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

Damir Baranas̆ić(Hammersmith Hospital), Matthias Hörtenhuber(Karolinska Institutet), Piotr J. Balwierz(Hammersmith Hospital), Tobias Zehnder(Hammersmith Hospital), Abdul Kadir Mukarram(Karolinska Institutet), Chirag Nepal(University of Copenhagen), Csilla Várnai(University of Birmingham), Yavor Hadzhiev(University of Birmingham), Ada Jiménez-González(University of Birmingham), Nan Li(University of Birmingham), Joseph W. Wragg(University of Birmingham), Fabio M. D’Orazio(University of Birmingham), Đorđe Relić(SIB Swiss Institute of Bioinformatics), Mikhail Pachkov(SIB Swiss Institute of Bioinformatics), Noèlia Díaz(Institut de Ciències del Mar), Benjamín Hernández-Rodríguez(Max Planck Institute for Molecular Biomedicine), Zelin Chen(Chinese Academy of Sciences), Marcus H. Stoiber(Lawrence Berkeley National Laboratory), Michael X. Dong(Karolinska Institutet), Irene Stevens(Karolinska Institutet), Samuel E. Ross(Garvan Institute of Medical Research), Anne Eagle(University of Oregon), Ryan Martin(University of Oregon), Oluwapelumi Obasaju(University of Birmingham), Sepand Rastegar(Karlsruhe Institute of Technology), Alison C. McGarvey(Max Delbrück Center), Wolfgang Kopp(Max Delbrück Center), Emily V. Chambers(University of Sheffield), Dennis Wang(Singapore Institute for Clinical Sciences), Hyejeong R. Kim(University of Sheffield), Rafael D. Acemel(Max Delbrück Center), Silvia Naranjo(Centro Andaluz de Biología del Desarrollo), Maciej Łapiński(International Institute of Molecular and Cell Biology), Vanessa Chong-Morrison(University of Oxford), Sinnakaruppan Mathavan(Sankara Nethralaya), Bernard Peers(University of Liège), Tatjana Sauka‐Spengler(University of Oxford), Martin Vingron(Max Planck Institute for Molecular Genetics), Piero Carninci(Human Technopole), Uwe Ohler(Max Delbrück Center), Scott A. Lacadie(Max Delbrück Center), Shawn M. Burgess(Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)), Cecilia Lanny Winata(International Institute of Molecular and Cell Biology), Fredericus J. M. van Eeden(University of Sheffield), Juan M. Vaquerizas(Hammersmith Hospital), José Luis Gómez-Skármeta(Centro Andaluz de Biología del Desarrollo), Daria Onichtchouk(University of Freiburg), James B. Brown(Lawrence Berkeley National Laboratory), Ozren Bogdanović(Garvan Institute of Medical Research), Erik van Nimwegen(SIB Swiss Institute of Bioinformatics), Monte Westerfield(University of Oregon), Fiona C. Wardle(King's College London), Carsten O. Daub(Science for Life Laboratory), Boris Lenhard(Hammersmith Hospital), Ferenc Müller(University of Birmingham)
Nature Genetics
July 1, 2022
10.1038/s41588-022-01089-w
Cited by 97Open Access
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Abstract

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

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