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

TitleMultiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Publication TypeJournal Article
Year of Publication2022
AuthorsBaranasic, D, Hörtenhuber, M, Balwierz, PJ, Zehnder, T, Mukarram, AKadir, 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, Kim, HR, Acemel, RD, Naranjo, S, Łapiński, M, Chong, V, Mathavan, S, Peers, B, Sauka-Spengler, T, Vingron, M, Carninci, P, Ohler, U, Lacadie, SAllen, Burgess, SM, Winata, C, van Eeden, F, Vaquerizas, JM, Gómez-Skarmeta, JLuis, Onichtchouk, D, Brown, BJames, Bogdanovic, O, van Nimwegen, E, Westerfield, M, Wardle, FC, Daub, CO, Lenhard, B, Müller, F
JournalNat Genet
Volume54
Issue7
Pagination1037-1050
Date Published2022 Jul
ISSN1546-1718
KeywordsAnimals, Chromatin, Databases, Genetic, Gene Expression Regulation, Developmental, Genome, Genomics, Humans, Mice, Molecular Sequence Annotation, Organogenesis, Regulatory Sequences, Nucleic Acid, Zebrafish, Zebrafish Proteins
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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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.

DOI10.1038/s41588-022-01089-w
Alternate JournalNat Genet
Citation Key125
PubMed ID35789323
PubMed Central IDPMC9279159
Grant ListU24 HG002659 / HG / NHGRI NIH HHS / United States
BB/R015457/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
MC_UP_1102/1 / MRC_ / Medical Research Council / United Kingdom
MC_EX_MR/S300007/1 / MRC_ / Medical Research Council / United Kingdom
106955 / WT_ / Wellcome Trust / United Kingdom
P61715 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
/ WT_ / Wellcome Trust / United Kingdom
MC_UP_1605/10 / MRC_ / Medical Research Council / United Kingdom

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