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

• DOI: 10.1038/s41588-022-01089-w
• Publication Date: 2022-07-04T16:03:30Z
• Authors: 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 Hernánde...; Zelin Chen; Marcus Stoiber; Michaël Dong; Irene Stevens; 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 Mat...; Bernard Peers; Tatjana Sauka-Spe...; Martin Vingron; Piero Carninci; Uwe Ohler; Scott Allen Lacadie; Shawn M. Burgess; Cecilia Winata; Freek van Eeden; Juan M. Vaquerizas; José Luis Gómez-S...; Daria Onichtchouk; Ben James Brown; Ozren Bogdanovic; Erik van Nimwegen; Monte Westerfield; Fiona C. Wardle; Carsten O. Daub; Boris Lenhard; Ferenc Müller
• Keywords: Danio; Functional Genomics; Model Organism; Epigenomics

Zebrafish, a popular organism for studying embryonic development and modeling human diseases, has so far lacked systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium created central repository store process zebrafish developmental genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines total of 1,802 sets unpublished re-analyzed published data, which used improve existing annotations show its utility experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity time space. delineated distance topology chromatin between regulatory active during zygotic genome activation organogenesis. Finally, matched epigenomic landscapes mouse predicted relationships them beyond sequence similarity, thus extending genomics mammals.