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

Baranasic, Damir and Hörtenhuber, Matthias and Balwierz, Piotr J. and Zehnder, Tobias and Mukarram, Abdul Kadir and Nepal, Chirag and Várnai, Csilla and Hadzhiev, Yavor and Jimenez-Gonzalez, Ada and Li, Nan and Wragg, Joseph and D'Orazio, Fabio M. and Relic, Dorde and Pachkov, Mikhail and Díaz, Noelia and Hernández-Rodríguez, Benjamín and Chen, Zelin and Stoiber, Marcus and Dong, Michaël and Stevens, Irene and Ross, Samuel E. and Eagle, Anne and Martin, Ryan and Obasaju, Oluwapelumi and Rastegar, Sepand and McGarvey, Alison C. and Kopp, Wolfgang and Chambers, Emily and Wang, Dennis and Kim, Hyejeong R. and Acemel, Rafael D. and Naranjo, Silvia and Łapiński, Maciej and Chong, Vanessa and Mathavan, Sinnakaruppan and Peers, Bernard and Sauka-Spengler, Tatjana and Vingron, Martin and Carninci, Piero and Ohler, Uwe and Lacadie, Scott Allen and Burgess, Shawn M. and Winata, Cecilia and van Eeden, Freek and Vaquerizas, Juan M. and Gómez-Skarmeta, José Luis and Onichtchouk, Daria and Brown, Ben James and Bogdanovic, Ozren and van Nimwegen, Erik and Westerfield, Monte and Wardle, Fiona C. and Daub, Carsten O. and Lenhard, Boris and Müller, Ferenc. (2022) Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics, 54 (7). pp. 1037-1050.

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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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
UniBasel Contributors:van Nimwegen, Erik and Relic, Dorde and Pachkov, Mikhail
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Nature Publishing Group
ISSN:1061-4036
e-ISSN:1546-1718
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:17 Aug 2022 13:09
Deposited On:17 Aug 2022 13:09

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