Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.

Animals Chromatin / genetics Databases, Genetic Gene Expression Regulation, Developmental Genome / genetics Genomics Humans Mice Molecular Sequence Annotation Organogenesis / genetics Regulatory Sequences, Nucleic Acid / genetics Zebrafish / embryology Zebrafish Proteins / genetics

Journal

Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904

Informations de publication

Date de publication:
07 2022
Historique:
received: 09 08 2021
accepted: 03 05 2022
pubmed: 6 7 2022
medline: 16 7 2022
entrez: 5 7 2022
Statut: ppublish

Résumé

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

Identifiants

DOI: 10.1038/s41588-022-01089-w PMID: 35789323 PMC: PMC9279159
pubmed: 35789323
doi: 10.1038/s41588-022-01089-w
pii: 10.1038/s41588-022-01089-w
pmc: PMC9279159
mid: EMS144747
doi:

Substances chimiques

Chromatin 0
Zebrafish Proteins 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1037-1050

Subventions

Organisme : NHGRI NIH HHS
ID : U24 HG002659
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R015457/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UP_1102/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_EX_MR/S300007/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 106955
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : P61715
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UP_1605/10
Pays : United Kingdom

Commentaires et corrections

Type : CommentIn

Informations de copyright

© 2022. Crown.

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Auteurs

Damir Baranasic (D)

MRC London Institute of Medical Sciences, London, UK.
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
ORCID: 0000-0001-5948-0932

Matthias Hörtenhuber (M)

Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
ORCID: 0000-0002-5599-5565

Piotr J Balwierz (PJ)

MRC London Institute of Medical Sciences, London, UK.
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
ORCID: 0000-0002-1548-4605

Tobias Zehnder (T)

MRC London Institute of Medical Sciences, London, UK.
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany.
ORCID: 0000-0002-4127-2673

Abdul Kadir Mukarram (AK)

Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.

Chirag Nepal (C)

Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Csilla Várnai (C)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
Centre for Computational Biology, University of Birmingham, Birmingham, UK.
ORCID: 0000-0003-0048-9507

Yavor Hadzhiev (Y)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
ORCID: 0000-0002-1134-4904

Ada Jimenez-Gonzalez (A)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
ORCID: 0000-0001-7702-6135

Nan Li (N)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
ORCID: 0000-0002-8919-2357

Joseph Wragg (J)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.

Fabio M D'Orazio (FM)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.

Dorde Relic (D)

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
ORCID: 0000-0001-6237-3345

Mikhail Pachkov (M)

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
ORCID: 0000-0001-7616-6435

Noelia Díaz (N)

Max Planck Institute for Molecular Biomedicine, Muenster, Germany.
Institute of Marine Sciences, Barcelona, Spain.
ORCID: 0000-0002-0319-3448

Benjamín Hernández-Rodríguez (B)

Max Planck Institute for Molecular Biomedicine, Muenster, Germany.
ORCID: 0000-0002-5118-8715

Zelin Chen (Z)

Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
ORCID: 0000-0002-8376-7367

Marcus Stoiber (M)

Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Michaël Dong (M)

Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
ORCID: 0000-0003-4084-3099

Irene Stevens (I)

Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
ORCID: 0000-0003-3823-1499

Samuel E Ross (SE)

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

Anne Eagle (A)

Institute of Neuroscience, University of Oregon, Eugene, OR, USA.

Ryan Martin (R)

Institute of Neuroscience, University of Oregon, Eugene, OR, USA.

Oluwapelumi Obasaju (O)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
ORCID: 0000-0001-5952-3103

Sepand Rastegar (S)

Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany.
ORCID: 0000-0003-4411-5646

Alison C McGarvey (AC)

Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.

Wolfgang Kopp (W)

Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
ORCID: 0000-0003-0376-0032

Emily Chambers (E)

Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK.
ORCID: 0000-0003-1252-8059

Dennis Wang (D)

Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK.
Singapore Institute for Clinical Sciences, Singapore, Singapore.
ORCID: 0000-0003-0068-1005

Hyejeong R Kim (HR)

Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK.

Rafael D Acemel (RD)

Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.
Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
ORCID: 0000-0003-4120-0140

Silvia Naranjo (S)

Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.
ORCID: 0000-0002-4529-3332

Maciej Łapiński (M)

International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
ORCID: 0000-0003-4892-976X

Vanessa Chong (V)

MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
ORCID: 0000-0002-2547-3694

Sinnakaruppan Mathavan (S)

Vision Research Foundation, Sankara Nethralayas, Chennai, India.

Bernard Peers (B)

Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium.

Tatjana Sauka-Spengler (T)

MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
ORCID: 0000-0001-9289-0263

Martin Vingron (M)

Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany.
ORCID: 0000-0002-1765-4241

Piero Carninci (P)

Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Fondazione Human Technopole, Milano, Italy.
ORCID: 0000-0001-7202-7243

Uwe Ohler (U)

Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
Institute of Biology, Humboldt University, Berlin, Germany.
ORCID: 0000-0002-0881-3116

Scott Allen Lacadie (SA)

Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.

Shawn M Burgess (SM)

Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
ORCID: 0000-0003-1147-0596

Cecilia Winata (C)

International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
ORCID: 0000-0002-7718-5248

Freek van Eeden (F)

Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK.
ORCID: 0000-0003-3483-8269

Juan M Vaquerizas (JM)

MRC London Institute of Medical Sciences, London, UK.
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
Max Planck Institute for Molecular Biomedicine, Muenster, Germany.
ORCID: 0000-0002-6583-6541

José Luis Gómez-Skarmeta (JL)

Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.
ORCID: 0000-0001-5125-4332

Daria Onichtchouk (D)

Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
ORCID: 0000-0001-6497-1445

Ben James Brown (BJ)

Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
ORCID: 0000-0002-5898-5848

Ozren Bogdanovic (O)

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
ORCID: 0000-0001-5680-0056

Erik van Nimwegen (E)

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
ORCID: 0000-0001-6338-1312

Monte Westerfield (M)

Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
ORCID: 0000-0003-1187-7839

Fiona C Wardle (FC)

Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK.
ORCID: 0000-0001-5444-1889

Carsten O Daub (CO)

Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden. carsten.daub@ki.se.
Science for Life Laboratory, Solna, Sweden. carsten.daub@ki.se.
ORCID: 0000-0002-3295-8729

Boris Lenhard (B)

MRC London Institute of Medical Sciences, London, UK. b.lenhard@imperial.ac.uk.
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK. b.lenhard@imperial.ac.uk.
ORCID: 0000-0002-1114-1509

Ferenc Müller (F)

Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK. f.mueller@bham.ac.uk.
ORCID: 0000-0002-0996-774X

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Multiomic atlas with functional stratification...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Multiomic atlas with functional stratification...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Multiomic atlas with functional stratification...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes au cours du développement › Multiomic atlas with functional stratification...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Multiomic atlas with functional stratification...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Multiomic atlas with functional stratification...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Multiomic atlas with functional stratification...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › Multiomic atlas with functional stratification...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Multiomic atlas with functional stratification...
questionsmedicales.fr › Phénomènes physiologiques des appareils urinaire et reproducteur › Phénomènes physiologiques de la reproduction › Reproduction › Développement embryonnaire et foetal › Organogenèse › Multiomic atlas with functional stratification...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Séquences d'acides nucléiques régulatrices › Multiomic atlas with functional stratification...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Poissons › Cypriniformes › Cyprinidae › Danio zébré › Multiomic atlas with functional stratification...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines de poisson › Protéines de poisson-zèbre › Multiomic atlas with functional stratification...