Journal Article

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

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

2022

Overview

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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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. The DANIO-CODE consortium leverages a large-scale multiomic dataset to improve zebrafish genome annotation. They identify ~140,000 cis -regulatory elements throughout development and perform a comparison with the mouse regulatory landscape.

• Publisher: Nature Publishing Group US,Nature Publishing Group,Nature Research
• Subject: 631/136 / 631/337/176 / 631/337/2019 / Agriculture / Animal Genetics and Genomics / Animal models / Animals / Annotations / BASIC BIOLOGICAL SCIENCES / Binding sites / Biochemistry, biophysics & molecular biology / Biochimie, biophysique & biologie moléculaire / Biomedical and Life Sciences / Biomedicine / Cancer Research / Chromatin / Chromatin - genetics / Danio rerio / Databases, Genetic / Datasets / Design of experiments / Disease / DNA methylation / Embryogenesis / Embryonic growth stage / Experimental design / Gene Expression Regulation, Developmental / Gene Function / Genes / Genetic engineering / Genetics / Genetics & Heredity / Genome / Genome - genetics / Genomes / Genomics / Human Genetics / Humans / Laboratories / Life sciences / Mammals / Metadata / Mice / Molecular Sequence Annotation / Organogenesis / Organogenesis - genetics / Regulatory sequences / Regulatory Sequences, Nucleic Acid - genetics / Sciences du vivant / Signal transduction / Topology / Zebrafish / Zebrafish - embryology / Zebrafish - genetics / Zebrafish Proteins / Zebrafish Proteins - genetics