1
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Liu X, Chen M, Qu X, Liu W, Dou Y, Liu Q, Shi D, Jiang M, Li H. Cis-Regulatory Elements in Mammals. Int J Mol Sci 2023; 25:343. [PMID: 38203513 PMCID: PMC10779164 DOI: 10.3390/ijms25010343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism. An in-depth exploration of enhancers and promoters can substantially enhance our understanding of gene regulatory networks, shedding new light on mammalian development, evolution and disease pathways. In this review, we provide a comprehensive overview of the intrinsic structural attributes, detection methodologies as well as the operational mechanisms of enhancers and promoters, coupled with the relevant novel and innovative investigative techniques used to explore their actions. We further elucidated the state-of-the-art research on the roles of enhancers and promoters in the realms of mammalian development, evolution and disease, and we conclude with forward-looking insights into prospective research avenues.
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Affiliation(s)
| | | | | | | | | | | | | | - Mingsheng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
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2
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Hadzhiev Y, Wheatley L, Cooper L, Ansaloni F, Whalley C, Chen Z, Finaurini S, Gustincich S, Sanges R, Burgess S, Beggs A, Müller F. The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. Dev Cell 2023; 58:155-170.e8. [PMID: 36693321 PMCID: PMC9904021 DOI: 10.1016/j.devcel.2022.12.007] [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: 08/11/2021] [Revised: 08/10/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023]
Abstract
In anamniote embryos, the major wave of zygotic genome activation starts during the mid-blastula transition. However, some genes escape global genome repression, are activated substantially earlier, and contribute to the minor wave of genome activation. The mechanisms underlying the minor wave of genome activation are little understood. We explored the genomic organization and cis-regulatory mechanisms of a transcription body, in which the minor wave of genome activation is first detected in zebrafish. We identified the miR-430 cluster as having excessive copy number and the highest density of Pol-II-transcribed promoters in the genome, and this is required for forming the transcription body. However, this transcription body is not essential for, nor does it encompasse, minor wave transcription globally. Instead, distinct minor-wave-specific promoter architecture suggests that promoter-autonomous mechanisms regulate the minor wave of genome activation. The minor-wave-specific features also suggest distinct transcription initiation mechanisms between the minor and major waves of genome activation.
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Affiliation(s)
- Yavor Hadzhiev
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Lucy Wheatley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ledean Cooper
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Federico Ansaloni
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy; Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Celina Whalley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhelin Chen
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Sara Finaurini
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy; Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Andrew Beggs
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ferenc Müller
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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3
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Begeman IJ, Emery B, Kurth A, Kang J. Regeneration and developmental enhancers are differentially compatible with minimal promoters. Dev Biol 2022; 492:47-58. [PMID: 36167150 PMCID: PMC10211259 DOI: 10.1016/j.ydbio.2022.09.007] [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: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/01/2022]
Abstract
Enhancers and promoters are cis-regulatory elements that control gene expression. Enhancers are activated in a cell type-, tissue-, and condition-specific manner to stimulate promoter function and transcription. Zebrafish have emerged as a powerful animal model for examining the activities of enhancers derived from various species through transgenic enhancer assays, in which an enhancer is coupled with a minimal promoter. However, the efficiency of minimal promoters and their compatibility with multiple developmental and regeneration enhancers have not been systematically tested in zebrafish. Thus, we assessed the efficiency of six minimal promoters and comprehensively interrogated the compatibility of the promoters with developmental and regeneration enhancers. We found that the fos minimal promoter and Drosophila synthetic core promoter (DSCP) yielded high rates of leaky expression that may complicate the interpretation of enhancer assays. Notably, the adenovirus E1b promoter, the zebrafish lepb 0.8-kb (P0.8) and lepb 2-kb (P2) promoters, and a new zebrafish synthetic promoter (ZSP) that combines elements of the E1b and P0.8 promoters drove little or no ectopic expression, making them suitable for transgenic assays. We also found significant differences in compatibility among specific combinations of promoters and enhancers, indicating the importance of promoters as key regulatory elements determining the specificity of gene expression. Our study provides guidelines for transgenic enhancer assays in zebrafish to aid in the discovery of functional enhancers regulating development and regeneration.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Benjamin Emery
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA; UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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4
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Toh K, Saunders D, Verd B, Steventon B. Zebrafish neuromesodermal progenitors undergo a critical state transition in vivo. iScience 2022; 25:105216. [PMID: 36274939 PMCID: PMC9579027 DOI: 10.1016/j.isci.2022.105216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
The transition state model of cell differentiation proposes that a transient window of gene expression stochasticity precedes entry into a differentiated state. Here, we assess this theoretical model in zebrafish neuromesodermal progenitors (NMps) in vivo during late somitogenesis stages. We observed an increase in gene expression variability at the 24 somite stage (24ss) before their differentiation into spinal cord and paraxial mesoderm. Analysis of a published 18ss scRNA-seq dataset showed that the NMp population is noisier than its derivatives. By building in silico composite gene expression maps from image data, we assigned an 'NM index' to in silico NMps based on the expression of neural and mesodermal markers and demonstrated that cell population heterogeneity peaked at 24ss. Further examination revealed cells with gene expression profiles incongruent with their prospective fate. Taken together, our work supports the transition state model within an endogenous cell fate decision making event.
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Affiliation(s)
- Kane Toh
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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5
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Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022; 54:1037-1050. [PMID: 35789323 PMCID: PMC9279159 DOI: 10.1038/s41588-022-01089-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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Affiliation(s)
- Damir Baranasic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Piotr J Balwierz
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Zehnder
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Abdul Kadir Mukarram
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nan Li
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joseph Wragg
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabio M D'Orazio
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dorde Relic
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Institute of Marine Sciences, Barcelona, Spain
| | | | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Marcus Stoiber
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michaël Dong
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Irene Stevens
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anne Eagle
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Ryan Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Oluwapelumi Obasaju
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alison C McGarvey
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Wolfgang Kopp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Emily Chambers
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Dennis Wang
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Hyejeong R Kim
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vanessa Chong
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Fondazione Human Technopole, Milano, Italy
| | - Uwe Ohler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Scott Allen Lacadie
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Shawn M Burgess
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Freek van Eeden
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Daria Onichtchouk
- Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ben James Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Fiona C Wardle
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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6
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Martinez-Ara M, Comoglio F, van Arensbergen J, van Steensel B. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome. Mol Cell 2022; 82:2519-2531.e6. [PMID: 35594855 PMCID: PMC9278412 DOI: 10.1016/j.molcel.2022.04.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/17/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Martinez-Ara
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Federico Comoglio
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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7
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Tsaryk R, Yucel N, Leonard EV, Diaz N, Bondareva O, Odenthal-Schnittler M, Arany Z, Vaquerizas JM, Schnittler H, Siekmann AF. Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites. Sci Rep 2022; 12:4795. [PMID: 35314737 PMCID: PMC8938417 DOI: 10.1038/s41598-022-08645-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Endothelial cells (ECs) lining blood vessels are exposed to mechanical forces, such as shear stress. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation. Despite a good understanding of the genes responding to shear stress, our insight into the transcriptional regulation of these genes is much more limited. Here, we set out to study alterations in the chromatin landscape of human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress. To do so, we performed ChIP-Seq for H3K27 acetylation, indicative of active enhancer elements and ATAC-Seq to mark regions of open chromatin in addition to RNA-Seq on HUVEC exposed to 6 h of laminar shear stress. Our results show a correlation of gained and lost enhancers with up and downregulated genes, respectively. DNA motif analysis revealed an over-representation of KLF transcription factor (TF) binding sites in gained enhancers, while lost enhancers contained more ETV/ETS motifs. We validated a subset of flow responsive enhancers using luciferase-based reporter constructs and CRISPR-Cas9 mediated genome editing. Lastly, we characterized the shear stress response in ECs of zebrafish embryos using RNA-Seq. Our results lay the groundwork for the exploration of shear stress responsive elements in controlling EC biology.
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Affiliation(s)
- Roman Tsaryk
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nora Yucel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Elvin V Leonard
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Noelia Diaz
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Olga Bondareva
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103, Leipzig, Germany
| | - Maria Odenthal-Schnittler
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Institute of Neuropathology, Westfälische Wilhelms-Universität Münster, Pottkamp 2, 48149, Münster, Germany
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Hans Schnittler
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Institute of Neuropathology, Westfälische Wilhelms-Universität Münster, Pottkamp 2, 48149, Münster, Germany
| | - Arndt F Siekmann
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany.
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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8
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Galouzis CC, Furlong EEM. Regulating specificity in enhancer-promoter communication. Curr Opin Cell Biol 2022; 75:102065. [PMID: 35240372 DOI: 10.1016/j.ceb.2022.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
Enhancers are cis-regulatory elements that can activate transcription remotely to regulate a specific pattern of a gene's expression. Genes typically have many enhancers that are often intermingled in the loci of other genes. To regulate expression, enhancers must therefore activate their correct promoter while ignoring others that may be in closer linear proximity. In this review, we discuss mechanisms by which enhancers engage with promoters, including recent findings on the role of cohesin and the Mediator complex, and how this specificity in enhancer-promoter communication is encoded. Genetic dissection of model loci, in addition to more recent findings using genome-wide approaches, highlight the core promoter sequence, its accessibility, cofactor-promoter preference, in addition to the surrounding genomic context, as key components.
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Affiliation(s)
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117, Heidelberg, Germany.
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9
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Kague E, Karasik D. Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models. Genes (Basel) 2022; 13:279. [PMID: 35205324 PMCID: PMC8872034 DOI: 10.3390/genes13020279] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
The advancement of human genomics has revolutionized our understanding of the genetic architecture of many skeletal diseases, including osteoporosis. However, interpreting results from human association studies remains a challenge, since index variants often reside in non-coding regions of the genome and do not possess an obvious regulatory function. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary, such as the one offered by animal models. These models enable us to identify causal mechanisms, clarify the underlying biology, and apply interventions. Over the past several decades, small teleost fishes, mostly zebrafish and medaka, have emerged as powerful systems for modeling the genetics of human diseases. Due to their amenability to genetic intervention and the highly conserved genetic and physiological features, fish have become indispensable for skeletal genomic studies. The goal of this review is to summarize the evidence supporting the utility of Zebrafish (Danio rerio) for accelerating our understanding of human skeletal genomics and outlining the remaining gaps in knowledge. We provide an overview of zebrafish skeletal morphophysiology and gene homology, shedding light on the advantages of human skeletal genomic exploration and validation. Knowledge of the biology underlying osteoporosis through animal models will lead to the translation into new, better and more effective therapeutic approaches.
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Affiliation(s)
- Erika Kague
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK;
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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10
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Hong CKY, Cohen BA. Genomic environments scale the activities of diverse core promoters. Genome Res 2022; 32:85-96. [PMID: 34961747 PMCID: PMC8744677 DOI: 10.1101/gr.276025.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022]
Abstract
A classical model of gene regulation is that enhancers provide specificity whereas core promoters provide a modular site for the assembly of the basal transcriptional machinery. However, examples of core promoter specificity have led to an alternate hypothesis in which specificity is achieved by core promoters with different sequence motifs that respond differently to genomic environments containing different enhancers and chromatin landscapes. To distinguish between these models, we measured the activities of hundreds of diverse core promoters in four different genomic locations and, in a complementary experiment, six different core promoters at thousands of locations across the genome. Although genomic locations had large effects on expression, the intrinsic activities of different classes of promoters were preserved across genomic locations, suggesting that core promoters are modular regulatory elements whose activities are independently scaled up or down by different genomic locations. This scaling of promoter activities is nonlinear and depends on the genomic location and the strength of the core promoter. Our results support the classical model of regulation in which diverse core promoter motifs set the intrinsic strengths of core promoters, which are then amplified or dampened by the activities of their genomic environments.
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Affiliation(s)
- Clarice K Y Hong
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
| | - Barak A Cohen
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, Missouri 63110, USA
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11
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Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics 2021; 219:iyab154. [PMID: 34849867 PMCID: PMC8664596 DOI: 10.1093/genetics/iyab154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene's overall expression pattern.
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Affiliation(s)
- Lily Li
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
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12
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Zaucker A, Mitchell CA, Coker HLE, Sampath K. Tools to Image Germplasm Dynamics During Early Zebrafish Development. Front Cell Dev Biol 2021; 9:712503. [PMID: 34485299 PMCID: PMC8414583 DOI: 10.3389/fcell.2021.712503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
During the first day of zebrafish development, ribonucleoprotein (RNP) complexes called germplasm form large aggregates that initially segregate asymmetrically during cleavage stages. After zygotic genome activation, the granules break into smaller fragments that associate with the nuclear membrane as perinuclear (germ) granules toward the end of gastrulation. The mechanisms underlying the highly dynamic behavior of germ granules are not well studied but thought to be facilitated by the cytoskeleton. Here, we present efficient mounting strategies using 3d-printed tools that generate wells on agarose-coated sample holders to allow high-resolution imaging of multiplexed embryos that are less than one day post-fertilization (dpf) on inverted (spinning disk confocal) as well as upright (lattice light-sheet and diSPIM) microscopes. In particular, our tools and methodology allow water dipping lenses to have direct access to mounted embryos, with no obstructions to the light path (e.g., through low melting agarose or methyl cellulose). Moreover, the multiplexed tight arrays of wells generated by our tools facilitate efficient mounting of early embryos (including cleavage stages) for live imaging. These methods and tools, together with new transgenic reporter lines, can facilitate the study of germ granule dynamics throughout their lifetime in detail, at high resolution and throughput, using live imaging technologies.
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Affiliation(s)
- Andreas Zaucker
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Claire A Mitchell
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Helena L E Coker
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Karuna Sampath
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
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13
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Jores T, Tonnies J, Wrightsman T, Buckler ES, Cuperus JT, Fields S, Queitsch C. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. NATURE PLANTS 2021; 7:842-855. [PMID: 34083762 PMCID: PMC10246763 DOI: 10.1038/s41477-021-00932-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 05/24/2023]
Abstract
Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements-notably the TATA box-as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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14
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Chen C, Gu Y, Philippe J, Zhang P, Bachman H, Zhang J, Mai J, Rufo J, Rawls JF, Davis EE, Katsanis N, Huang TJ. Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae. Nat Commun 2021; 12:1118. [PMID: 33602914 PMCID: PMC7892888 DOI: 10.1038/s41467-021-21373-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Modern biomedical research and preclinical pharmaceutical development rely heavily on the phenotyping of small vertebrate models for various diseases prior to human testing. In this article, we demonstrate an acoustofluidic rotational tweezing platform that enables contactless, high-speed, 3D multispectral imaging and digital reconstruction of zebrafish larvae for quantitative phenotypic analysis. The acoustic-induced polarized vortex streaming achieves contactless and rapid (~1 s/rotation) rotation of zebrafish larvae. This enables multispectral imaging of the zebrafish body and internal organs from different viewing perspectives. Moreover, we develop a 3D reconstruction pipeline that yields accurate 3D models based on the multi-view images for quantitative evaluation of basic morphological characteristics and advanced combinations of metrics. With its contactless nature and advantages in speed and automation, our acoustofluidic rotational tweezing system has the potential to be a valuable asset in numerous fields, especially for developmental biology, small molecule screening in biochemistry, and pre-clinical drug development in pharmacology.
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Affiliation(s)
- Chuyi Chen
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Yuyang Gu
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Julien Philippe
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Peiran Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Hunter Bachman
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Jinxin Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - John Mai
- Alfred E. Mann Institute for Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Joseph Rufo
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA.
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15
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Westhoff JH, Steenbergen PJ, Thomas LSV, Heigwer J, Bruckner T, Cooper L, Tönshoff B, Hoffmann GF, Gehrig J. In vivo High-Content Screening in Zebrafish for Developmental Nephrotoxicity of Approved Drugs. Front Cell Dev Biol 2020; 8:583. [PMID: 32754590 PMCID: PMC7366291 DOI: 10.3389/fcell.2020.00583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
Despite widespread drug exposure, for example during gestation or in prematurely born children, organ-specific developmental toxicity of most drugs is poorly understood. Developmental and functional abnormalities are a major cause of kidney diseases during childhood; however, the potential causal relationship to exposure with nephrotoxic drugs during nephrogenesis is widely unknown. To identify developmental nephrotoxic drugs in a large scale, we established and performed an automated high-content screen to score for phenotypic renal alterations in the Tg(wt1b:EGFP) zebrafish line. During early nephrogenesis, embryos were exposed to a compound library of approved drugs. After treatment, embryos were aligned within microtiter plates using 3D-printed orientation tools enabling the robust acquisition of consistent dorsal views of pronephric kidneys by automated microscopy. To qualitatively and quantitatively score and visualize phenotypes, we developed software tools for the semi-automated analysis, processing and visualization of this large image-based dataset. Using this scoring scheme, we were able to categorize compounds based on their potential developmental nephrotoxic effects. About 10% of tested drugs induced pronephric phenotypes including glomerular and tubular malformations, or overall changes in kidney morphology. Major chemical compound groups identified to cause glomerular and tubular alterations included dihydropyridine derivatives, HMG CoA reductase inhibitors, fibrates, imidazole, benzimidazole and triazole derivatives, corticosteroids, glucocorticoids, acetic acid derivatives and propionic acid derivatives. In conclusion, the presented study demonstrates the large-scale screening of kidney-specific toxicity of approved drugs in a live vertebrate embryo. The associated technology and tool-sets can be easily adapted for other organ systems providing a unique platform for in vivo large-scale assessment of organ-specific developmental toxicity or other biomedical applications. Ultimately, the presented data and associated visualization and browsing tools provide a resource for potentially nephrotoxic drugs and for further investigations.
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Affiliation(s)
- Jens H. Westhoff
- Department of Pediatrics I, University Children’s Hospital, Heidelberg, Germany
| | | | - Laurent S. V. Thomas
- Department of Pediatrics I, University Children’s Hospital, Heidelberg, Germany
- DITABIS, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
- ACQUIFER Imaging GmbH, Heidelberg, Germany
| | - Jana Heigwer
- Department of Pediatrics I, University Children’s Hospital, Heidelberg, Germany
| | - Thomas Bruckner
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | | | - Burkhard Tönshoff
- Department of Pediatrics I, University Children’s Hospital, Heidelberg, Germany
| | - Georg F. Hoffmann
- Department of Pediatrics I, University Children’s Hospital, Heidelberg, Germany
| | - Jochen Gehrig
- DITABIS, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
- ACQUIFER Imaging GmbH, Heidelberg, Germany
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16
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Thomas LSV, Gehrig J. Multi-template matching: a versatile tool for object-localization in microscopy images. BMC Bioinformatics 2020; 21:44. [PMID: 32024462 PMCID: PMC7003318 DOI: 10.1186/s12859-020-3363-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/13/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The localization of objects of interest is a key initial step in most image analysis workflows. For biomedical image data, classical image-segmentation methods like thresholding or edge detection are typically used. While those methods perform well for labelled objects, they are reaching a limit when samples are poorly contrasted with the background, or when only parts of larger structures should be detected. Furthermore, the development of such pipelines requires substantial engineering of analysis workflows and often results in case-specific solutions. Therefore, we propose a new straightforward and generic approach for object-localization by template matching that utilizes multiple template images to improve the detection capacity. RESULTS We provide a new implementation of template matching that offers higher detection capacity than single template approach, by enabling the detection of multiple template images. To provide an easy-to-use method for the automatic localization of objects of interest in microscopy images, we implemented multi-template matching as a Fiji plugin, a KNIME workflow and a python package. We demonstrate its application for the localization of entire, partial and multiple biological objects in zebrafish and medaka high-content screening datasets. The Fiji plugin can be installed by activating the Multi-Template-Matching and IJ-OpenCV update sites. The KNIME workflow is available on nodepit and KNIME Hub. Source codes and documentations are available on GitHub (https://github.com/multi-template-matching). CONCLUSION The novel multi-template matching is a simple yet powerful object-localization algorithm, that requires no data-pre-processing or annotation. Our implementation can be used out-of-the-box by non-expert users for any type of 2D-image. It is compatible with a large variety of applications including, for instance, analysis of large-scale datasets originating from automated microscopy, detection and tracking of objects in time-lapse assays, or as a general image-analysis step in any custom processing pipelines. Using different templates corresponding to distinct object categories, the tool can also be used for classification of the detected regions.
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Affiliation(s)
- Laurent S V Thomas
- Acquifer is a division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany. .,Centre of Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany.
| | - Jochen Gehrig
- Acquifer is a division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany.
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17
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Pandey G, Westhoff JH, Schaefer F, Gehrig J. A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model. Int J Mol Sci 2019; 20:ijms20061290. [PMID: 30875791 PMCID: PMC6471943 DOI: 10.3390/ijms20061290] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/25/2019] [Accepted: 03/10/2019] [Indexed: 12/19/2022] Open
Abstract
The zebrafish is being increasingly used in biomedical research and drug discovery to conduct large-scale compound screening. However, there is a lack of accessible methodologies to enable automated imaging and scoring of tissue-specific phenotypes at enhanced resolution. Here, we present the development of an automated imaging pipeline to identify chemical modifiers of glomerular cyst formation in a zebrafish model for human cystic kidney disease. Morpholino-mediated knockdown of intraflagellar transport protein Ift172 in Tg(wt1b:EGFP) embryos was used to induce large glomerular cysts representing a robustly scorable phenotypic readout. Compound-treated embryos were consistently aligned within the cavities of agarose-filled microplates. By interfacing feature detection algorithms with automated microscopy, a smart imaging workflow for detection, centring and zooming in on regions of interests was established, which enabled the automated capturing of standardised higher resolution datasets of pronephric areas. High-content screening datasets were processed and analysed using custom-developed heuristic algorithms implemented in common open-source image analysis software. The workflow enables highly efficient profiling of entire compound libraries and scoring of kidney-specific morphological phenotypes in thousands of zebrafish embryos. The demonstrated toolset covers all the aspects of a complex whole organism screening assay and can be adapted to other organs, specimens or applications.
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Affiliation(s)
- Gunjan Pandey
- Acquifer is a division of Ditabis, Digital Biomedical Imaging Systems AG, 75179 Pforzheim, Germany.
- Department of Pediatrics I, University Children's Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Jens H Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Franz Schaefer
- Department of Pediatrics I, University Children's Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Jochen Gehrig
- Acquifer is a division of Ditabis, Digital Biomedical Imaging Systems AG, 75179 Pforzheim, Germany.
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18
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Bakos K, Kovacs R, Balogh E, Sipos DK, Reining M, Gyomorei-Neuberger O, Balazs A, Kriszt B, Bencsik D, Csepeli A, Gazsi G, Hadzhiev Y, Urbanyi B, Mueller F, Kovacs B, Csenki Z. Estrogen sensitive liver transgenic zebrafish (Danio rerio) line (Tg(vtg1:mCherry)) suitable for the direct detection of estrogenicity in environmental samples. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 208:157-167. [PMID: 30677711 DOI: 10.1016/j.aquatox.2019.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 05/19/2023]
Abstract
Environmental estrogens are a serious concern worldwide due to their ubiquity and adverse ecotoxicological and health effects. Chemical structure of these substances is highly diverse, therefore estrogenicity cannot be predicted on the basis of molecular structure. Furthermore, estimation of estrogenicity of environmental samples based on chemical analytics of suspects is difficult given the complex interaction of chemicals and the impact on estrogenicity. The full estrogenic impact of an environmental sample can thus only be revealed by a series of sensitive in vitro and in vivo ecotoxicological tests. Herein we describe a vitellogenin reporter transgenic zebrafish line (Tg(vtg1:mCherry)) that enables the detection of estrogenicity in the environmentally relevant, low concentration ranges in embryonic tests that are in accordance with 3Rs and relevant animal welfare regulations. The transgene construct used for the development of Tg(vtg1:mCherry) carried a long (3.4 kbp) natural vitellogenin-1 promoter sequence with a high number of ERE sites. A test protocol was developed based on our finding that the endogenous vitellogenin and the reporter show similar spatial expression pattern and both endogenous and vitellogenin reporter is only produced in the left hepatic lobe of 5 dpf zebrafish embryos. Seven generations of Tg(vtg1:mCherry) have been established, and the estrogen responsiveness was tested with different estrogenic substances and wastewater samples. Embryos were exposed from 3 to 5 days post fertilization (dpf). Fluorescence in embryos could be detected upon treatment with 17-ß-estradiol from a concentration of 100 ng/L, 17-α-ethynilestradiol from 1 ng/L, zearalenone from 100 ng/L and bisphenol-A from 1 mg/L. In the adult stage transgene activity appeared to be more sensitive to estrogen treatment, with detectable transgene activity from 5 ng/L 17-ß-estradiol concentration. The transgenic line Tg(vtg1:mCherry) was also suitable for the direct measurement of estrogenicity in wastewater samples without sample extraction. The detection of estrogenic activity using the reporter line was confirmed by the bioluminescent yeast estrogen screen.
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Affiliation(s)
- Katalin Bakos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Robert Kovacs
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Erna Balogh
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Dora Kanaine Sipos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Marta Reining
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Orsolya Gyomorei-Neuberger
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Adrienn Balazs
- Department of Environmental Safety and Ecotoxicology, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Balazs Kriszt
- Department of Environmental Safety and Ecotoxicology, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Dora Bencsik
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Andrea Csepeli
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Gyongyi Gazsi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, Edgbaston, Birmingham, United Kingdom
| | - Bela Urbanyi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary
| | - Ferenc Mueller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, Edgbaston, Birmingham, United Kingdom
| | - Balazs Kovacs
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary.
| | - Zsolt Csenki
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Páter Károly St., H-2100 Gödöllő, Hungary.
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19
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Korzh V, Kondrychyn I, Winata C. The Zebrafish as a New Model System for Experimental Biology. CYTOL GENET+ 2018. [DOI: 10.3103/s009545271806004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Quillien A, Abdalla M, Yu J, Ou J, Zhu LJ, Lawson ND. Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. Cell Rep 2018; 20:709-720. [PMID: 28723572 DOI: 10.1016/j.celrep.2017.06.070] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 02/08/2023] Open
Abstract
Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis. However, robust detection of these regulatory elements remains challenging, especially in vertebrate genomes. Here, we apply fluorescent-activated nuclei sorting (FANS) followed by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to identify developmentally active endothelial enhancers in the zebrafish genome. ATAC-seq of nuclei from Tg(fli1a:egfp)y1 transgenic embryos revealed expected patterns of nucleosomal positioning at transcriptional start sites throughout the genome and association with active histone modifications. Comparison of ATAC-seq from GFP-positive and -negative nuclei identified more than 5,000 open elements specific to endothelial cells. These elements flanked genes functionally important for vascular development and that displayed endothelial-specific gene expression. Importantly, a majority of tested elements drove endothelial gene expression in zebrafish embryos. Thus, FANS-assisted ATAC-seq using transgenic zebrafish embryos provides a robust approach for genome-wide identification of active tissue-specific enhancer elements.
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Affiliation(s)
- Aurelie Quillien
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Mary Abdalla
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jun Yu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jianhong Ou
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan D Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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21
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Soukup V, Mrstakova S, Kozmik Z. Asymmetric pitx2 expression in medaka epithalamus is regulated by nodal signaling through an intronic enhancer. Dev Genes Evol 2018; 228:131-139. [PMID: 29663064 DOI: 10.1007/s00427-018-0611-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/03/2018] [Indexed: 12/23/2022]
Abstract
The epithalamic region of fishes shows prominent left-right asymmetries that are executed by nodal signaling upstream of the asymmetry-determining transcription factor pitx2. Previous reports have identified that nodal controls the left-sided pitx2 expression in the lateral plate mesoderm through an enhancer present in the last intron of this gene. However, whether similar regulation occurs also in the case of epithalamic asymmetry is currently unresolved. Here, we address some of the cis-regulatory information that control asymmetric pitx2 expression in epithalamus by presenting a Tg(pitx2:EGFP) 116-17 transgenic medaka model, which expresses enhanced green fluorescent protein (EGFP) under control of an intronic enhancer. We show that this transgene recapitulates epithalamic expression of the endogenous pitx2 and that it responds to nodal signaling inhibition. Further, we identify that three foxh1-binding sites present in this enhancer modulate expression of the transgene and that the second site is absolutely necessary for the left-sided epithalamic expression while the other two sites may have subtler regulative roles. We provide evidence that left-sided epithalamic pitx2 expression is controlled through an enhancer present in the last intron of this gene and that the regulatory logic underlying asymmetric pitx2 expression is shared between epithalamic and lateral plate mesoderm regions.
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Affiliation(s)
- Vladimir Soukup
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44, Prague, Czech Republic.
| | - Simona Mrstakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
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22
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Gehrig J, Pandey G, Westhoff JH. Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases. Front Pediatr 2018; 6:183. [PMID: 30003073 PMCID: PMC6031734 DOI: 10.3389/fped.2018.00183] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
Genetic disorders account for a wide range of renal diseases emerging during childhood and adolescence. Due to the utilization of modern biochemical and biomedical techniques, the number of identified disease-associated genes is increasing rapidly. Modeling of congenital human disease in animals is key to our understanding of the biological mechanism underlying pathological processes and thus developing novel potential treatment options. The zebrafish (Danio rerio) has been established as a versatile small vertebrate organism that is widely used for studying human inherited diseases. Genetic accessibility in combination with elegant experimental methods in zebrafish permit modeling of human genetic diseases and dissecting the perturbation of underlying cellular networks and physiological processes. Beyond its utility for genetic analysis and pathophysiological and mechanistic studies, zebrafish embryos, and larvae are amenable for phenotypic screening approaches employing high-content and high-throughput experiments using automated microscopy. This includes large-scale chemical screening experiments using genetic models for searching for disease-modulating compounds. Phenotype-based approaches of drug discovery have been successfully performed in diverse zebrafish-based screening applications with various phenotypic readouts. As a result, these can lead to the identification of candidate substances that are further examined in preclinical and clinical trials. In this review, we discuss zebrafish models for inherited kidney disease as well as requirements and considerations for the technical realization of drug screening experiments in zebrafish.
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Affiliation(s)
- Jochen Gehrig
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
| | - Gunjan Pandey
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany.,Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Jens H Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
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23
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White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017; 6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022] Open
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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Affiliation(s)
| | - John E Collins
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Zsofia Digby
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Matthew P Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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24
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Quintero-Cadena P, Sternberg PW. Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes. G3 (BETHESDA, MD.) 2016; 6:4167-4174. [PMID: 27799341 PMCID: PMC5144984 DOI: 10.1534/g3.116.036228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/15/2016] [Indexed: 01/08/2023]
Abstract
Enhancers physically interact with transcriptional promoters, looping over distances that can span multiple regulatory elements. Given that enhancer-promoter (EP) interactions generally occur via common protein complexes, it is unclear whether EP pairing is predominantly deterministic or proximity guided. Here, we present cross-organismic evidence suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions. By reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that nonspecific EP interactions can explain such correlation, and that EP distance acts as a scaling factor for the transcriptional influence of an enhancer. We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation.
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Affiliation(s)
- Porfirio Quintero-Cadena
- Division of Biology and Biological Engineering, California Institute of Technology, Howard Hughes Medical Institute, Pasadena, California 91125
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Howard Hughes Medical Institute, Pasadena, California 91125
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25
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Zabidi MA, Stark A. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet 2016; 32:801-814. [PMID: 27816209 DOI: 10.1016/j.tig.2016.10.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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26
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Deal S, Wambaugh J, Judson R, Mosher S, Radio N, Houck K, Padilla S. Development of a quantitative morphological assessment of toxicant-treated zebrafish larvae using brightfield imaging and high-content analysis. J Appl Toxicol 2016; 36:1214-22. [PMID: 26924781 DOI: 10.1002/jat.3290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/22/2015] [Accepted: 12/15/2015] [Indexed: 11/11/2022]
Abstract
One of the rate-limiting procedures in a developmental zebrafish screen is the morphological assessment of each larva. Most researchers opt for a time-consuming, structured visual assessment by trained human observer(s). The present studies were designed to develop a more objective, accurate and rapid method for screening zebrafish for dysmorphology. Instead of the very detailed human assessment, we have developed the computational malformation index, which combines the use of high-content imaging with a very brief human visual assessment. Each larva was quickly assessed by a human observer (basic visual assessment), killed, fixed and assessed for dysmorphology with the Zebratox V4 BioApplication using the Cellomics® ArrayScan® V(TI) high-content image analysis platform. The basic visual assessment adds in-life parameters, and the high-content analysis assesses each individual larva for various features (total area, width, spine length, head-tail length, length-width ratio, perimeter-area ratio). In developing the computational malformation index, a training set of hundreds of embryos treated with hundreds of chemicals were visually assessed using the basic or detailed method. In the second phase, we assessed both the stability of these high-content measurements and its performance using a test set of zebrafish treated with a dose range of two reference chemicals (trans-retinoic acid or cadmium). We found the measures were stable for at least 1 week and comparison of these automated measures to detailed visual inspection of the larvae showed excellent congruence. Our computational malformation index provides an objective manner for rapid phenotypic brightfield assessment of individual larva in a developmental zebrafish assay. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Samantha Deal
- National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC, USA.,Division of Pediatrics Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, 6701, Fannin St., Houston, TX, USA
| | - John Wambaugh
- National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Richard Judson
- National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Shad Mosher
- ORISE Fellow, National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Nick Radio
- Thermo Fisher Scientific, Cellular Imaging and Analysis, Pittsburgh, PA, USA
| | - Keith Houck
- National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Stephanie Padilla
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC, USA
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27
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Rastegar S, Strähle U. The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes. GENETICS, GENOMICS AND FISH PHENOMICS 2016; 95:195-216. [DOI: 10.1016/bs.adgen.2016.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Martinez NJ, Titus SA, Wagner AK, Simeonov A. High-throughput fluorescence imaging approaches for drug discovery using in vitro and in vivo three-dimensional models. Expert Opin Drug Discov 2015; 10:1347-61. [PMID: 26394277 DOI: 10.1517/17460441.2015.1091814] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION High-resolution microscopy using fluorescent probes is a powerful tool to investigate individual cell structure and function, cell subpopulations and mechanisms underlying cellular responses to drugs. Additionally, responses to drugs more closely resemble those seen in vivo when cells are physically connected in three-dimensional (3D) systems (either 3D cell cultures or whole organisms), as opposed to traditional monolayer cultures. Combined, the use of imaging-based 3D models in the early stages of drug development has the potential to generate biologically relevant data that will increase the likelihood of success for drug candidates in human studies. AREAS COVERED The authors discuss current methods for the culturing of cells in 3D as well as approaches for the imaging of whole-animal models and 3D cultures that are amenable to high-throughput settings and could be implemented to support drug discovery campaigns. Furthermore, they provide critical considerations when discussing imaging these 3D systems for high-throughput chemical screenings. EXPERT OPINION Despite widespread understanding of the limitations imposed by the two-dimensional versus the 3D cellular paradigm, imaging-based drug screening of 3D cellular models is still limited, with only a few screens found in the literature. Image acquisition in high throughput, accurate interpretation of fluorescent signal, and uptake of staining reagents can be challenging, as the samples are in essence large aggregates of cells. The authors recognize these shortcomings that need to be overcome before the field can accelerate the utilization of these technologies in large-scale chemical screens.
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Affiliation(s)
- Natalia J Martinez
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
| | - Steven A Titus
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
| | - Amanda K Wagner
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
| | - Anton Simeonov
- a National Institutes of Health, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA
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29
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Pindyurin AV, de Jong J, Akhtar W. TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes. Genomics 2015; 106:171-177. [PMID: 26080039 DOI: 10.1016/j.ygeno.2015.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/01/2015] [Accepted: 06/09/2015] [Indexed: 11/25/2022]
Abstract
Enhancers are regulatory elements that promote gene expression in a spatio-temporal way and are involved in a wide range of developmental and disease processes. Both the identification and subsequent functional dissection of enhancers are key steps in understanding these processes. Several high-throughput approaches were recently developed for these purposes; however, in almost all cases enhancers are being tested outside their native chromatin context. Until recently, the analysis of enhancer activities at their native genomic locations was low throughput, laborious and time-consuming. Here, we discuss the potential of a powerful approach, TRIP, to study the functioning of enhancers in their native chromatin environments by introducing sensor constructs directly in the genome. TRIP allows for simultaneously analyzing the quantitative readout of numerous sensor constructs integrated at random locations in the genome. The high-throughput and flexible nature of TRIP opens up potential to study different aspects of enhancer biology at an unprecedented level.
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Affiliation(s)
- Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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30
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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31
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Ordas A, Raterink RJ, Cunningham F, Jansen HJ, Wiweger MI, Jong-Raadsen S, Bos S, Bates RH, Barros D, Meijer AH, Vreeken RJ, Ballell-Pages L, Dirks RP, Hankemeier T, Spaink HP. Testing tuberculosis drug efficacy in a zebrafish high-throughput translational medicine screen. Antimicrob Agents Chemother 2015; 59:753-62. [PMID: 25385118 PMCID: PMC4335901 DOI: 10.1128/aac.03588-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/05/2014] [Indexed: 12/17/2022] Open
Abstract
The translational value of zebrafish high-throughput screens can be improved when more knowledge is available on uptake characteristics of potential drugs. We investigated reference antibiotics and 15 preclinical compounds in a translational zebrafish-rodent screening system for tuberculosis. As a major advance, we have developed a new tool for testing drug uptake in the zebrafish model. This is important, because despite the many applications of assessing drug efficacy in zebrafish research, the current methods for measuring uptake using mass spectrometry do not take into account the possible adherence of drugs to the larval surface. Our approach combines nanoliter sampling from the yolk using a microneedle, followed by mass spectrometric analysis. To date, no single physicochemical property has been identified to accurately predict compound uptake; our method offers a great possibility to monitor how any novel compound behaves within the system. We have correlated the uptake data with high-throughput drug-screening data from Mycobacterium marinum-infected zebrafish larvae. As a result, we present an improved zebrafish larva drug-screening platform which offers new insights into drug efficacy and identifies potential false negatives and drugs that are effective in zebrafish and rodents. We demonstrate that this improved zebrafish drug-screening platform can complement conventional models of in vivo Mycobacterium tuberculosis-infected rodent assays. The detailed comparison of two vertebrate systems, fish and rodent, may give more predictive value for efficacy of drugs in humans.
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Affiliation(s)
- Anita Ordas
- IBL, Leiden University, Leiden, The Netherlands
| | - Robert-Jan Raterink
- Division of Analytical BioSciences, Leiden Academic Centre for Drug Research and Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
| | | | | | - Malgorzata I Wiweger
- IBL, Leiden University, Leiden, The Netherlands ZF-screens B.V., Leiden, The Netherlands
| | | | - Sabine Bos
- Division of Analytical BioSciences, Leiden Academic Centre for Drug Research and Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
| | | | | | | | - Rob J Vreeken
- Division of Analytical BioSciences, Leiden Academic Centre for Drug Research and Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
| | | | | | - Thomas Hankemeier
- Division of Analytical BioSciences, Leiden Academic Centre for Drug Research and Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
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32
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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33
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Wittbrodt JN, Liebel U, Gehrig J. Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing. BMC Biotechnol 2014; 14:36. [PMID: 24886511 PMCID: PMC4021294 DOI: 10.1186/1472-6750-14-36] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/24/2014] [Indexed: 01/26/2023] Open
Abstract
Background The zebrafish has been established as the main vertebrate model system for whole organism screening applications. However, the lack of consistent positioning of zebrafish embryos within wells of microtiter plates remains an obstacle for the comparative analysis of images acquired in automated screening assays. While technical solutions to the orientation problem exist, dissemination is often hindered by the lack of simple and inexpensive ways of distributing and duplicating tools. Results Here, we provide a cost effective method for the production of 96-well plate compatible zebrafish orientation tools using a desktop 3D printer. The printed tools enable the positioning and orientation of zebrafish embryos within cavities formed in agarose. Their applicability is demonstrated by acquiring lateral and dorsal views of zebrafish embryos arrayed within microtiter plates using an automated screening microscope. This enables the consistent visualization of morphological phenotypes and reporter gene expression patterns. Conclusions The designs are refined versions of previously demonstrated devices with added functionality and strongly reduced production costs. All corresponding 3D models are freely available and digital design can be easily shared electronically. In combination with the increasingly widespread usage of 3D printers, this provides access to the developed tools to a wide range of zebrafish users. Finally, the design files can serve as templates for other additive and subtractive fabrication methods.
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34
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Seth A, Stemple DL, Barroso I. The emerging use of zebrafish to model metabolic disease. Dis Model Mech 2014; 6:1080-8. [PMID: 24046387 PMCID: PMC3759328 DOI: 10.1242/dmm.011346] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The zebrafish research community is celebrating! The zebrafish genome has recently been sequenced, the Zebrafish Mutation Project (launched by the Wellcome Trust Sanger Institute) has published the results of its first large-scale ethylnitrosourea (ENU) mutagenesis screen, and a host of new techniques, such as the genome editing technologies TALEN and CRISPR-Cas, are enabling specific mutations to be created in model organisms and investigated in vivo. The zebrafish truly seems to be coming of age. These powerful resources invoke the question of whether zebrafish can be increasingly used to model human disease, particularly common, chronic diseases of metabolism such as obesity and type 2 diabetes. In recent years, there has been considerable success, mainly from genomic approaches, in identifying genetic variants that are associated with these conditions in humans; however, mechanistic insights into the role of implicated disease loci are lacking. In this Review, we highlight some of the advantages and disadvantages of zebrafish to address the organism’s utility as a model system for human metabolic diseases.
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Affiliation(s)
- Asha Seth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Tat J, Liu M, Wen XY. Zebrafish cancer and metastasis models for in vivo drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 10:e83-9. [PMID: 24050234 DOI: 10.1016/j.ddtec.2012.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
There is a great need for more efficient methods to discover new cancer therapeutics, as traditional drug development processes are slow and expensive. The use of zebrafish as a whole-organism screen is a time and cost-effective means of improving the efficiency and efficacy of drug development. This review features zebrafish genetic and cell transplantation models of cancer and metastasis, and current imaging and automation technologies that, together, will significantly advance the field of anti-cancer drug discovery.
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Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest AR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014; 507:455-461. [PMID: 24670763 PMCID: PMC5215096 DOI: 10.1038/nature12787] [Citation(s) in RCA: 1722] [Impact Index Per Article: 172.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 10/16/2013] [Indexed: 02/07/2023]
Abstract
Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Irene Miguel-Escalada
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ilka Hoof
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Jette Bornholdt
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Xiaobei Zhao
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christian Schmidl
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Takahiro Suzuki
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Evgenia Ntini
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Bldg. 1130, DK-8000 Aarhus, Denmark
| | - Erik Arner
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Eivind Valen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- Department of Molecular and Cellular Biology, Harvard University, USA
| | - Kang Li
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Lucia Schwarzfischer
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Berit Lilje
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Nicolas Rapin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet and Danish Stem Cell Centre (DanStem), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Denmark
| | - Frederik Otzen Bagger
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet and Danish Stem Cell Centre (DanStem), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Denmark
| | - Mette Jørgensen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Peter Refsing Andersen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Bldg. 1130, DK-8000 Aarhus, Denmark
| | - Nicolas Bertin
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Owen Rackham
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - A. Maxwell Burroughs
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - J. Kenneth Baillie
- Roslin Institute, Edinburgh University, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Yuri Ishizu
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yuri Shimizu
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Shiori Maeda
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yutaka Negishi
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Christopher J. Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 64-121, Berkeley, CA 94720, USA
| | - Terrence F. Meehan
- EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD
| | - Timo Lassmann
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Naoto Kondo
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Jun Kawai
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Stockholm, Sweden
| | - Carsten O. Daub
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Stockholm, Sweden
| | - Peter Heutink
- Department of Clinical Genetics, VU University Medical Center, van der Boechorststraat 7, 1081 BT Amsterdam, Netherlands
| | - David A. Hume
- Roslin Institute, Edinburgh University, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Bldg. 1130, DK-8000 Aarhus, Denmark
| | - Harukazu Suzuki
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Ferenc Müller
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alistair R.R. Forrest
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
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Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014. [DOI: 10.10.1038/nature12787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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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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Stegmaier J, Shahid M, Takamiya M, Yang L, Rastegar S, Reischl M, Strähle U, Mikut R. Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. Bioinformatics 2014; 30:726-33. [PMID: 24135262 DOI: 10.1093/bioinformatics/btt600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION To reliably assess the effects of unknown chemicals on the development of fluorescently labeled sensory-, moto- and interneuron populations in the spinal cord of zebrafish, automated data analysis is essential. RESULTS For the evaluation of a high-throughput screen of a large chemical library, we developed a new method for the automated extraction of quantitative information from green fluorescent protein (eGFP) and red fluorescent protein (RFP) labeled spinal cord neurons in double-transgenic zebrafish embryos. The methodology comprises region of interest detection, intensity profiling with reference comparison and neuron distribution histograms. All methods were validated on a manually evaluated pilot study using a Notch inhibitor dose-response experiment. The automated evaluation showed superior performance to manual investigation regarding time consumption, information detail and reproducibility. AVAILABILITY AND IMPLEMENTATION Being part of GNU General Public Licence (GNU-GPL) licensed open-source MATLAB toolbox Gait-CAD, an implementation of the presented methods is publicly available for download at http://sourceforge.net/projects/zebrafishimage/.
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Affiliation(s)
- Johannes Stegmaier
- Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
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Kinkema M, Geijskes J, Delucca P, Palupe A, Shand K, Coleman HD, Brinin A, Williams B, Sainz M, Dale JL. Improved molecular tools for sugar cane biotechnology. PLANT MOLECULAR BIOLOGY 2014; 84:497-508. [PMID: 24150836 DOI: 10.1007/s11103-013-0147-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/16/2013] [Indexed: 06/02/2023]
Abstract
Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.
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Affiliation(s)
- Mark Kinkema
- Syngenta Centre for Sugar Cane Biofuels Development, Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, 4001, Australia,
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Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WFJ, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature 2014; 507:381-385. [PMID: 24531765 PMCID: PMC4820030 DOI: 10.1038/nature12974] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 12/23/2013] [Indexed: 12/17/2022]
Abstract
A core promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulatory inputs1 and recruits general transcription factors to initiate transcription2. The nature and causative relationship of DNA sequence and chromatin signals that govern the selection of most TSS by RNA polymerase II remain unresolved. Maternal to zygotic transition (MZT) represents the most dramatic change of the transcriptome repertoire in vertebrate life cycle3-6. Early embryonic development in zebrafish is characterized by a series of transcriptionally silent cell cycles regulated by inherited maternal gene products: zygotic genome activation commences at the 10th cell cycle, marking the midblastula transition (MBT)7. This transition provides a unique opportunity to study the rules of TSS selection and the hierarchy of events linking transcription initiation with key chromatin modifications. We analysed TSS usage during zebrafish early embryonic development at high resolution using cap analysis of gene expression (CAGE)8 and determined the positions of H3K4me3-marked promoter-associated nucleosomes9. We show that the transition from maternal to zygotic transcriptome is characterised by a switch between two fundamentally different modes of defining transcription initiation, which drive the dynamic change of TSS usage and promoter shape. A maternal-specific TSS selection, which requires an A/T-rich (W-box) motif, is replaced with a zygotic TSS selection grammar characterized by broader patterns of dinucleotide enrichments, precisely aligned with the first downstream (+1) nucleosome. The developmental dynamics of the H3K4me3-marked nucleosomes reveals their DNA sequence-associated positioning at promoters prior to zygotic transcription and subsequent transcription-independent adjustment to the final position downstream of zygotic TSS. The two TSS-defining grammars coexist often in physical overlap in core promoters of constitutively expressed genes to enable their expression in the two regulatory environments. The dissection of overlapping core promoter determinants represents a framework for future studies of promoter structure and function across different regulatory contexts.
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Affiliation(s)
- Vanja Haberle
- Department of Biology, University of Bergen, Thormøhlensgate 53A, N-5008 Bergen, Norway.,Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom
| | - Nan Li
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yavor Hadzhiev
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Charles Plessy
- RIKEN Omics Science Center, Yokohama, Kanagawa, 230-0045 Japan (ceased to exist on 01 April 2013 due to RIKEN reorganisation).,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Christopher Previti
- Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Chirag Nepal
- Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Jochen Gehrig
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Xianjun Dong
- Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Altuna Akalin
- Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Ana Maria Suzuki
- RIKEN Omics Science Center, Yokohama, Kanagawa, 230-0045 Japan (ceased to exist on 01 April 2013 due to RIKEN reorganisation).,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Wilfred F J van IJcken
- Erasmus Medical Center, Center for Biomics, Room Ee679b, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Olivier Armant
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany
| | - Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany
| | - Piero Carninci
- RIKEN Omics Science Center, Yokohama, Kanagawa, 230-0045 Japan (ceased to exist on 01 April 2013 due to RIKEN reorganisation).,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Boris Lenhard
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom.,Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
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42
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Kishi S. Using zebrafish models to explore genetic and epigenetic impacts on evolutionary developmental origins of aging. Transl Res 2014; 163:123-35. [PMID: 24239812 PMCID: PMC3969878 DOI: 10.1016/j.trsl.2013.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 01/10/2023]
Abstract
Can we reset, reprogram, rejuvenate, or reverse the organismal aging process? Certain genetic manipulations could at least reset and reprogram epigenetic dynamics beyond phenotypic plasticity and elasticity in cells, which can be manipulated further into organisms. However, in a whole complex aging organism, how can we rejuvenate intrinsic resources and infrastructures in an intact and noninvasive manner? The incidence of diseases increases exponentially with age, accompanied by progressive deteriorations of physiological functions in organisms. Aging-associated diseases are sporadic but essentially inevitable complications arising from senescence. Senescence is often considered the antithesis of early development, but yet there may be factors and mechanisms in common between these 2 phenomena to rejuvenate over the dynamic process of aging. The association between early development and late-onset disease with advancing age is thought to come from a consequence of developmental plasticity, the phenomenon by which one genotype can give rise to a range of physiologically and/or morphologically adaptive states based on diverse epigenotypes in response to intrinsic or extrinsic environmental cues and genetic perturbations. We hypothesized that the future aging process can be predictive based on adaptivity during the early developmental period. Modulating the thresholds and windows of plasticity and its robustness by molecular genetic and chemical epigenetic approaches, we have successfully conducted experiments to isolate zebrafish mutants expressing apparently altered senescence phenotypes during their embryonic and/or larval stages ("embryonic/larval senescence"). Subsequently, at least some of these mutant animals were found to show a shortened life span, whereas others would be expected to live longer into adulthood. We anticipate that previously uncharacterized developmental genes may mediate the aging process and play a pivotal role in senescence. On the other hand, unexpected senescence-related genes might also be involved in the early developmental process and its regulation. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes, genotypes, and epigenotypes that can be linked to the senescence phenotype, which facilitates searching for the evolutionary and developmental origins of aging in vertebrates.
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Affiliation(s)
- Shuji Kishi
- Department of Metabolism & Aging, The Scripps Research Institute, Scripps Florida, Jupiter, Fla.
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43
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Atkinson TJ, Halfon MS. Regulation of gene expression in the genomic context. Comput Struct Biotechnol J 2014; 9:e201401001. [PMID: 24688749 PMCID: PMC3962188 DOI: 10.5936/csbj.201401001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/10/2013] [Accepted: 12/29/2013] [Indexed: 11/22/2022] Open
Abstract
Metazoan life is dependent on the proper temporal and spatial control of gene expression within the many cells-essentially all with the identical genome-that make up the organism. While much is understood about how individual gene regulatory elements function, many questions remain about how they interact to maintain correct regulation globally throughout the genome. In this review we summarize the basic features and functions of the crucial regulatory elements promoters, enhancers, and insulators and discuss some of the ways in which proper interactions between these elements is realized. We focus in particular on the role of core promoter sequences and propose explanations for some of the contradictory results seen in experiments aimed at understanding insulator function. We suggest that gene regulation depends on local genomic context and argue that more holistic in vivo investigations that take into account multiple local features will be necessary to understand how genome-wide gene regulation is maintained.
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Affiliation(s)
- Taylor J Atkinson
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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44
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Parker HJ, Sauka-Spengler T, Bronner M, Elgar G. A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancers. PLoS One 2014; 9:e85492. [PMID: 24416417 PMCID: PMC3887057 DOI: 10.1371/journal.pone.0085492] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/05/2013] [Indexed: 11/27/2022] Open
Abstract
The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.
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Affiliation(s)
- Hugo J. Parker
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Tatjana Sauka-Spengler
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Marianne Bronner
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Greg Elgar
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- * E-mail:
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45
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Development of an automated imaging pipeline for the analysis of the zebrafish larval kidney. PLoS One 2013; 8:e82137. [PMID: 24324758 PMCID: PMC3852951 DOI: 10.1371/journal.pone.0082137] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/21/2013] [Indexed: 01/01/2023] Open
Abstract
The analysis of kidney malformation caused by environmental influences during nephrogenesis or by hereditary nephropathies requires animal models allowing the in vivo observation of developmental processes. The zebrafish has emerged as a useful model system for the analysis of vertebrate organ development and function, and it is suitable for the identification of organotoxic or disease-modulating compounds on a larger scale. However, to fully exploit its potential in high content screening applications, dedicated protocols are required allowing the consistent visualization of inner organs such as the embryonic kidney. To this end, we developed a high content screening compatible pipeline for the automated imaging of standardized views of the developing pronephros in zebrafish larvae. Using a custom designed tool, cavities were generated in agarose coated microtiter plates allowing for accurate positioning and orientation of zebrafish larvae. This enabled the subsequent automated acquisition of stable and consistent dorsal views of pronephric kidneys. The established pipeline was applied in a pilot screen for the analysis of the impact of potentially nephrotoxic drugs on zebrafish pronephros development in the Tg(wt1b:EGFP) transgenic line in which the developing pronephros is highlighted by GFP expression. The consistent image data that was acquired allowed for quantification of gross morphological pronephric phenotypes, revealing concentration dependent effects of several compounds on nephrogenesis. In addition, applicability of the imaging pipeline was further confirmed in a morpholino based model for cilia-associated human genetic disorders associated with different intraflagellar transport genes. The developed tools and pipeline can be used to study various aspects in zebrafish kidney research, and can be readily adapted for the analysis of other organ systems.
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Ferg M, Armant O, Yang L, Dickmeis T, Rastegar S, Strähle U. Gene transcription in the zebrafish embryo: regulators and networks. Brief Funct Genomics 2013; 13:131-43. [PMID: 24152666 DOI: 10.1093/bfgp/elt044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
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Affiliation(s)
- Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany.
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Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AMM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CEM, van der Sloot AAJ, van Ijcken WFJ, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B, Müller F. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res 2013; 23:1938-50. [PMID: 24002785 PMCID: PMC3814893 DOI: 10.1101/gr.153692.112] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.
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Affiliation(s)
- Chirag Nepal
- Department of Biology, University of Bergen, Bergen N-5008, Norway
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Mikut R, Dickmeis T, Driever W, Geurts P, Hamprecht FA, Kausler BX, Ledesma-Carbayo MJ, Marée R, Mikula K, Pantazis P, Ronneberger O, Santos A, Stotzka R, Strähle U, Peyriéras N. Automated processing of zebrafish imaging data: a survey. Zebrafish 2013; 10:401-21. [PMID: 23758125 PMCID: PMC3760023 DOI: 10.1089/zeb.2013.0886] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.
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Affiliation(s)
- Ralf Mikut
- Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Annila T, Lihavainen E, Marques IJ, Williams DR, Yli-Harja O, Ribeiro A. ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. BMC Bioinformatics 2013; 14 Suppl 10:S5. [PMID: 24267347 PMCID: PMC3750475 DOI: 10.1186/1471-2105-14-s10-s5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Zebrafish embryos have recently been established as a xenotransplantation model of the metastatic behaviour of primary human tumours. Current tools for automated data extraction from the microscope images are restrictive concerning the developmental stage of the embryos, usually require laborious manual image preprocessing, and, in general, cannot characterize the metastasis as a function of the internal organs. Methods We present a tool, ZebIAT, that allows both automatic or semi-automatic registration of the outer contour and inner organs of zebrafish embryos. ZebIAT provides a registration at different stages of development and an automatic analysis of cancer metastasis per organ, thus allowing to study cancer progression. The semi-automation relies on a graphical user interface. Results We quantified the performance of the registration method, and found it to be accurate, except in some of the smallest organs. Our results show that the accuracy of registering small organs can be improved by introducing few manual corrections. We also demonstrate the applicability of the tool to studies of cancer progression. Conclusions ZebIAT offers major improvement relative to previous tools by allowing for an analysis on a per-organ or region basis. It should be of use in high-throughput studies of cancer metastasis in zebrafish embryos.
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Pfriem A, Pylatiuk C, Alshut R, Ziegener B, Schulz S, Bretthauer G. A modular, low-cost robot for zebrafish handling. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2012:980-3. [PMID: 23366058 DOI: 10.1109/embc.2012.6346097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The zebrafish (danio rerio) is one of the most important model organisms in modern drug discovery and disease modeling. Handling and analyzing large numbers of zebrafish larvae require an immense manpower and involve time-consuming manual processes. A novel modular, robotic platform for high-throughput screening is being developed at BioRobotLab (KIT). In this article the fish sorter, which is a robotic device for the automation of a manual process in bio analysis, is presented. The fish sorter detects randomly spread zebrafish eggs and larvae up to an age of 120 hours post fertilization (hpf) in Petri dishes and transfers them to standard 96- or 384- well plates. The robot is controlled by an advanced algorithm with sensor-based process control. Fast and precise hardware components lead to a high working speed and success rate >= 95%.
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Affiliation(s)
- Alexander Pfriem
- Institute of Applied Computer Science, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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