of SheffieldSheffieldUK
- Present address:
CeSASt, University of CagliariCagliariItaly
| | | | | | - Mar Marzo
- School of BiosciencesUniversity of SheffieldSheffieldUK
| | | | - Fan‐Suo Geng
- Brain and Mind Research Institute, University of SydneySydneyNew South WalesAustralia
- Present address:
Data Science Institute, The University of Technology SydneySydneyAustralia
| | - Kazutomo Yokoya
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's HospitalLondonUK
| | - Robert D. Knight
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's HospitalLondonUK
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2
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Bordeira-Carriço R, Teixeira J, Duque M, Galhardo M, Ribeiro D, Acemel RD, Firbas PN, Tena JJ, Eufrásio A, Marques J, Ferreira FJ, Freitas T, Carneiro F, Goméz-Skarmeta JL, Bessa J. Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers. Nat Commun 2022; 13:1945. [PMID: 35410466 PMCID: PMC9001708 DOI: 10.1038/s41467-022-29551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
The pancreas is a central organ for human diseases. Most alleles uncovered by genome-wide association studies of pancreatic dysfunction traits overlap with non-coding sequences of DNA. Many contain epigenetic marks of cis-regulatory elements active in pancreatic cells, suggesting that alterations in these sequences contribute to pancreatic diseases. Animal models greatly help to understand the role of non-coding alterations in disease. However, interspecies identification of equivalent cis-regulatory elements faces fundamental challenges, including lack of sequence conservation. Here we combine epigenetic assays with reporter assays in zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis-regulatory elements, regardless of sequence conservation. Among other potential disease-relevant enhancers, we identify a zebrafish ptf1a distal-enhancer whose deletion causes pancreatic agenesis, a phenotype previously found to be induced by mutations in a distal-enhancer of PTF1A in humans, further supporting the causality of this condition in vivo. This approach helps to uncover interspecies functionally equivalent cis-regulatory elements and their potential role in human disease. Alterations in cis-regulatory elements (CREs) can contribute to pancreatic diseases. Here the authors combine chromatin profiling and interaction points with in vivo reporter assays in zebrafish to uncover functionally equivalent human CREs, helping to predict disease-relevant enhancers.
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Bhatia S, Kleinjan DJ, Uttley K, Mann A, Dellepiane N, Bickmore WA. Quantitative spatial and temporal assessment of regulatory element activity in zebrafish. eLife 2021; 10:65601. [PMID: 34796872 PMCID: PMC8604437 DOI: 10.7554/elife.65601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Mutations or genetic variation in noncoding regions of the genome harbouring cis-regulatory elements (CREs), or enhancers, have been widely implicated in human disease and disease risk. However, our ability to assay the impact of these DNA sequence changes on enhancer activity is currently very limited because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type and disease-associated mutant human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. The activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing simultaneous visualisation of where and when in development the wild-type allele is active and how this activity is altered by mutation.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan Kleinjan
- Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsty Uttley
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Anita Mann
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Nefeli Dellepiane
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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4
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Crespo D, Assis LHC, Zhang YT, Safian D, Furmanek T, Skaftnesmo KO, Norberg B, Ge W, Choi YC, den Broeder MJ, Legler J, Bogerd J, Schulz RW. Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells. Commun Biol 2021; 4:204. [PMID: 33589679 PMCID: PMC7884674 DOI: 10.1038/s42003-021-01708-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/13/2021] [Indexed: 01/31/2023] Open
Abstract
Pituitary hormones can use local signaling molecules to regulate target tissue functions. In adult zebrafish testes, follicle-stimulating hormone (Fsh) strongly increases the production of insulin-like 3 (Insl3), a Leydig cell-derived growth factor found in all vertebrates. Little information is available regarding Insl3 function in adult spermatogenesis. The Insl3 receptors Rxfp2a and 2b were expressed by type A spermatogonia and Sertoli and myoid cells, respectively, in zebrafish testis tissue. Loss of insl3 increased germ cell apoptosis in males starting at 9 months of age, but spermatogenesis appeared normal in fully fertile, younger adults. Insl3 changed the expression of 409 testicular genes. Among others, retinoic acid (RA) signaling was up- and peroxisome proliferator-activated receptor gamma (Pparg) signaling was down-regulated. Follow-up studies showed that RA and Pparg signaling mediated Insl3 effects, resulting in the increased production of differentiating spermatogonia. This suggests that Insl3 recruits two locally active nuclear receptor pathways to implement pituitary (Fsh) stimulation of spermatogenesis.
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Affiliation(s)
- Diego Crespo
- grid.5477.10000000120346234Reproductive Biology Group, Division Developmental Biology, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands ,grid.10917.3e0000 0004 0427 3161Present Address: Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Luiz H. C. Assis
- grid.5477.10000000120346234Reproductive Biology Group, Division Developmental Biology, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
| | - Yu Ting Zhang
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Fujian, PR China ,grid.449133.80000 0004 1764 3555Present Address: Institute of Oceanography, Minjiang University, Fuzhou, PR China
| | - Diego Safian
- grid.5477.10000000120346234Reproductive Biology Group, Division Developmental Biology, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Experimental Zoology Group and Aquaculture and Fisheries Group, Department of Animal Science, Wageningen University, Wageningen, The Netherlands
| | - Tomasz Furmanek
- grid.10917.3e0000 0004 0427 3161Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Kai Ove Skaftnesmo
- grid.10917.3e0000 0004 0427 3161Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Birgitta Norberg
- grid.10917.3e0000 0004 0427 3161Institute of Marine Research, Austevoll Research Station, Storebø, Norway
| | - Wei Ge
- grid.437123.00000 0004 1794 8068Center of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau China
| | - Yung-Ching Choi
- grid.437123.00000 0004 1794 8068Center of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau China
| | - Marjo J. den Broeder
- grid.5477.10000000120346234Division of Toxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Juliette Legler
- grid.5477.10000000120346234Division of Toxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jan Bogerd
- grid.5477.10000000120346234Reproductive Biology Group, Division Developmental Biology, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
| | - Rüdiger W. Schulz
- grid.5477.10000000120346234Reproductive Biology Group, Division Developmental Biology, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands ,grid.10917.3e0000 0004 0427 3161Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
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Zhang G, Ferg M, Lübke L, Takamiya M, Beil T, Gourain V, Diotel N, Strähle U, Rastegar S. Bone morphogenetic protein signaling regulates Id1-mediated neural stem cell quiescence in the adult zebrafish brain via a phylogenetically conserved enhancer module. Stem Cells 2020; 38:875-889. [PMID: 32246536 DOI: 10.1002/stem.3182] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022]
Abstract
In the telencephalon of adult zebrafish, the inhibitor of DNA binding 1 (id1) gene is expressed in radial glial cells (RGCs), behaving as neural stem cells (NSCs), during constitutive and regenerative neurogenesis. Id1 controls the balance between resting and proliferating states of RGCs by promoting quiescence. Here, we identified a phylogenetically conserved cis-regulatory module (CRM) mediating the specific expression of id1 in RGCs. Systematic deletion mapping and mutation of conserved transcription factor binding sites in stable transgenic zebrafish lines reveal that this CRM operates via conserved smad1/5 and 4 binding motifs under both homeostatic and regenerative conditions. Transcriptome analysis of injured and uninjured telencephala as well as pharmacological inhibition experiments identify a crucial role of bone morphogenetic protein (BMP) signaling for the function of the CRM. Our data highlight that BMP signals control id1 expression and thus NSC proliferation during constitutive and induced neurogenesis.
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Affiliation(s)
- Gaoqun Zhang
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Marco Ferg
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Luisa Lübke
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tanja Beil
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Victor Gourain
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Nicolas Diotel
- Université de La Réunion, INSERM, UMR 1188, Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Uwe Strähle
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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6
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Mann A, Bhatia S. Zebrafish: A Powerful Model for Understanding the Functional Relevance of Noncoding Region Mutations in Human Genetic Diseases. Biomedicines 2019; 7:E71. [PMID: 31527394 PMCID: PMC6784013 DOI: 10.3390/biomedicines7030071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Determining aetiology of genetic disorders caused by damaging mutations in protein-coding genes is well established. However, understanding how mutations in the vast stretches of the noncoding genome contribute to genetic abnormalities remains a huge challenge. Cis-regulatory elements (CREs) or enhancers are an important class of noncoding elements. CREs function as the primary determinants of precise spatial and temporal regulation of their target genes during development by serving as docking sites for tissue-specific transcription factors. Although a large number of potential disease-associated CRE mutations are being identified in patients, lack of robust methods for mechanistically linking these mutations to disease phenotype is currently hampering the understanding of their roles in disease aetiology. Here, we have described the various systems available for testing the CRE potential of stretches of noncoding regions harbouring mutations implicated in human disease. We highlight advances in the field leading to the establishment of zebrafish as a powerful system for robust and cost-effective functional assays of CRE activity, enabling rapid identification of causal variants in regulatory regions and the validation of their role in disruption of appropriate gene expression.
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Affiliation(s)
- Anita Mann
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Shipra Bhatia
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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7
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Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons. Genes (Basel) 2018; 9:genes9120630. [PMID: 30551672 PMCID: PMC6316676 DOI: 10.3390/genes9120630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022] Open
Abstract
Although transposon-mediated enhancer trapping (ET) is successfully applied in diverse models, the efficiency of various transposon systems varies significantly, and little information is available regarding efficiency of enhancer trapping by various transposons in zebrafish. Most potential enhancers (Ens) still lack evidence of actual En activity. Here, we compared the differences in ET efficiency between sleeping beauty (SB), piggyBac (PB) and Tol2 transposons. Tol2 represented the highest germline transfer efficiencies at 55.56% (NF0 = 165), followed by SB (38.36%, NF0 = 151) and PB (32.65%, NF0 = 149). ET lines generated by the Tol2 transposon tended to produce offspring with a single expression pattern per line, while PB and SB tended to generate embryos with multiple expression patterns. In our tests, 10 putative Ens (En1–10) were identified by splinkerette PCR and comparative genomic analysis. Combining the GFP expression profiles and mRNA expression patterns revealed that En1 and En2 may be involved in regulation of the expression of dlx1a and dlx2a, while En6 may be involved in regulation of the expression of line TK4 transgene and rps26, and En7 may be involved in the regulation of the expression of wnt1 and wnt10b. Most identified Ens were found to be transcribed in zebrafish embryos, and their regulatory function may involve eRNAs.
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Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W, Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M, Padilla S, Reif DM, Tanguay RL, Hamm J. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 2016; 33:435-452. [PMID: 27328013 PMCID: PMC5270630 DOI: 10.14573/altex.1601281] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Small freshwater fish models, especially zebrafish, offer advantages over traditional rodent models, including low maintenance and husbandry costs, high fecundity, genetic diversity, physiology similar to that of traditional biomedical models, and reduced animal welfare concerns. The Collaborative Workshop on Aquatic Models and 21st Century Toxicology was held at North Carolina State University on May 5-6, 2014, in Raleigh, North Carolina, USA. Participants discussed the ways in which small fish are being used as models to screen toxicants and understand mechanisms of toxicity. Workshop participants agreed that the lack of standardized protocols is an impediment to broader acceptance of these models, whereas development of standardized protocols, validation, and subsequent regulatory acceptance would facilitate greater usage. Given the advantages and increasing application of small fish models, there was widespread interest in follow-up workshops to review and discuss developments in their use. In this article, we summarize the recommendations formulated by workshop participants to enhance the utility of small fish species in toxicology studies, as well as many of the advances in the field of toxicology that resulted from using small fish species, including advances in developmental toxicology, cardiovascular toxicology, neurotoxicology, and immunotoxicology. We alsoreview many emerging issues that will benefit from using small fish species, especially zebrafish, and new technologies that will enable using these organisms to yield results unprecedented in their information content to better understand how toxicants affect development and health.
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Affiliation(s)
- Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carolyn J. Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - David Allen
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David Hinton
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Jyotshna Kanungo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Seth W. Kullman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Tamara Tal
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Maria Bondesson
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | | | - Con Sullivan
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Carol Kim
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Mamta Behl
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Stephanie Padilla
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Jon Hamm
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
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Rinkwitz S, Geng FS, Manning E, Suster M, Kawakami K, Becker TS. BAC transgenic zebrafish reveal hypothalamic enhancer activity around obesity associated SNP rs9939609 within the human FTO gene. Genesis 2015; 53:640-51. [PMID: 26271004 PMCID: PMC5054831 DOI: 10.1002/dvg.22884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/05/2015] [Accepted: 08/12/2015] [Indexed: 12/22/2022]
Abstract
Single Nucleotide Polymorphisms in FTO intron 1 have been associated with obesity risk, leading to the hypothesis that FTO is the obesity‐related gene. However, other studies have shown that the FTO gene is part of the regulatory domain of the neighboring IRX3 gene and that enhancers in FTO intron 1 regulate IRX3. While Irx3 activity was shown to be necessary in the hypothalamus for the metabolic function of Irx3 in mouse, no enhancers with hypothalamic activity have been demonstrated in the risk‐associated region within FTO. In order to identify potential enhancers at the human FTO locus in vivo, we tested regulatory activity in FTO intron 1 using BAC transgenesis in zebrafish. A minimal gata2 promoter‐GFP cassette was inserted 1.3 kb upstream of the obesity associated SNP rs9939609 in a human FTO BAC plasmid. In addition to the previously identified expression domains in notochord and kidney, human FTO BAC:GFP transgenic zebrafish larvae expressed GFP in the ventral posterior tuberculum, the posterior hypothalamus and the anterior brainstem, which are also expression domains of zebrafish irx3a. In contrast, an in‐frame insertion of a GFP cassette at the FTO start codon resulted in weak ubiquitous GFP expression indicating that the promoter of FTO does likely not react to enhancers located in the obesity risk‐associated region. genesis 53:640–651, 2015. © 2015 The Authors. genesis Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Silke Rinkwitz
- Brain and Mind Research Institute, School of Medicine, University of Sydney, Camperdown, New South Wales, Australia.,Department of Physiology, School of Medicine, University of Sydney, Australia
| | - Fan-Suo Geng
- Brain and Mind Research Institute, School of Medicine, University of Sydney, Camperdown, New South Wales, Australia
| | - Elizabeth Manning
- Brain and Mind Research Institute, School of Medicine, University of Sydney, Camperdown, New South Wales, Australia
| | | | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Thomas S Becker
- Brain and Mind Research Institute, School of Medicine, University of Sydney, Camperdown, New South Wales, Australia.,Department of Physiology, School of Medicine, University of Sydney, Australia
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Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene. Hum Genet 2015; 134:1163-82. [PMID: 26337422 DOI: 10.1007/s00439-015-1594-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/16/2015] [Indexed: 10/23/2022]
Abstract
Protein-coding mutations in the transcription factor-encoding gene ARX cause various forms of intellectual disability (ID) and epilepsy. In contrast, variations in surrounding non-coding sequences are correlated with milder forms of non-syndromic ID and autism and had suggested the importance of ARX gene regulation in the etiology of these disorders. We compile data on several novel and some already identified patients with or without ID that carry duplications of ARX genomic region and consider likely genetic mechanisms underlying the neurodevelopmental defects. We establish the long-range regulatory domain of ARX and identify its brain region-specific autoregulation. We conclude that neurodevelopmental disturbances in the patients may not simply arise from increased dosage due to ARX duplication. This is further exemplified by a small duplication involving a non-functional ARX copy, but with duplicated enhancers. ARX enhancers are located within a 504-kb region and regulate expression specifically in the forebrain in developing and adult zebrafish. Transgenic enhancer-reporter lines were used as in vivo tools to delineate a brain region-specific negative and positive autoregulation of ARX. We find autorepression of ARX in the telencephalon and autoactivation in the ventral thalamus. Fluorescently labeled brain regions in the transgenic lines facilitated the identification of neuronal outgrowth and pathfinding disturbances in the ventral thalamus and telencephalon that occur when arxa dosage is diminished. In summary, we have established a model for how breakpoints in long-range gene regulation alter the expression levels of a target gene brain region-specifically, and how this can cause subtle neuronal phenotypes relating to the etiology of associated neuropsychiatric disease.
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11
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Bhatia S, Gordon CT, Foster RG, Melin L, Abadie V, Baujat G, Vazquez MP, Amiel J, Lyonnet S, van Heyningen V, Kleinjan DA. Functional assessment of disease-associated regulatory variants in vivo using a versatile dual colour transgenesis strategy in zebrafish. PLoS Genet 2015; 11:e1005193. [PMID: 26030420 PMCID: PMC4452300 DOI: 10.1371/journal.pgen.1005193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/02/2015] [Indexed: 11/26/2022] Open
Abstract
Disruption of gene regulation by sequence variation in non-coding regions of the genome is now recognised as a significant cause of human disease and disease susceptibility. Sequence variants in cis-regulatory elements (CREs), the primary determinants of spatio-temporal gene regulation, can alter transcription factor binding sites. While technological advances have led to easy identification of disease-associated CRE variants, robust methods for discerning functional CRE variants from background variation are lacking. Here we describe an efficient dual-colour reporter transgenesis approach in zebrafish, simultaneously allowing detailed in vivo comparison of spatio-temporal differences in regulatory activity between putative CRE variants and assessment of altered transcription factor binding potential of the variant. We validate the method on known disease-associated elements regulating SHH, PAX6 and IRF6 and subsequently characterise novel, ultra-long-range SOX9 enhancers implicated in the craniofacial abnormality Pierre Robin Sequence. The method provides a highly cost-effective, fast and robust approach for simultaneously unravelling in a single assay whether, where and when in embryonic development a disease-associated CRE-variant is affecting its regulatory function. Cis-regulatory elements (CREs) play a vital role in gene regulation by providing spatial and temporal specificity to the expression of their target genes. Understanding how these regions of the genome work is of vital importance for human health as it has been demonstrated that genetic changes in these regions can result in incorrect gene expression, leading to a variety of human diseases. Functional characterization of putative CREs and the effects of mutations on their activity is currently a major bottleneck in many studies towards understanding the causes and mechanisms of disease and disease susceptibility. We describe a robust in-vivo approach using dual-colour reporter transgenesis in zebrafish for unambiguous assessment of the effects of disease-associated CRE mutations on CRE activity during the entire time-course of embryonic development. The highly efficient, cost-effective and modular design of the assay allows rapid analysis of several CRE-variants in parallel. We illustrate the robustness of our approach using examples of CRE-variants associated with a broad spectrum of genetic diseases including brain, limb, eye and jaw disorders. In a single assay the method can address where and when in development the CRE variant affects its activity, what potential target genes are misregulated by the change and what upstream trans-acting factors are likely to mediate this effect.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (SB); (VvH); (DAK)
| | - Christopher T. Gordon
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
| | - Robert G. Foster
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Lucie Melin
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
| | - Véronique Abadie
- Service de Pédiatrie Générale, Université Paris Descartes, Hôpital Necker-Enfants Malades, Paris, France
| | - Geneviève Baujat
- Departement de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris France
| | - Marie-Paule Vazquez
- Service de Chirurgie Maxillo-Faciale et Plastique, CRMR des Malformations de la Face et de la Cavité Buccale, Hôpital Necker-Enfants Malades, Paris, France
| | - Jeanne Amiel
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
- Departement de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris France
| | - Stanislas Lyonnet
- INSERM U781, Hôpital Necker-Enfants Malades and Université Paris Descartes-Sorbonne Paris Cité, Institute Imagine, Paris, France
- Departement de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris France
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (SB); (VvH); (DAK)
| | - Dirk A. Kleinjan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (SB); (VvH); (DAK)
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Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. Nat Commun 2015; 6:6904. [PMID: 25908307 PMCID: PMC4423230 DOI: 10.1038/ncomms7904] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 03/12/2015] [Indexed: 01/31/2023] Open
Abstract
Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression. Enhancers regulate the transcription of genes over long genomic distances. Here, the authors show that enhancer function is correlated with maintenance of linkage between non-coding elements and neighbouring genes in the human X chromosome and that enhancers in zebrafish drive expression in a pattern consistent with the expression of a linked gene.
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13
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Fogarty MP, Cannon ME, Vadlamudi S, Gaulton KJ, Mohlke KL. Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus. PLoS Genet 2014; 10:e1004633. [PMID: 25211022 PMCID: PMC4161327 DOI: 10.1371/journal.pgen.1004633] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/28/2014] [Indexed: 12/28/2022] Open
Abstract
Many of the type 2 diabetes loci identified through genome-wide association studies localize to non-protein-coding intronic and intergenic regions and likely contain variants that regulate gene transcription. The CDC123/CAMK1D type 2 diabetes association signal on chromosome 10 spans an intergenic region between CDC123 and CAMK1D and also overlaps the CDC123 3'UTR. To gain insight into the molecular mechanisms underlying the association signal, we used open chromatin, histone modifications and transcription factor ChIP-seq data sets from type 2 diabetes-relevant cell types to identify SNPs overlapping predicted regulatory regions. Two regions containing type 2 diabetes-associated variants were tested for enhancer activity using luciferase reporter assays. One SNP, rs11257655, displayed allelic differences in transcriptional enhancer activity in 832/13 and MIN6 insulinoma cells as well as in human HepG2 hepatocellular carcinoma cells. The rs11257655 risk allele T showed greater transcriptional activity than the non-risk allele C in all cell types tested. Using electromobility shift and supershift assays we demonstrated that the rs11257655 risk allele showed allele-specific binding to FOXA1 and FOXA2. We validated FOXA1 and FOXA2 enrichment at the rs11257655 risk allele using allele-specific ChIP in human islets. These results suggest that rs11257655 affects transcriptional activity through altered binding of a protein complex that includes FOXA1 and FOXA2, providing a potential molecular mechanism at this GWAS locus.
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Affiliation(s)
- Marie P. Fogarty
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Maren E. Cannon
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Marsh EK, Balciuniene J, Balciunas D, Müller F. Targeted transgene integration overcomes variability of position effects in zebrafish. Development 2014; 141:715-24. [PMID: 24449846 DOI: 10.1242/dev.100347] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Zebrafish transgenesis is increasingly popular owing to the optical transparency and external development of embryos, which provide a scalable vertebrate model for in vivo experimentation. The ability to express transgenes in a tightly controlled spatio-temporal pattern is an important prerequisite for exploitation of zebrafish in a wide range of biomedical applications. However, conventional transgenesis methods are plagued by position effects: the regulatory environment of genomic integration sites leads to variation of expression patterns of transgenes driven by engineered cis-regulatory modules. This limitation represents a bottleneck when studying the precise function of cis-regulatory modules and their subtle variants or when various effector proteins are to be expressed for labelling and manipulation of defined sets of cells. Here, we provide evidence for the efficient elimination of variability of position effects by developing a PhiC31 integrase-based targeting method. To detect targeted integration events, a simple phenotype scoring of colour change in the lens of larvae is used. We compared PhiC31-based integration and Tol2 transgenesis in the analysis of the activity of a novel conserved enhancer from the developmentally regulated neural-specific esrrga gene. Reporter expression was highly variable among independent lines generated with Tol2, whereas all lines generated with PhiC31 into a single integration site displayed nearly identical, enhancer-specific reporter expression in brain nuclei. Moreover, we demonstrate that a modified integrase system can also be used for the detection of enhancer activity in transient transgenesis. These results demonstrate the power of the PhiC31-based transgene integration for the annotation and fine analysis of transcriptional regulatory elements and it promises to be a generally desirable tool for a range of applications, which rely on highly reproducible patterns of transgene activity in zebrafish.
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Affiliation(s)
- Jennifer Anne Roberts
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos. Dev Biol 2014; 387:214-28. [PMID: 24440152 DOI: 10.1016/j.ydbio.2014.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/29/2013] [Accepted: 01/11/2014] [Indexed: 11/22/2022]
Abstract
Biological differences between cell types and developmental processes are characterised by differences in gene expression profiles. Gene-distal enhancers are key components of the regulatory networks that specify the tissue-specific expression patterns driving embryonic development and cell fate decisions, and variations in their sequences are a major contributor to genetic disease and disease susceptibility. Despite advances in the methods for discovery of putative cis-regulatory sequences, characterisation of their spatio-temporal enhancer activities in a mammalian model system remains a major bottle-neck. We employed a strategy that combines gnathostome sequence conservation with transgenic mouse and zebrafish reporter assays to survey the genomic locus of the developmental control gene PAX6 for the presence of novel cis-regulatory elements. Sequence comparison between human and the cartilaginous elephant shark (Callorhinchus milii) revealed several ancient gnathostome conserved non-coding elements (agCNEs) dispersed widely throughout the PAX6 locus, extending the range of the known PAX6 cis-regulatory landscape to contain the full upstream PAX6-RCN1 intergenic region. Our data indicates that ancient conserved regulatory sequences can be tested effectively in transgenic zebrafish even when not conserved in zebrafish themselves. The strategy also allows efficient dissection of compound regulatory regions previously assessed in transgenic mice. Remarkable overlap in expression patterns driven by sets of agCNEs indicates that PAX6 resides in a landscape of multiple tissue-specific regulatory archipelagos.
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