King's College London

Research portal

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

Research output: Contribution to journalArticlepeer-review

Damir Baranasic, Matthias Hörtenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Várnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio M. D’Orazio, Dorde Relic, Mikhail Pachkov, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens & 35 more Samuel E. Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Łapiński, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn M. Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Müller

Original languageEnglish
Pages (from-to)1037-1050
Number of pages14
JournalNature genetics
Volume54
Issue number7
DOIs
Accepted/In press2022
PublishedJul 2022

Bibliographical note

Funding Information: We are indebted to the late Jose Luis Gomez Skarmeta for his devoted support of the DANIO-CODE programme. We thank M. Haussler at UCSC and D. Zerbino at EBI for facilitating access of DANIO-CODE track hubs in the UCSC and Ensembl genome browsers, respectively. We thank ZFIN for hosting the DANIO-CODE DCC and raw data. We thank J. Horsefield for creating the DANIO-CODE logo. We thank data producers (for the list of laboratories visit the DANIO-CODE DCC) who directly uploaded data and provided metadata directly. We thank DNANexus for providing computer time for the reprocessing of public datasets. We thank our main funders, the Horizon 2020 MSCA-ITN project ZENCODE-ITN by the European Commission to F.M., B.L., C.O.D., J.M.V. and B.P. (GA no: 643062), BBSRC support (DanioPeaks, P61715) to B.L., F.M. and F.C.W., Wellcome Trust (Joint-Investigator award 106955/Z/15/Z) to F.M. and B.L. and AQUA-FAANG (Horizon 2020, GA 817923) to B.L., D.B. and F.M. and BBSRC (BB/R015457/1) to F.vE and Key Special Project for Introduced Talents Team to Z.C. (GML2019ZD0401) and PrecisionTox project by the European Commission (GA no: 965406). We thank SNP&SEQ Technology Platform in Uppsala, Sweden (CAGE sequencing), MRC LMS Genomics Facility and Genomics Birmingham facilities UK. D.B. was awarded the Rutherford Fund Fellowship. Funding Information: We are indebted to the late Jose Luis Gomez Skarmeta for his devoted support of the DANIO-CODE programme. We thank M. Haussler at UCSC and D. Zerbino at EBI for facilitating access of DANIO-CODE track hubs in the UCSC and Ensembl genome browsers, respectively. We thank ZFIN for hosting the DANIO-CODE DCC and raw data. We thank J. Horsefield for creating the DANIO-CODE logo. We thank data producers (for the list of laboratories visit the DANIO-CODE DCC) who directly uploaded data and provided metadata directly. We thank DNANexus for providing computer time for the reprocessing of public datasets. We thank our main funders, the Horizon 2020 MSCA-ITN project ZENCODE-ITN by the European Commission to F.M., B.L., C.O.D., J.M.V. and B.P. (GA no: 643062), BBSRC support (DanioPeaks, P61715) to B.L., F.M. and F.C.W., Wellcome Trust (Joint-Investigator award 106955/Z/15/Z) to F.M. and B.L. and AQUA-FAANG (Horizon 2020, GA 817923) to B.L., D.B. and F.M. and BBSRC (BB/R015457/1) to F.vE and Key Special Project for Introduced Talents Team to Z.C. (GML2019ZD0401) and PrecisionTox project by the European Commission (GA no: 965406 ) . We thank SNP&SEQ Technology Platform in Uppsala, Sweden (CAGE sequencing), MRC LMS Genomics Facility and Genomics Birmingham facilities UK. D.B. was awarded the Rutherford Fund Fellowship. Publisher Copyright: © 2022, Crown.

King's Authors

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.

View graph of relations

© 2020 King's College London | Strand | London WC2R 2LS | England | United Kingdom | Tel +44 (0)20 7836 5454