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

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 Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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.

Metadata

Item Type:	Article
Authors/Creators:	Baranasic, D Hörtenhuber, M Balwierz, PJ Zehnder, T Mukarram, AK Nepal, C Várnai, C Hadzhiev, Y Jimenez-Gonzalez, A Li, N Wragg, J D’Orazio, FM Relic, D Pachkov, M Díaz, N Hernández-Rodríguez, B Chen, Z Stoiber, M Dong, M Stevens, I Ross, SE Eagle, A Martin, R Obasaju, O Rastegar, S McGarvey, AC Kopp, W Chambers, E Wang, D https://orcid.org/0000-0003-0068-1005 Kim, HR Acemel, RD Naranjo, S Łapiński, M Chong, V Mathavan, S Peers, B Sauka-Spengler, T Vingron, M Carninci, P Ohler, U Lacadie, SA Burgess, SM Winata, C van Eeden, F Vaquerizas, JM Gómez-Skarmeta, JL Onichtchouk, D Brown, BJ Bogdanovic, O van Nimwegen, E Westerfield, M Wardle, FC Daub, CO Lenhard, B Müller, F
Copyright, Publisher and Additional Information:	© Crown 2022. Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Dates:	Published: July 2022 Published (online): 4 July 2022 Accepted: 3 May 2022
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > Department of Neuroscience (Sheffield)
Funding Information:	Funder Grant number BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL BB/R015457/1
Depositing User:	Symplectic Sheffield
Date Deposited:	19 Jul 2022 16:29
Last Modified:	19 Jul 2022 16:29
Status:	Published
Publisher:	Springer Science and Business Media LLC
Refereed:	Yes
Identification Number:	10.1038/s41588-022-01089-w
Related URLs:	PubMed URL
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:189200

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

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