1
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García-González J, Brock AJ, Parker MO, Riley RJ, Joliffe D, Sudwarts A, Teh MT, Busch-Nentwich EM, Stemple DL, Martineau AR, Kaprio J, Palviainen T, Kuan V, Walton RT, Brennan CH. Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour. eLife 2020; 9:e51295. [PMID: 32209227 PMCID: PMC7096180 DOI: 10.7554/elife.51295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/25/2020] [Indexed: 01/08/2023] Open
Abstract
To facilitate smoking genetics research we determined whether a screen of mutagenized zebrafish for nicotine preference could predict loci affecting smoking behaviour. From 30 screened F3 sibling groups, where each was derived from an individual ethyl-nitrosurea mutagenized F0 fish, two showed increased or decreased nicotine preference. Out of 25 inactivating mutations carried by the F3 fish, one in the slit3 gene segregated with increased nicotine preference in heterozygous individuals. Focussed SNP analysis of the human SLIT3 locus in cohorts from UK (n=863) and Finland (n=1715) identified two variants associated with cigarette consumption and likelihood of cessation. Characterisation of slit3 mutant larvae and adult fish revealed decreased sensitivity to the dopaminergic and serotonergic antagonist amisulpride, known to affect startle reflex that is correlated with addiction in humans, and increased htr1aa mRNA expression in mutant larvae. No effect on neuronal pathfinding was detected. These findings reveal a role for SLIT3 in development of pathways affecting responses to nicotine in zebrafish and smoking in humans.
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Affiliation(s)
- Judit García-González
- School of Biological and Chemical Sciences, Queen Mary, University of LondonLondonUnited Kingdom
| | - Alistair J Brock
- School of Biological and Chemical Sciences, Queen Mary, University of LondonLondonUnited Kingdom
| | - Matthew O Parker
- School of Pharmacy and Biomedical Science, University of PortsmouthPortsmouthUnited Kingdom
| | - Riva J Riley
- School of Biological and Chemical Sciences, Queen Mary, University of LondonLondonUnited Kingdom
| | - David Joliffe
- Barts and The London School of Medicine and Dentistry, Blizard InstituteLondonUnited Kingdom
| | - Ari Sudwarts
- School of Biological and Chemical Sciences, Queen Mary, University of LondonLondonUnited Kingdom
| | - Muy-Teck Teh
- Centre for Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and DentistryLondonUnited Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
| | | | - Adrian R Martineau
- Barts and The London School of Medicine and Dentistry, Blizard InstituteLondonUnited Kingdom
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM, HiLIFEHelsinkiFinland
- Department of Public Health, Faculty of Medicine, University of HelsinkiHelsinkiFinland
| | | | - Valerie Kuan
- Institute of Cardiovascular Science, University College LondonLondonUnited Kingdom
| | - Robert T Walton
- Barts and The London School of Medicine and Dentistry, Blizard InstituteLondonUnited Kingdom
| | - Caroline H Brennan
- School of Biological and Chemical Sciences, Queen Mary, University of LondonLondonUnited Kingdom
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2
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Kim J, Lana B, Torelli S, Ryan D, Catapano F, Ala P, Luft C, Stevens E, Konstantinidis E, Louzada S, Fu B, Paredes‐Redondo A, Chan AWE, Yang F, Stemple DL, Liu P, Ketteler R, Selwood DL, Muntoni F, Lin Y. A new patient-derived iPSC model for dystroglycanopathies validates a compound that increases glycosylation of α-dystroglycan. EMBO Rep 2019; 20:e47967. [PMID: 31566294 PMCID: PMC6832011 DOI: 10.15252/embr.201947967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/24/2019] [Accepted: 08/29/2019] [Indexed: 12/24/2022] Open
Abstract
Dystroglycan, an extracellular matrix receptor, has essential functions in various tissues. Loss of α-dystroglycan-laminin interaction due to defective glycosylation of α-dystroglycan underlies a group of congenital muscular dystrophies often associated with brain malformations, referred to as dystroglycanopathies. The lack of isogenic human dystroglycanopathy cell models has limited our ability to test potential drugs in a human- and neural-specific context. Here, we generated induced pluripotent stem cells (iPSCs) from a severe dystroglycanopathy patient with homozygous FKRP (fukutin-related protein gene) mutation. We showed that CRISPR/Cas9-mediated gene correction of FKRP restored glycosylation of α-dystroglycan in iPSC-derived cortical neurons, whereas targeted gene mutation of FKRP in wild-type cells disrupted this glycosylation. In parallel, we screened 31,954 small molecule compounds using a mouse myoblast line for increased glycosylation of α-dystroglycan. Using human FKRP-iPSC-derived neural cells for hit validation, we demonstrated that compound 4-(4-bromophenyl)-6-ethylsulfanyl-2-oxo-3,4-dihydro-1H-pyridine-5-carbonitrile (4BPPNit) significantly augmented glycosylation of α-dystroglycan, in part through upregulation of LARGE1 glycosyltransferase gene expression. Together, isogenic human iPSC-derived cells represent a valuable platform for facilitating dystroglycanopathy drug discovery and therapeutic development.
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Affiliation(s)
- Jihee Kim
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Beatrice Lana
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Silvia Torelli
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - David Ryan
- Wellcome Sanger InstituteHinxtonCambridgeUK
| | | | - Pierpaolo Ala
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - Christin Luft
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | | | - Evangelos Konstantinidis
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | | | - Beiyuan Fu
- Wellcome Sanger InstituteHinxtonCambridgeUK
| | - Amaia Paredes‐Redondo
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - AW Edith Chan
- The Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | | | | | - Pentao Liu
- Wellcome Sanger InstituteHinxtonCambridgeUK
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - David L Selwood
- The Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | - Francesco Muntoni
- UCL Great Ormond Street Institute of Child HealthLondonUK
- NIHR Biomedical Research Centre at Great Ormond Street HospitalLondonUK
| | - Yung‐Yao Lin
- Centre for Genomics and Child HealthBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Stem Cell LaboratoryNational Bowel Research CentreBlizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
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3
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Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Common and distinct transcriptional signatures of mammalian embryonic lethality. Nat Commun 2019; 10:2792. [PMID: 31243271 PMCID: PMC6594971 DOI: 10.1038/s41467-019-10642-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.
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Affiliation(s)
- John E Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Richard J White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicole Staudt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ian Packham
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cecilia Mazzeo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Green
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emma Siragher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Irene Papatheodoru
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Stefan H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Wolfgang J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Antonella Galli
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Myriam Hemberger
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Derek L Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Camena Bioscience, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Elizabeth Robertson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - James C Smith
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Timothy Mohun
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
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4
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Dooley CM, Wali N, Sealy IM, White RJ, Stemple DL, Collins JE, Busch-Nentwich EM. The gene regulatory basis of genetic compensation during neural crest induction. PLoS Genet 2019; 15:e1008213. [PMID: 31199790 PMCID: PMC6594659 DOI: 10.1371/journal.pgen.1008213] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/26/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors. NC induction robustness is ensured through the ability of some of these transcription factors to compensate loss of function of gene family members. However the gene regulatory events underlying compensation are poorly understood. We have used gene knockout and RNA sequencing strategies to dissect NC induction and compensation in zebrafish. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that compensation through a single wild-type allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, but many target genes have abnormal expression levels and therefore show sensitivity to the reduced tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. We also identify the 15 somites stage as the peak of the molecular phenotype which strongly diminishes at 24 hpf even as the morphological phenotype becomes more apparent. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation. This work extends and refines the NC GRN while also uncovering the transcriptional basis of genetic compensation via paralogues. Embryonic development is an intricate process that requires genes to be active at the right time and place. Organisms have evolved mechanisms that ensure faithful execution of developmental programmes even if genes fail to function. For example, in a process called genetic compensation, one or more genes become activated in response to loss of function of another. In this work we use the zebrafish model to investigate how two related genes, tfap2a and tfap2c, interact to ensure establishment of the neural crest, a vertebrate-specific cell type that contributes to many different tissues. Losing tfap2a activity causes mild morphological defects and losing tfap2c has no visible effect. Yet when both are inactive, embryos are severely abnormal due to lack of neural crest-derived tissues. Here we show that loss of tfap2a triggers upregulation of tfap2c which prevents the loss of neural crest tissue. However, the genes normally regulated by tfap2a respond differently to tfap2c allowing us to identify the first tier of the Ap2 network and new players in neural crest biology. Our work demonstrates that the expression signature of partial, but morphologically sufficient, genetic compensation provides an opportunity to dissect gene regulatory networks.
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Affiliation(s)
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ian M. Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Richard J. White
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - John E. Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elisabeth M. Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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5
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Nelson AC, Cutty SJ, Gasiunas SN, Deplae I, Stemple DL, Wardle FC. In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors. Cell Rep 2018; 19:2782-2795. [PMID: 28658625 PMCID: PMC5494305 DOI: 10.1016/j.celrep.2017.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/28/2017] [Accepted: 05/31/2017] [Indexed: 01/15/2023] Open
Abstract
T-box transcription factors T/Brachyury homolog A (Ta) and Tbx16 are essential for correct mesoderm development in zebrafish. The downstream transcriptional networks guiding their functional activities are poorly understood. Additionally, important contributions elsewhere are likely masked due to redundancy. Here, we exploit functional genomic strategies to identify Ta and Tbx16 targets in early embryogenesis. Surprisingly, we discovered they not only activate mesodermal gene expression but also redundantly regulate key endodermal determinants, leading to substantial loss of endoderm in double mutants. To further explore the gene regulatory networks (GRNs) governing endoderm formation, we identified targets of Ta/Tbx16-regulated homeodomain transcription factor Mixl1, which is absolutely required in zebrafish for endoderm formation. Interestingly, we find many endodermal determinants coordinately regulated through common genomic occupancy by Mixl1, Eomesa, Smad2, Nanog, Mxtx2, and Pou5f3. Collectively, these findings augment the endoderm GRN and reveal a panel of target genes underlying the Ta, Tbx16, and Mixl1 mutant phenotypes.
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Affiliation(s)
- Andrew C Nelson
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Stephen J Cutty
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Saule N Gasiunas
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Isabella Deplae
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fiona C Wardle
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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6
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Scahill CM, Digby Z, Sealy IM, White RJ, Wali N, Collins JE, Stemple DL, Busch-Nentwich EM. The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish. Wellcome Open Res 2018; 2:77. [PMID: 29568807 PMCID: PMC5840683 DOI: 10.12688/wellcomeopenres.12530.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 12/03/2022] Open
Abstract
Background: Mutations in proteins involved in telomere maintenance lead to a range of human diseases, including dyskeratosis congenita, idiopathic pulmonary fibrosis and cancer. Telomerase functions to add telomeric repeats back onto the ends of chromosomes, however non-canonical roles of components of telomerase have recently been suggested. Methods: Here we use a zebrafish telomerase mutant which harbours a nonsense mutation in
tert to investigate the adult phenotypes of fish derived from heterozygous parents of different ages. Furthermore we use whole genome sequencing data to estimate average telomere lengths. Results: We show that homozygous offspring from older heterozygotes exhibit signs of body wasting at a younger age than those of younger parents, and that offspring of older heterozygous parents weigh less irrespective of genotype. We also demonstrate that
tert homozygous mutant fish have a male sex bias, and that clutches from older parents also have a male sex bias in the heterozygous and wild-type populations. Telomere length analysis reveals that the telomeres of younger heterozygous parents are shorter than those of older heterozygous parents. Conclusions: These data indicate that the phenotypes observed in offspring from older parents cannot be explained by telomere length. Instead we propose that Tert functions outside of telomere length maintenance in an age-dependent manner to influence the adult phenotypes of the next generation.
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Affiliation(s)
| | - Zsofia Digby
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Richard J White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Neha Wali
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - John E Collins
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
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7
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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: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Praissman JL, Willer T, Sheikh MO, Toi A, Chitayat D, Lin YY, Lee H, Stalnaker SH, Wang S, Prabhakar PK, Nelson SF, Stemple DL, Moore SA, Moremen KW, Campbell KP, Wells L. The functional O-mannose glycan on α-dystroglycan contains a phospho-ribitol primed for matriglycan addition. eLife 2016; 5. [PMID: 27130732 PMCID: PMC4924997 DOI: 10.7554/elife.14473] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/28/2016] [Indexed: 12/24/2022] Open
Abstract
Multiple glycosyltransferases are essential for the proper modification of alpha-dystroglycan, as mutations in the encoding genes cause congenital/limb-girdle muscular dystrophies. Here we elucidate further the structure of an O-mannose-initiated glycan on alpha-dystroglycan that is required to generate its extracellular matrix-binding polysaccharide. This functional glycan contains a novel ribitol structure that links a phosphotrisaccharide to xylose. ISPD is a CDP-ribitol (ribose) pyrophosphorylase that generates the reduced sugar nucleotide for the insertion of ribitol in a phosphodiester linkage to the glycoprotein. TMEM5 is a UDP-xylosyl transferase that elaborates the structure. We demonstrate in a zebrafish model as well as in a human patient that defects in TMEM5 result in muscular dystrophy in combination with abnormal brain development. Thus, we propose a novel structure—a ribitol in a phosphodiester linkage—for the moiety on which TMEM5, B4GAT1, and LARGE act to generate the functional receptor for ECM proteins having LG domains. DOI:http://dx.doi.org/10.7554/eLife.14473.001
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Affiliation(s)
- Jeremy L Praissman
- Complex Carbohydrate Research Center, University of Georgia, Athens, United States
| | - Tobias Willer
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, United States.,Howard Hughes Medical Institute, University of Iowa, Iowa City, United States.,Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, United States.,Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - M Osman Sheikh
- Complex Carbohydrate Research Center, University of Georgia, Athens, United States
| | - Ants Toi
- Department of Medical Imaging, Mount Sinai Hospital, Toronto, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Canada.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Yung-Yao Lin
- Blizard Institute, London, United Kingdom.,Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.,Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Hane Lee
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, United States
| | | | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, United States
| | | | - Stanley F Nelson
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States.,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Derek L Stemple
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Steven A Moore
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, United States
| | - Kevin P Campbell
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, United States.,Howard Hughes Medical Institute, University of Iowa, Iowa City, United States.,Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, United States.,Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, United States
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9
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Brocal I, White RJ, Dooley CM, Carruthers SN, Clark R, Hall A, Busch-Nentwich EM, Stemple DL, Kettleborough RNW. Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish. BMC Genomics 2016; 17:259. [PMID: 27009152 PMCID: PMC4806435 DOI: 10.1186/s12864-016-2563-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/02/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The CRISPR/Cas9 system is a prokaryotic immune system that infers resistance to foreign genetic material and is a sort of 'adaptive immunity'. It has been adapted to enable high throughput genome editing and has revolutionised the generation of targeted mutations. RESULTS We have developed a scalable analysis pipeline to identify CRISPR/Cas9 induced mutations in hundreds of samples using next generation sequencing (NGS) of amplicons. We have used this system to investigate the best way to screen mosaic Zebrafish founder individuals for germline transmission of induced mutations. Screening sperm samples from potential founders provides much better information on germline transmission rates and crucially the sequence of the particular insertions/deletions (indels) that will be transmitted. This enables us to combine screening with archiving to create a library of cryopreserved samples carrying known mutations. It also allows us to design efficient genotyping assays, making identifying F1 carriers straightforward. CONCLUSIONS The methods described will streamline the production of large numbers of knockout alleles in selected genes for phenotypic analysis, complementing existing efforts using random mutagenesis.
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Affiliation(s)
- Isabel Brocal
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard J. White
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Christopher M. Dooley
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Samantha N. Carruthers
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard Clark
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Amanda Hall
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | | | - Derek L. Stemple
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Ross N. W. Kettleborough
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- />Twist Bioscience, 455 Mission Bay Boulevard South, San Francisco, CA 94158 United States
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10
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Lorent K, Gong W, Koo KA, Waisbourd-Zinman O, Karjoo S, Zhao X, Sealy I, Kettleborough RN, Stemple DL, Windsor PA, Whittaker SJ, Porter JR, Wells RG, Pack M. Identification of a plant isoflavonoid that causes biliary atresia. Sci Transl Med 2016; 7:286ra67. [PMID: 25947162 DOI: 10.1126/scitranslmed.aaa1652] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biliary atresia (BA) is a rapidly progressive and destructive fibrotic disorder of unknown etiology affecting the extrahepatic biliary tree of neonates. Epidemiological studies suggest that an environmental factor, such as a virus or toxin, is the cause of the disease, although none have been definitively established. Several naturally occurring outbreaks of BA in Australian livestock have been associated with the ingestion of unusual plants by pregnant animals during drought conditions. We used a biliary secretion assay in zebrafish to isolate a previously undescribed isoflavonoid, biliatresone, from Dysphania species implicated in a recent BA outbreak. This compound caused selective destruction of the extrahepatic, but not intrahepatic, biliary system of larval zebrafish. A mutation that enhanced biliatresone toxicity mapped to a region of the zebrafish genome that has conserved synteny with an established human BA susceptibility locus. The toxin also caused loss of cilia in neonatal mouse extrahepatic cholangiocytes in culture and disrupted cell polarity and monolayer integrity in cholangiocyte spheroids. Together, these findings provide direct evidence that BA could be initiated by perinatal exposure to an environmental toxin.
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Affiliation(s)
- Kristin Lorent
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weilong Gong
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyung A Koo
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104, USA
| | - Orith Waisbourd-Zinman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sara Karjoo
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xiao Zhao
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian Sealy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ross N Kettleborough
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peter A Windsor
- Faculty of Veterinary Science, University of Sydney, Camden, New South Wales 2570, Australia
| | - Stephen J Whittaker
- Hume Livestock Health and Pest Authority, Albury, New South Wales 2640, Australia
| | - John R Porter
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA 19104, USA
| | - Rebecca G Wells
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Michael Pack
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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11
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Bielczyk-Maczyńska E, Lam Hung L, Ferreira L, Fleischmann T, Weis F, Fernández-Pevida A, Harvey SA, Wali N, Warren AJ, Barroso I, Stemple DL, Cvejic A. The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish. PLoS Genet 2015; 11:e1005677. [PMID: 26624285 PMCID: PMC4666468 DOI: 10.1371/journal.pgen.1005677] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
Ribosome biogenesis is a ubiquitous and essential process in cells. Defects in ribosome biogenesis and function result in a group of human disorders, collectively known as ribosomopathies. In this study, we describe a zebrafish mutant with a loss-of-function mutation in nol9, a gene that encodes a non-ribosomal protein involved in rRNA processing. nol9sa1022/sa1022 mutants have a defect in 28S rRNA processing. The nol9sa1022/sa1022 larvae display hypoplastic pancreas, liver and intestine and have decreased numbers of hematopoietic stem and progenitor cells (HSPCs), as well as definitive erythrocytes and lymphocytes. In addition, ultrastructural analysis revealed signs of pathological processes occurring in endothelial cells of the caudal vein, emphasizing the complexity of the phenotype observed in nol9sa1022/sa1022 larvae. We further show that both the pancreatic and hematopoietic deficiencies in nol9sa1022/sa1022 embryos were due to impaired cell proliferation of respective progenitor cells. Interestingly, genetic loss of Tp53 rescued the HSPCs but not the pancreatic defects. In contrast, activation of mRNA translation via the mTOR pathway by L-Leucine treatment did not revert the erythroid or pancreatic defects. Together, we present the nol9sa1022/sa1022 mutant, a novel zebrafish ribosomopathy model, which recapitulates key human disease characteristics. The use of this genetically tractable model will enhance our understanding of the tissue-specific mechanisms following impaired ribosome biogenesis in the context of an intact vertebrate.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Laure Lam Hung
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tobias Fleischmann
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Félix Weis
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Antonio Fernández-Pevida
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Steven A. Harvey
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alan J. Warren
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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12
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Sztal TE, Zhao M, Williams C, Oorschot V, Parslow AC, Giousoh A, Yuen M, Hall TE, Costin A, Ramm G, Bird PI, Busch-Nentwich EM, Stemple DL, Currie PD, Cooper ST, Laing NG, Nowak KJ, Bryson-Richardson RJ. Zebrafish models for nemaline myopathy reveal a spectrum of nemaline bodies contributing to reduced muscle function. Acta Neuropathol 2015; 130:389-406. [PMID: 25931053 PMCID: PMC4541704 DOI: 10.1007/s00401-015-1430-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 12/22/2022]
Abstract
Nemaline myopathy is characterized by muscle weakness and the presence of rod-like (nemaline) bodies. The genetic etiology of nemaline myopathy is becoming increasingly understood with mutations in ten genes now known to cause the disease. Despite this, the mechanism by which skeletal muscle weakness occurs remains elusive, with previous studies showing no correlation between the frequency of nemaline bodies and disease severity. To investigate the formation of nemaline bodies and their role in pathogenesis, we generated overexpression and loss-of-function zebrafish models for skeletal muscle α-actin (ACTA1) and nebulin (NEB). We identify three distinct types of nemaline bodies and visualize their formation in vivo, demonstrating these nemaline bodies not only exhibit different subcellular origins, but also have distinct pathological consequences within the skeletal muscle. One subtype is highly dynamic and upon breakdown leads to the accumulation of cytoplasmic actin contributing to muscle weakness. Examination of a Neb-deficient model suggests this mechanism may be common in nemaline myopathy. Another subtype results from a reduction of actin and forms a more stable cytoplasmic body. In contrast, the final type originates at the Z-disk and is associated with myofibrillar disorganization. Analysis of zebrafish and muscle biopsies from ACTA1 nemaline myopathy patients demonstrates that nemaline bodies also possess a different protein signature. In addition, we show that the ACTA1D286G mutation causes impaired actin incorporation and localization in the sarcomere. Together these data provide a novel examination of nemaline body origins and dynamics in vivo and identifies pathological changes that correlate with muscle weakness.
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Affiliation(s)
- Tamar E. Sztal
- />School of Biological Sciences, Monash University, Melbourne, VIC Australia
| | - Mo Zhao
- />School of Biological Sciences, Monash University, Melbourne, VIC Australia
| | - Caitlin Williams
- />School of Biological Sciences, Monash University, Melbourne, VIC Australia
| | - Viola Oorschot
- />Monash Micro-Imaging, Monash University, Melbourne, VIC Australia
| | - Adam C. Parslow
- />School of Biological Sciences, Monash University, Melbourne, VIC Australia
| | - Aminah Giousoh
- />Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia
| | - Michaela Yuen
- />Institute for Neuroscience and Muscle Research, The Children’s Hospital at Westmead, Sydney, NSW Australia
| | - Thomas E. Hall
- />Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD Australia
| | - Adam Costin
- />Monash Micro-Imaging, Monash University, Melbourne, VIC Australia
| | - Georg Ramm
- />Monash Micro-Imaging, Monash University, Melbourne, VIC Australia
- />Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia
| | - Phillip I. Bird
- />Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC Australia
| | | | - Derek L. Stemple
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire UK
| | - Peter D. Currie
- />Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC Australia
| | - Sandra T. Cooper
- />Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Nigel G. Laing
- />Harry Perkins Institute of Medical Research and the Centre for Medical Research, University of Western Australia, Perth, WA Australia
| | - Kristen J. Nowak
- />Harry Perkins Institute of Medical Research and the Centre for Medical Research, University of Western Australia, Perth, WA Australia
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13
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Collins JE, Wali N, Sealy IM, Morris JA, White RJ, Leonard SR, Jackson DK, Jones MC, Smerdon NC, Zamora J, Dooley CM, Carruthers SN, Barrett JC, Stemple DL, Busch-Nentwich EM. High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping. BMC Genomics 2015; 16:578. [PMID: 26238335 PMCID: PMC4524448 DOI: 10.1186/s12864-015-1788-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. RESULTS Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. CONCLUSIONS This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.
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Affiliation(s)
- John E Collins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Neha Wali
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - James A Morris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Richard J White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Steven R Leonard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - David K Jackson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Matthew C Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nathalie C Smerdon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jorge Zamora
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Christopher M Dooley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Samantha N Carruthers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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14
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Abstract
The initial phases of embryonic development occur in the absence of de novo transcription and are instead controlled by maternally inherited mRNAs and proteins. During this initial period, cell cycles are synchronous and lack gap phases. Following this period of transcriptional silence, zygotic transcription begins, the maternal influence on development starts to decrease, and dramatic changes to the cell cycle take place. Here, we discuss recent work that is shedding light on the maternal to zygotic transition and the interrelated but distinct mechanisms regulating the onset of zygotic transcription and changes to the cell cycle during early embryonic development.
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Affiliation(s)
- Alexander R Langley
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - James C Smith
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Derek L Stemple
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Steven A Harvey
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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15
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Kenyon EJ, Campos I, Bull JC, Williams PH, Stemple DL, Clark MD. Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling. Dev Biol 2014; 397:212-24. [PMID: 25478908 PMCID: PMC4294769 DOI: 10.1016/j.ydbio.2014.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/03/2014] [Accepted: 11/11/2014] [Indexed: 01/08/2023]
Abstract
The RAB5 gene family is the best characterised of all human RAB families and is essential for in vitro homotypic fusion of early endosomes. In recent years, the disruption or activation of Rab5 family proteins has been used as a tool to understand growth factor signal transduction in whole animal systems such as Drosophila melanogaster and zebrafish. In this study we have examined the functions for four rab5 genes in zebrafish. Disruption of rab5ab expression by antisense morpholino oligonucleotide (MO) knockdown abolishes nodal signalling in early zebrafish embryos, whereas overexpression of rab5ab mRNA leads to ectopic expression of markers that are normally downstream of nodal signalling. By contrast MO disruption of other zebrafish rab5 genes shows little or no effect on expression of markers of dorsal organiser development. We conclude that rab5ab is essential for nodal signalling and organizer specification in the developing zebrafish embryo. We have examined the activities of each of the zebrafish Rab5 genes using morpholino knockdowns. Loss of one Rab5 isoform, Rab5ab, affects formation of the dorsal organizer. Rab5ab overexpression leads to ectopic expression of dorsal markers.
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Affiliation(s)
- Emma J Kenyon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Isabel Campos
- Champalimaud Centre for the Unknown, Fundação Champalimaud, Lisboa, Portugal
| | - James C Bull
- Department of Biosciences, Swansea University, Swansea SA2 8PP, United Kingdom
| | - P Huw Williams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
| | - Matthew D Clark
- Sequencing Technology Development, The Genome Analysis Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
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16
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Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AEE, Wardle FC. Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biol 2014; 12:81. [PMID: 25277163 PMCID: PMC4206766 DOI: 10.1186/s12915-014-0081-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/27/2022] Open
Abstract
Background Nodal signalling is an absolute requirement for normal mesoderm and endoderm formation in vertebrate embryos, yet the transcriptional networks acting directly downstream of Nodal and the extent to which they are conserved is largely unexplored, particularly in vivo. Eomesodermin also plays a role in patterning mesoderm and endoderm in vertebrates, but its mechanisms of action and how it interacts with the Nodal signalling pathway are still unclear. Results Using a combination of expression analysis and chromatin immunoprecipitation with deep sequencing (ChIP-seq) we identify direct targets of Smad2, the effector of Nodal signalling in blastula stage zebrafish embryos, including many novel target genes. Through comparison of these data with published ChIP-seq data in human, mouse and Xenopus we show that the transcriptional network driven by Smad2 in mesoderm and endoderm is conserved in these vertebrate species. We also show that Smad2 and zebrafish Eomesodermin a (Eomesa) bind common genomic regions proximal to genes involved in mesoderm and endoderm formation, suggesting Eomesa forms a general component of the Smad2 signalling complex in zebrafish. Combinatorial perturbation of Eomesa and Smad2-interacting factor Foxh1 results in loss of both mesoderm and endoderm markers, confirming the role of Eomesa in endoderm formation and its functional interaction with Foxh1 for correct Nodal signalling. Finally, we uncover a novel role for Eomesa in repressing ectodermal genes in the early blastula. Conclusions Our data demonstrate that evolutionarily conserved developmental functions of Nodal signalling occur through maintenance of the transcriptional network directed by Smad2. This network is modulated by Eomesa in zebrafish which acts to promote mesoderm and endoderm formation in combination with Nodal signalling, whilst Eomesa also opposes ectoderm gene expression. Eomesa, therefore, regulates the formation of all three germ layers in the early zebrafish embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0081-5) contains supplementary material, which is available to authorized users.
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17
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Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A, Richardson J, Jones D, Raine K, Watson IR, Wu CJ, Cheng J, Martincorena I, Nik-Zainal S, Mudie L, Moreau Y, Marshall J, Ramakrishna M, Tarpey P, Shlien A, Whitmore I, Gamble S, Latimer C, Langdon E, Kaufman C, Dovey M, Taylor A, Menzies A, McLaren S, O'Meara S, Butler A, Teague J, Lister J, Chin L, Campbell P, Adams DJ, Zon LI, Patton EE, Stemple DL, Futreal PA. The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome Biol 2014; 14:R113. [PMID: 24148783 PMCID: PMC3983654 DOI: 10.1186/gb-2013-14-10-r113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022] Open
Abstract
Background Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even with germline mutated p53, these engineered melanomas present with variable onset and pathology, implicating additional somatic mutations in a multi-hit tumorigenic process. Results To decipher the genetics of these melanomas, we sequence the protein coding exons of 53 primary melanomas generated from several BRAFV600E or NRASQ61K driven transgenic zebrafish lines. We find that engineered zebrafish melanomas show an overall low mutation burden, which has a strong, inverse association with the number of initiating germline drivers. Although tumors reveal distinct mutation spectrums, they show mostly C > T transitions without UV light exposure, and enrichment of mutations in melanogenesis, p53 and MAPK signaling. Importantly, a recurrent amplification occurring with pre-configured drivers BRAFV600E and p53-/- suggests a novel path of BRAF cooperativity through the protein kinase A pathway. Conclusion This is the first analysis of a melanoma mutational landscape in the absence of UV light, where tumors manifest with remarkably low mutation burden and high heterogeneity. Genotype specific amplification of protein kinase A in cooperation with BRAF and p53 mutation suggests the involvement of melanogenesis in these tumors. This work is important for defining the spectrum of events in BRAF or NRAS driven melanoma in the absence of UV light, and for informed exploitation of models such as transgenic zebrafish to better understand mechanisms leading to human melanoma formation.
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18
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Bielczyk-Maczyńska E, Serbanovic-Canic J, Ferreira L, Soranzo N, Stemple DL, Ouwehand WH, Cvejic A. A loss of function screen of identified genome-wide association study Loci reveals new genes controlling hematopoiesis. PLoS Genet 2014; 10:e1004450. [PMID: 25010335 PMCID: PMC4091788 DOI: 10.1371/journal.pgen.1004450] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/02/2014] [Indexed: 01/01/2023] Open
Abstract
The formation of mature cells by blood stem cells is very well understood at the cellular level and we know many of the key transcription factors that control fate decisions. However, many upstream signalling and downstream effector processes are only partially understood. Genome wide association studies (GWAS) have been particularly useful in providing new directions to dissect these pathways. A GWAS meta-analysis identified 68 genetic loci controlling platelet size and number. Only a quarter of those genes, however, are known regulators of hematopoiesis. To determine function of the remaining genes we performed a medium-throughput genetic screen in zebrafish using antisense morpholino oligonucleotides (MOs) to knock down protein expression, followed by histological analysis of selected genes using a wide panel of different hematopoietic markers. The information generated by the initial knockdown was used to profile phenotypes and to position candidate genes hierarchically in hematopoiesis. Further analysis of brd3a revealed its essential role in differentiation but not maintenance and survival of thrombocytes. Using the from-GWAS-to-function strategy we have not only identified a series of genes that represent novel regulators of thrombopoiesis and hematopoiesis, but this work also represents, to our knowledge, the first example of a functional genetic screening strategy that is a critical step toward obtaining biologically relevant functional data from GWA study for blood cell traits.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Jovana Serbanovic-Canic
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield, United Kingdom
- Department of Cardiovascular Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicole Soranzo
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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19
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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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20
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Abstract
The need for scalable strategies to probe the biological consequences of candidate cancer genes has never been more pressing. The zebrafish, with its capacity for high-throughput transgenesis, in vivo imaging and chemical/genetic screening, has ideal features for undertaking this task. Unique biological insights from zebrafish have already led to the identification of novel oncogenic drivers and small molecules being used to treat the human cancer. This review summarizes the recent main findings and describes pertinent areas where the zebrafish can greatly contribute to our understanding of cancer biology and treatment.
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Affiliation(s)
- Jennifer Yen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Richard M White
- Memorial Sloan Kettering Cancer Center and Weill-Cornell Medical College, New York, NY 11788, United States
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom.
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21
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Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird G, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper JD, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley C, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SMJ, Enright A, Geisler R, Plasterk RHA, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Volhard CN, Hubbard TJP, Crollius HR, Rogers J, Stemple DL. Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013. [DOI: 10.1038/nature12813] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher JP, Clark KJ, Stemple DL, Klee EW, Ekker SC, Scaria V, Sivasubbu S. A sequence-based variation map of zebrafish. Zebrafish 2013; 10:15-20. [PMID: 23590399 DOI: 10.1089/zeb.2012.0848] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zebrafish (Danio rerio) is a popular vertebrate model organism largely deployed using outbred laboratory animals. The nonisogenic nature of the zebrafish as a model system offers the opportunity to understand natural variations and their effect in modulating phenotype. In an effort to better characterize the range of natural variation in this model system and to complement the zebrafish reference genome project, the whole genome sequence of a wild zebrafish at 39-fold genome coverage was determined. Comparative analysis with the zebrafish reference genome revealed approximately 5.2 million single nucleotide variations and over 1.6 million insertion-deletion variations. This dataset thus represents a new catalog of genetic variations in the zebrafish genome. Further analysis revealed selective enrichment for variations in genes involved in immune function and response to the environment, suggesting genome-level adaptations to environmental niches. We also show that human disease gene orthologs in the sequenced wild zebrafish genome show a lower ratio of nonsynonymous to synonymous single nucleotide variations.
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Affiliation(s)
- Ashok Patowary
- CSIR- Institute of Genomics and Integrative Biology, Delhi, India
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23
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Dooley CM, Scahill C, Fényes F, Kettleborough RN, Stemple DL, Busch-Nentwich EM. Multi-allelic phenotyping--a systematic approach for the simultaneous analysis of multiple induced mutations. Methods 2013; 62:197-206. [PMID: 23624102 PMCID: PMC3770900 DOI: 10.1016/j.ymeth.2013.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 01/01/2023] Open
Abstract
The zebrafish mutation project (ZMP) aims to generate a loss of function allele for every protein-coding gene, but importantly to also characterise the phenotypes of these alleles during the first five days of development. Such a large-scale screen requires a systematic approach both to identifying phenotypes, and also to linking those phenotypes to specific mutations. This phenotyping pipeline simultaneously assesses the consequences of multiple alleles in a two-step process. First, mutations that do not produce a visible phenotype during the first five days of development are identified, while a second round of phenotyping focuses on detailed analysis of those alleles that are suspected to cause a phenotype. Allele-specific PCR single nucleotide polymorphism (SNP) assays are used to genotype F2 parents and individual F3 fry for mutations known to be present in the F1 founder. With this method specific phenotypes can be linked to induced mutations. In addition a method is described for cryopreserving sperm samples of mutagenised males and their subsequent use for in vitro fertilisation to generate F2 families for phenotyping. Ultimately this approach will lead to the functional annotation of the zebrafish genome, which will deepen our understanding of gene function in development and disease.
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24
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Kettleborough RNW, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E, Stemple DL. A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature 2013; 496:494-7. [PMID: 23594742 PMCID: PMC3743023 DOI: 10.1038/nature11992] [Citation(s) in RCA: 442] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 02/07/2013] [Indexed: 01/11/2023]
Abstract
Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in model vertebrate organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes, this number falls considerably short of the more than 22,000 mouse protein-coding genes. Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning, insertional mutagenesis, antisense morpholino oligonucleotides, targeted re-sequencing, and zinc finger and TAL endonucleases have made substantial contributions to our understanding of the biological activity of vertebrate genes, but again the number of genes studied falls well short of the more than 26,000 zebrafish protein-coding genes. Importantly, for both mice and zebrafish, none of these strategies are particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Here we describe an active project that aims to identify and phenotype the disruptive mutations in every zebrafish protein-coding gene, using a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis. So far we have identified potentially disruptive mutations in more than 38% of all known zebrafish protein-coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1,000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.
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Affiliation(s)
- Ross N W Kettleborough
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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25
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Grønskov K, Dooley CM, Østergaard E, Kelsh RN, Hansen L, Levesque MP, Vilhelmsen K, Møllgård K, Stemple DL, Rosenberg T. Mutations in c10orf11, a melanocyte-differentiation gene, cause autosomal-recessive albinism. Am J Hum Genet 2013; 92:415-21. [PMID: 23395477 DOI: 10.1016/j.ajhg.2013.01.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/17/2012] [Accepted: 01/23/2013] [Indexed: 11/28/2022] Open
Abstract
Autosomal-recessive albinism is a hypopigmentation disorder with a broad phenotypic range. A substantial fraction of individuals with albinism remain genetically unresolved, and it has been hypothesized that more genes are to be identified. By using homozygosity mapping of an inbred Faroese family, we identified a 3.5 Mb homozygous region (10q22.2-q22.3) on chromosome 10. The region contains five protein-coding genes, and sequencing of one of these, C10orf11, revealed a nonsense mutation that segregated with the disease and showed a recessive inheritance pattern. Investigation of additional albinism-affected individuals from the Faroe Islands revealed that five out of eight unrelated affected persons had the nonsense mutation in C10orf11. Screening of a cohort of autosomal-recessive-albinism-affected individuals residing in Denmark showed a homozygous 1 bp duplication in C10orf11 in an individual originating from Lithuania. Immunohistochemistry showed localization of C10orf11 in melanoblasts and melanocytes in human fetal tissue, but no localization was seen in retinal pigment epithelial cells. Knockdown of the zebrafish (Danio rerio) homolog with the use of morpholinos resulted in substantially decreased pigmentation and a reduction of the apparent number of pigmented melanocytes. The morphant phenotype was rescued by wild-type C10orf11, but not by mutant C10orf11. In conclusion, we have identified a melanocyte-differentiation gene, C10orf11, which when mutated causes autosomal-recessive albinism in humans.
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Affiliation(s)
- Karen Grønskov
- Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
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26
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Buysse K, Riemersma M, Powell G, van Reeuwijk J, Chitayat D, Roscioli T, Kamsteeg EJ, van den Elzen C, van Beusekom E, Blaser S, Babul-Hirji R, Halliday W, Wright GJ, Stemple DL, Lin YY, Lefeber DJ, van Bokhoven H. Missense mutations in β-1,3-N-acetylglucosaminyltransferase 1 (B3GNT1) cause Walker-Warburg syndrome. Hum Mol Genet 2013; 22:1746-54. [PMID: 23359570 PMCID: PMC3613162 DOI: 10.1093/hmg/ddt021] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Several known or putative glycosyltransferases are required for the synthesis of laminin-binding glycans on alpha-dystroglycan (αDG), including POMT1, POMT2, POMGnT1, LARGE, Fukutin, FKRP, ISPD and GTDC2. Mutations in these glycosyltransferase genes result in defective αDG glycosylation and reduced ligand binding by αDG causing a clinically heterogeneous group of congenital muscular dystrophies, commonly referred to as dystroglycanopathies. The most severe clinical form, Walker–Warburg syndrome (WWS), is characterized by congenital muscular dystrophy and severe neurological and ophthalmological defects. Here, we report two homozygous missense mutations in the β-1,3-N-acetylglucosaminyltransferase 1 (B3GNT1) gene in a family affected with WWS. Functional studies confirmed the pathogenicity of the mutations. First, expression of wild-type but not mutant B3GNT1 in human prostate cancer (PC3) cells led to increased levels of αDG glycosylation. Second, morpholino knockdown of the zebrafish b3gnt1 orthologue caused characteristic muscular defects and reduced αDG glycosylation. These functional studies identify an important role of B3GNT1 in the synthesis of the uncharacterized laminin-binding glycan of αDG and implicate B3GNT1 as a novel causative gene for WWS.
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Affiliation(s)
- Karen Buysse
- Department of Human Genetics 855, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
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27
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Nelson AC, Pillay N, Henderson S, Presneau N, Tirabosco R, Halai D, Berisha F, Flicek P, Stemple DL, Stern CD, Wardle FC, Flanagan AM. An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma. J Pathol 2012; 228:274-85. [PMID: 22847733 PMCID: PMC6089345 DOI: 10.1002/path.4082] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/16/2012] [Accepted: 07/14/2012] [Indexed: 12/31/2022]
Abstract
Chordoma is a rare malignant tumour of bone, the molecular marker of which is the expression of the transcription factor, brachyury. Having recently demonstrated that silencing brachyury induces growth arrest in a chordoma cell line, we now seek to identify its downstream target genes. Here we use an integrated functional genomics approach involving shRNA-mediated brachyury knockdown, gene expression microarray, ChIP-seq experiments, and bioinformatics analysis to achieve this goal. We confirm that the T-box binding motif of human brachyury is identical to that found in mouse, Xenopus, and zebrafish development, and that brachyury acts primarily as an activator of transcription. Using human chordoma samples for validation purposes, we show that brachyury binds 99 direct targets and indirectly influences the expression of 64 other genes, thereby acting as a master regulator of an elaborate oncogenic transcriptional network encompassing diverse signalling pathways including components of the cell cycle, and extracellular matrix components. Given the wide repertoire of its active binding and the relative specific localization of brachyury to the tumour cells, we propose that an RNA interference-based gene therapy approach is a plausible therapeutic avenue worthy of investigation.
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Affiliation(s)
- Andrew C Nelson
- Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, Guy’s Campus, London, SE1 1UL, UK
| | - Nischalan Pillay
- Cancer Institute, University College London, London, WC1E 6BT, UK
- Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
| | | | - Nadège Presneau
- Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
| | - Dina Halai
- Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
| | - Fitim Berisha
- Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Fiona C Wardle
- Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, Guy’s Campus, London, SE1 1UL, UK
| | - Adrienne M Flanagan
- Cancer Institute, University College London, London, WC1E 6BT, UK
- Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
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28
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Abstract
Ensembl gene annotation provides a comprehensive catalog of transcripts aligned to the reference sequence. It relies on publicly available species-specific and orthologous transcripts plus their inferred protein sequence. The accuracy of gene models is improved by increasing the species-specific component that can be cost-effectively achieved using RNA-seq. Two zebrafish gene annotations are presented in Ensembl version 62 built on the Zv9 reference sequence. Firstly, RNA-seq data from five tissues and seven developmental stages were assembled into 25,748 gene models. A 3′-end capture and sequencing protocol was developed to predict the 3′ ends of transcripts, and 46.1% of the original models were subsequently refined. Secondly, a standard Ensembl genebuild, incorporating carefully filtered elements from the RNA-seq-only build, followed by a merge with the manually curated VEGA database, produced a comprehensive annotation of 26,152 genes represented by 51,569 transcripts. The RNA-seq-only and the Ensembl/VEGA genebuilds contribute contrasting elements to the final genebuild. The RNA-seq genebuild was used to adjust intron/exon boundaries of orthologous defined models, confirm their expression, and improve 3′ untranslated regions. Importantly, the inferred protein alignments within the Ensembl genebuild conferred proof of model contiguity for the RNA-seq models. The zebrafish gene annotation has been enhanced by the incorporation of RNA-seq data and the pipeline will be used for other organisms. Organisms with little species-specific cDNA data will generally benefit the most.
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Affiliation(s)
- John E Collins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.
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29
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Brieu N, Navab N, Serbanovic-Canic J, Ouwehand WH, Stemple DL, Cvejic A, Groher M. Image-based characterization of thrombus formation in time-lapse DIC microscopy. Med Image Anal 2012; 16:915-31. [PMID: 22482997 PMCID: PMC3740235 DOI: 10.1016/j.media.2012.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 02/01/2012] [Accepted: 02/02/2012] [Indexed: 11/19/2022]
Abstract
The characterization of thrombus formation in time-lapse DIC microscopy is of increased interest for identifying genes which account for atherothrombosis and coronary artery diseases (CADs). In particular, we are interested in large-scale studies on zebrafish, which result in large amount of data, and require automatic processing. In this work, we present an image-based solution for the automatized extraction of parameters quantifying the temporal development of thrombotic plugs. Our system is based on the joint segmentation of thrombotic and aortic regions over time. This task is made difficult by the low contrast and the high dynamic conditions observed in vivo DIC microscopic scenes. Our key idea is to perform this segmentation by distinguishing the different motion patterns in image time series rather than by solving standard image segmentation tasks in each image frame. Thus, we are able to compensate for the poor imaging conditions. We model motion patterns by energies based on the idea of dynamic textures, and regularize the model by two prior energies on the shape of the aortic region and on the topological relationship between the thrombus and the aorta. We demonstrate the performance of our segmentation algorithm by qualitative and quantitative experiments on synthetic examples as well as on real in vivo microscopic sequences.
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Affiliation(s)
- Nicolas Brieu
- Computer Aided Medical Procedures, Technische Universität München (TUM), Garching bei München 85748, Germany
- Corresponding author. Address: TUM, Institut für Informatik, CAMP-I16, Boltzmannstrasse 3, Garching bei München 85748, Germany. Tel.: +49 89 289 19405.
| | - Nassir Navab
- Computer Aided Medical Procedures, Technische Universität München (TUM), Garching bei München 85748, Germany
| | - Jovana Serbanovic-Canic
- Department of Hematology, University of Cambridge & NHS Blood and Transplant, Cambridge CB2 0PT, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Willem H. Ouwehand
- Department of Hematology, University of Cambridge & NHS Blood and Transplant, Cambridge CB2 0PT, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Derek L. Stemple
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Ana Cvejic
- Department of Hematology, University of Cambridge & NHS Blood and Transplant, Cambridge CB2 0PT, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Martin Groher
- Computer Aided Medical Procedures, Technische Universität München (TUM), Garching bei München 85748, Germany
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30
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Abstract
The pipid frog Xenopus tropicalis has emerged as a powerful new model system for combining genetic and genomic analysis of tetrapod development with robust embryological, molecular, and biochemical assays. Its early development closely resembles that of its well-understood relative X. laevis, from which techniques and reagents can be readily transferred. In contrast to the tetraploid X. laevis, X. tropicalis has a compact diploid genome with strong synteny to those of amniotes. Recently, advances in high-throughput sequencing together with solution-hybridization whole-exome enrichment technology offer powerful strategies for cloning novel mutations as well as reverse genetic identification of sequence lesions in specific genes of interest. Further advantages include the wide range of functional and molecular assays available, the large number of embryos/meioses produced, and the ease of haploid genetics and gynogenesis. The addition of these genetic tools to X. tropicalis provides a uniquely flexible platform for analysis of gene function in vertebrate development.
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Affiliation(s)
- Timothy J. Geach
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA United Kingdom
| | | | - Lyle B. Zimmerman
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA United Kingdom
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31
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Sinzelle L, Thuret R, Hwang HY, Herszberg B, Paillard E, Bronchain OJ, Stemple DL, Dhorne-Pollet S, Pollet N. Characterization of a novel Xenopus tropicalis cell line as a model for in vitro studies. Genesis 2011; 50:316-24. [PMID: 22083648 PMCID: PMC3503257 DOI: 10.1002/dvg.20822] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/21/2011] [Accepted: 10/26/2011] [Indexed: 11/08/2022]
Abstract
Cell lines are useful tools to facilitate in vitro studies of many biological and molecular processes. We describe a new permanent fibroblast-type cell line obtained from disaggregated Xenopus tropicalis limb bud. The cell line population doubling time was ∼ 24 h. Its karyotype was genetically stable with a chromosome number of 2n = 21 and a chromosome 10 trisomy. These cells could be readily transfected and expressed transgenes faithfully. We obtained stable transformants using transposon-based gene transfer technology. These cells responded to thyroid hormone and thus can provide a complementary research tool to study thyroid hormone signaling events. In conclusion, this cell line baptized “Speedy” should prove useful to couple in vitro and in vivo biological studies in the X. tropicalisfrog model. genesis 50:316–324, 2012. © 2011 Wiley Periodicals, Inc.
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Affiliation(s)
- Ludivine Sinzelle
- Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry Val d'Essonne, Genavenir 3-Genopole campus 3, 1 rue Pierre Fontaine, Evry, France
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32
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Wells DE, Gutierrez L, Xu Z, Krylov V, Macha J, Blankenburg KP, Hitchens M, Bellot LJ, Spivey M, Stemple DL, Kowis A, Ye Y, Pasternak S, Owen J, Tran T, Slavikova R, Tumova L, Tlapakova T, Seifertova E, Scherer SE, Sater AK. A genetic map of Xenopus tropicalis. Dev Biol 2011; 354:1-8. [PMID: 21458440 PMCID: PMC3098391 DOI: 10.1016/j.ydbio.2011.03.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 03/05/2011] [Accepted: 03/11/2011] [Indexed: 01/22/2023]
Abstract
We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132cM in length, and 4 smaller linkage groups between 7 and 40cM. The total effective size of the map is 1658cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis.
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Affiliation(s)
- Dan E Wells
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston TX 77204-5001, USA
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Ferrante MI, Kiff RM, Goulding DA, Stemple DL. Troponin T is essential for sarcomere assembly in zebrafish skeletal muscle. Development 2011. [DOI: 10.1242/dev.065185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lin YY, White RJ, Torelli S, Cirak S, Muntoni F, Stemple DL. Zebrafish Fukutin family proteins link the unfolded protein response with dystroglycanopathies. Hum Mol Genet 2011; 20:1763-75. [PMID: 21317159 PMCID: PMC3071672 DOI: 10.1093/hmg/ddr059] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Allelic mutations in putative glycosyltransferase genes, fukutin and fukutin-related protein (fkrp), lead to a wide range of muscular dystrophies associated with hypoglycosylation of α-dystroglycan, commonly referred to as dystroglycanopathies. Defective glycosylation affecting dystroglycan–ligand interactions is considered to underlie the disease pathogenesis. We have modelled dystroglycanopathies in zebrafish using a novel loss-of-function dystroglycan allele and by inhibition of Fukutin family protein activities. We show that muscle pathology in embryos lacking Fukutin or FKRP is different from loss of dystroglycan. In addition to hypoglycosylated α-dystroglycan, knockdown of Fukutin or FKRP leads to a notochord defect and a perturbation of laminin expression before muscle degeneration. These are a consequence of endoplasmic reticulum stress and activation of the unfolded protein response (UPR), preceding loss of dystroglycan–ligand interactions. Together, our results suggest that Fukutin family proteins may play important roles in protein secretion and that the UPR may contribute to the phenotypic spectrum of some dystroglycanopathies in humans.
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Affiliation(s)
- Yung-Yao Lin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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35
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Abstract
In striated muscle, the basic contractile unit is the sarcomere, which comprises myosin-rich thick filaments intercalated with thin filaments made of actin, tropomyosin and troponin. Troponin is required to regulate Ca(2+)-dependent contraction, and mutant forms of troponins are associated with muscle diseases. We have disrupted several genes simultaneously in zebrafish embryos and have followed the progression of muscle degeneration in the absence of troponin. Complete loss of troponin T activity leads to loss of sarcomere structure, in part owing to the destructive nature of deregulated actin-myosin activity. When troponin T and myosin activity are simultaneously disrupted, immature sarcomeres are rescued. However, tropomyosin fails to localise to sarcomeres, and intercalating thin filaments are missing from electron microscopic cross-sections, indicating that loss of troponin T affects thin filament composition. If troponin activity is only partially disrupted, myofibrils are formed but eventually disintegrate owing to deregulated actin-myosin activity. We conclude that the troponin complex has at least two distinct activities: regulation of actin-myosin activity and, independently, a role in the proper assembly of thin filaments. Our results also indicate that sarcomere assembly can occur in the absence of normal thin filaments.
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Affiliation(s)
- Maria I Ferrante
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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36
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Abstract
There is an increasing requirement for efficient reverse genetics in the zebrafish, Here we describe a method that takes advantage of conventional mutagenized libraries (identical to ones used in forward screens) and re-sequencing to identify ENU-induced mutations in genes of interest. The efficiency of TILLING (Targeting Induced Local Legions IN Genomes) depends on the rate of mutagenesis in the library being screened, the amount of base pairs screened, and the ability to effectively identify and retrieve mutations on interest. Here we show that by improving the mutagenesis protocol, using in silico methods to predict codon changes for target selection, efficient PCR and re-sequencing, and accurate mutation detection we can vastly improve current TILLING protocols. Importantly it is also possible to use this method for screening for splice and mis-sense mutations, and with even a relatively small library, there is a high chance of identifying mutations across any given gene.
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Cvejic A, Serbanovic-Canic J, Stemple DL, Ouwehand WH. The role of meis1 in primitive and definitive hematopoiesis during zebrafish development. Haematologica 2010; 96:190-8. [PMID: 21048033 DOI: 10.3324/haematol.2010.027698] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The Meis1 protein represents an important cofactor for Hox and Pbx1 and is implicated in human and murine leukemias. Though much is known about the role of meis1 in leukemogenesis, its function in normal hematopoiesis remains largely unclear. Here we characterized the role of the proto-oncogene, meis1, during zebrafish primitive and definitive hematopoiesis. DESIGN AND METHODS Zebrafish embryos were stained with o-dianisidine to detect hemoglobin-containing cells and Sudan black to quantify neutrophils. The numbers of other cells (scl-, gata1- and alas2-positive cells) were also quantified by measuring the corresponding stained areas of the embryos. We used anti-Meis1 antibody and whole mount immunohistochemistry to determine the pattern of expression of Meis1 during zebrafish development and then analyzed the functional role of Meis1 by knocking-down the meis1 gene. RESULTS Using antisense morpholino oligomers to interrupt meis1 expression we found that, although primitive macrophage development could occur unhampered, posterior erythroid differentiation required meis1, and its absence resulted in a severe decrease in the number of mature erythrocytes. Furthermore a picture emerged that meis1 exerts important effects on later stages of erythrocyte maturation and that these effects are independent of gata1, but under the control of scl. In addition, meis1 morpholino knock-down led to dramatic single arteriovenous tube formation. We also found that knock-down of pbx1 resulted in a phenotype that was strikingly similar to that of meis1 knock-down zebrafish. CONCLUSIONS These results imply that meis1, jointly with pbx1, regulates primitive hematopoiesis as well as vascular development.
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Affiliation(s)
- Ana Cvejic
- Department of Haematology, University of Cambridge, Long Road, Cambridge CB2 0PT, UK
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Jacoby AS, Busch-Nentwich E, Bryson-Richardson RJ, Hall TE, Berger J, Berger S, Sonntag C, Sachs C, Geisler R, Stemple DL, Currie PD. The zebrafish dystrophic mutant softy maintains muscle fibre viability despite basement membrane rupture and muscle detachment. Development 2009; 136:3367-76. [PMID: 19736328 DOI: 10.1242/dev.034561] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The skeletal muscle basement membrane fulfils several crucial functions during development and in the mature myotome and defects in its composition underlie certain forms of muscular dystrophy. A major component of this extracellular structure is the laminin polymer, which assembles into a resilient meshwork that protects the sarcolemma during contraction. Here we describe a zebrafish mutant, softy, which displays severe embryonic muscle degeneration as a result of initial basement membrane failure. The softy phenotype is caused by a mutation in the lamb2 gene, identifying laminin beta2 as an essential component of this basement membrane. Uniquely, softy homozygotes are able to recover and survive to adulthood despite the loss of myofibre adhesion. We identify the formation of ectopic, stable basement membrane attachments as a novel means by which detached fibres are able to maintain viability. This demonstration of a muscular dystrophy model possessing innate fibre viability following muscle detachment suggests basement membrane augmentation as a therapeutic strategy to inhibit myofibre loss.
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Affiliation(s)
- Arie S Jacoby
- The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Ferrante MI, Romio L, Castro S, Collins JE, Goulding DA, Stemple DL, Woolf AS, Wilson SW. Convergent extension movements and ciliary function are mediated by ofd1, a zebrafish orthologue of the human oral-facial-digital type 1 syndrome gene. Hum Mol Genet 2008; 18:289-303. [PMID: 18971206 PMCID: PMC2638777 DOI: 10.1093/hmg/ddn356] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In humans, OFD1 is mutated in oral-facial-digital type I syndrome leading to prenatal death in hemizygous males and dysmorphic faces and brain malformations, with polycystic kidneys presenting later in life in heterozygous females. To elucidate the function of Ofd1, we have studied its function during zebrafish embryonic development. In wild-type embryos, ofd1 mRNA is widely expressed and Ofd1-green fluorescent protein (GFP) fusion localizes to the centrosome/basal body. Disrupting Ofd1 using antisense morpholinos (MOs) led to bent body axes, hydrocephalus and oedema. Laterality was randomized in the brain, heart and viscera, likely a consequence of shorter cilia with disrupted axonemes and perturbed intravesicular fluid flow in Kupffer's vesicle. Embryos injected with ofd1 MOs also displayed convergent extension (CE) defects, which were enhanced by loss of Slb/Wnt11 or Tri/Vangl2, two proteins functioning in a non-canonical Wnt/Planar Cell Polarity (PCP) pathway. Pronephric glomerular midline fusion was compromised in vangl2 and ofd1 loss of function embryos and we suggest this anomaly may be a novel CE defect. Thus, Ofd1 is required for ciliary motility and function in zebrafish, supporting data showing that Ofd1 is essential for primary cilia function in mice. In addition, our data show that Ofd1 is important for CE during gastrulation, consistent with data linking primary cilia and non-canonical Wnt/PCP signalling.
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Affiliation(s)
- Maria I Ferrante
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
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40
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Noël ES, Casal-Sueiro A, Busch-Nentwich E, Verkade H, Dong PDS, Stemple DL, Ober EA. Organ-specific requirements for Hdac1 in liver and pancreas formation. Dev Biol 2008; 322:237-50. [PMID: 18687323 PMCID: PMC3710974 DOI: 10.1016/j.ydbio.2008.06.040] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 05/28/2008] [Accepted: 06/20/2008] [Indexed: 12/14/2022]
Abstract
Liver, pancreas and lung originate from the presumptive foregut in temporal and spatial proximity. This requires precisely orchestrated transcriptional activation and repression of organ-specific gene expression within the same cell. Here, we show distinct roles for the chromatin remodelling factor and transcriptional repressor Histone deacetylase 1 (Hdac1) in endodermal organogenesis in zebrafish. Loss of Hdac1 causes defects in timely liver specification and in subsequent differentiation. Mosaic analyses reveal a cell-autonomous requirement for hdac1 within the hepatic endoderm. Our studies further reveal specific functions for Hdac1 in pancreas development. Loss of hdac1 causes the formation of ectopic endocrine clusters anteriorly to the main islet, as well as defects in exocrine pancreas specification and differentiation. In addition, we observe defects in extrahepatopancreatic duct formation and morphogenesis. Finally, loss of hdac1 results in an expansion of the foregut endoderm in the domain from which the liver and pancreas originate. Our genetic studies demonstrate that Hdac1 is crucial for regulating distinct steps in endodermal organogenesis. This suggests a model in which Hdac1 may directly or indirectly restrict foregut fates while promoting hepatic and exocrine pancreatic specification and differentiation, as well as pancreatic endocrine islet morphogenesis. These findings establish zebrafish as a tractable system to investigate chromatin remodelling factor functions in controlling gene expression programmes in vertebrate endodermal organogenesis.
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Affiliation(s)
- Emily S Noël
- National Institute for Medical Research, Division of Developmental Biology, The Ridgeway, Mill Hill, London, UK
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41
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Ekker SC, Stemple DL, Clark M, Chien CB, Rasooly RS, Javois LC. Zebrafish genome project: bringing new biology to the vertebrate genome field. Zebrafish 2008; 4:239-51. [PMID: 18284331 DOI: 10.1089/zeb.2007.9979] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Rochester, Minnesota 55905, USA.
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42
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Pei W, Williams PH, Clark MD, Stemple DL, Feldman B. Environmental and genetic modifiers of squint penetrance during zebrafish embryogenesis. Dev Biol 2007; 308:368-78. [PMID: 17583692 PMCID: PMC1994576 DOI: 10.1016/j.ydbio.2007.05.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 05/01/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
The Nodal-related subgroup of the TGFbeta superfamily of secreted cytokines regulates the specification of the mesodermal and endodermal germ layers during gastrulation. Two Nodal-related proteins - Squint (Sqt) and Cyclops (Cyc) - are expressed during germ-layer specification in zebrafish. Genetic sqt mutant phenotypes have defined a variable requirement for zygotic Sqt, but not for maternal Sqt, in midline mesendoderm development. However a comparison of phenotypes arising from oocytes or zygotes injected with Sqt antisense morpholinos has suggested a novel requirement for maternal Sqt in dorsal specification. In this study we examined maternal-zygotic mutants for each of two sqt alleles and we also compared phenotypes of closely related zygotic and maternal-zygotic sqt mutants. Each of these approaches indicated there is no general requirement for maternal Sqt. To better understand the dispensability of maternal and zygotic Sqt, we sought out developmental contexts that more rigorously demand intact Sqt signalling. We found that sqt penetrance is influenced by genetic modifiers, by environmental temperature, by levels of residual Activin-like activity and by Heat-Shock Protein 90 (HSP90) activity. Therefore, Sqt may confer an evolutionary advantage by protecting early-stage embryos against detrimental interacting alleles and environmental challenges.
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Affiliation(s)
- Wuhong Pei
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - P. Huw Williams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Matthew D. Clark
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
- *Corresponding Authors: Derek L. Stemple, ; Benjamin Feldman,
| | - Benjamin Feldman
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- *Corresponding Authors: Derek L. Stemple, ; Benjamin Feldman,
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Abstract
DNA amplification is essential to most nucleic acid testing strategies, but established techniques require sophisticated equipment or complex experimental procedures, and their uptake outside specialised laboratories has been limited. Our novel approach, recombinase polymerase amplification (RPA), couples isothermal recombinase-driven primer targeting of template material with strand-displacement DNA synthesis. It achieves exponential amplification with no need for pretreatment of sample DNA. Reactions are sensitive, specific, and rapid and operate at constant low temperature. We have also developed a probe-based detection system. Key aspects of the combined RPA amplification/detection process are illustrated by a test for the pathogen methicillin-resistant
Staphylococcus aureus. The technology proves to be sensitive to fewer than ten copies of genomic DNA. Furthermore, products can be detected in a simple sandwich assay, thereby establishing an instrument-free DNA testing system. This unique combination of properties is a significant advance in the development of portable and widely accessible nucleic acid–based tests.
The authors describe a new technology for the amplification of target DNA that does not require thermocycling, which could find applications in detection of pathogens or bioterror agents in the field.
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Affiliation(s)
| | | | - Derek L Stemple
- 2Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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44
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Feldman B, Pei W, Williams H, Clark M, Stemple DL. Squint protects early embryos from temperature-induced dysmorphology. Dev Biol 2006. [DOI: 10.1016/j.ydbio.2006.04.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB. Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS Genet 2006; 2:e91. [PMID: 16789825 PMCID: PMC1475704 DOI: 10.1371/journal.pgen.0020091] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 04/28/2006] [Indexed: 11/18/2022] Open
Abstract
We present here the results of forward and reverse genetic screens for chemically-induced mutations in Xenopus tropicalis. In our forward genetic screen, we have uncovered 77 candidate phenotypes in diverse organogenesis and differentiation processes. Using a gynogenetic screen design, which minimizes time and husbandry space expenditures, we find that if a phenotype is detected in the gynogenetic F2 of a given F1 female twice, it is highly likely to be a heritable abnormality (29/29 cases). We have also demonstrated the feasibility of reverse genetic approaches for obtaining carriers of mutations in specific genes, and have directly determined an induced mutation rate by sequencing specific exons from a mutagenized population. The Xenopus system, with its well-understood embryology, fate map, and gain-of-function approaches, can now be coupled with efficient loss-of-function genetic strategies for vertebrate functional genomics and developmental genetics.
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Affiliation(s)
- Tadahiro Goda
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Anita Abu-Daya
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Samantha Carruthers
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthew D Clark
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L Stemple
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * To whom correspondence should be addressed. E-mail: (DLS); (LBZ)
| | - Lyle B Zimmerman
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
- * To whom correspondence should be addressed. E-mail: (DLS); (LBZ)
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46
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Pollard SM, Parsons MJ, Kamei M, Kettleborough RNW, Thomas KA, Pham VN, Bae MK, Scott A, Weinstein BM, Stemple DL. Essential and overlapping roles for laminin alpha chains in notochord and blood vessel formation. Dev Biol 2006; 289:64-76. [PMID: 16321372 DOI: 10.1016/j.ydbio.2005.10.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 09/23/2005] [Accepted: 10/03/2005] [Indexed: 01/13/2023]
Abstract
Laminins are major constituents of basement membranes and have wide ranging functions during development and in the adult. They are a family of heterotrimeric molecules created through association of an alpha, beta and gamma chain. We previously reported that two zebrafish loci, grumpy (gup) and sleepy (sly), encode laminin beta1 and gamma1, which are important both for notochord differentiation and for proper intersegmental blood vessel (ISV) formation. In this study we show that bashful (bal) encodes laminin alpha1 (lama1). Although the strongest allele, bal(m190), is fully penetrant, when compared to gup or sly mutant embryos, bal mutants are not as severely affected, as only anterior notochord fails to differentiate and ISVs are unaffected. This suggests that other alpha chains, and hence other isoforms, act redundantly to laminin 1 in posterior notochord and ISV development. We identified cDNA sequences for lama2, lama4 and lama5 and disrupted the expression of each alone or in mutant embryos also lacking laminin alpha1. When expression of laminin alpha4 and laminin alpha1 are simultaneously disrupted, notochord differentiation and ISVs are as severely affected as sly or gup mutants. Moreover, live imaging of transgenic embryos expressing enhanced green fluorescent protein in forming ISVs reveals that the vascular defects in these embryos are due to an inability of ISV sprouts to migrate correctly along the intersegmental, normally laminin-rich regions.
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Affiliation(s)
- Steven M Pollard
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK
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47
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Abstract
Research using Xenopus laevis has made enormous contributions to our understanding of vertebrate development, control of the eukaryotic cell cycle and the cytoskeleton. One limitation, however, has been the lack of systematic genetic studies in Xenopus to complement molecular and cell biological investigations. Work with the closely related diploid frog Xenopus tropicalis is beginning to address this limitation. Here, we review the resources that will make genetic studies using X. tropicalis a reality.
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Affiliation(s)
- Samantha Carruthers
- Vertebrate Development and Genetics, The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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Bosman EA, Penn AC, Ambrose JC, Kettleborough R, Stemple DL, Steel KP. Multiple mutations in mouse Chd7 provide models for CHARGE syndrome. Hum Mol Genet 2005; 14:3463-76. [PMID: 16207732 DOI: 10.1093/hmg/ddi375] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mouse ENU mutagenesis programmes have yielded a series of independent mutations on proximal chromosome 4 leading to dominant head-bobbing and circling behaviour due to truncations of the lateral semicircular canal of the inner ear. Here, we report the identification of mutations in the Chd7 gene in nine of these mutant alleles including six nonsense and three splice site mutations. The human CHD7 gene is known to be involved in CHARGE syndrome, which also shows inner ear malformations and a variety of other features with varying penetrance and appears to be due to frequent de novo mutation. We found widespread expression of Chd7 in early development of the mouse in organs affected in CHARGE syndrome including eye, olfactory epithelium, inner ear and vascular system. Closer inspection of heterozygous mutant mice revealed a range of defects with reduced penetrance, such as cleft palate, choanal atresia, septal defects of the heart, haemorrhages, prenatal death, vulva and clitoral defects and keratoconjunctivitis sicca. Many of these defects mimic the features of CHARGE syndrome. There were no obvious features of the gene that might make it more mutable than other genes. We conclude that the large number of mouse mutants and human de novo mutations may be due to the combination of the Chd7 gene being a large target and the fact that many heterozygous carriers of the mutations are viable individuals with a readily detectable phenotype.
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Affiliation(s)
- Erika A Bosman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Abstract
The notochord is the defining structure of the chordates, and has essential roles in vertebrate development. It serves as a source of midline signals that pattern surrounding tissues and as a major skeletal element of the developing embryo. Genetic and embryological studies over the past decade have informed us about the development and function of the notochord. In this review, I discuss the embryonic origin, signalling roles and ultimate fate of the notochord, with an emphasis on structural aspects of notochord biology.
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Affiliation(s)
- Derek L Stemple
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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50
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Affiliation(s)
- Annabelle Scott
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
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