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| Item Type: | Article |
|---|---|
| Title: | Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements |
| Creators Name: | Baranasic, D. and Hörtenhuber, M. and Balwierz, P.J. and Zehnder, T. and Mukarram, A.K. and Nepal, C. and Várnai, C. and Hadzhiev, Y. and Jimenez-Gonzalez, A. and Li, N. and Wragg, J. and D'Orazio, F.M. and Relic, D. and Pachkov, M. and Díaz, N. and Hernández-Rodríguez, B. and Chen, Z. and Stoiber, M. and Dong, M. and Stevens, I. and Ross, S.E. and Eagle, A. and Martin, R. and Obasaju, O. and Rastegar, S. and McGarvey, A.C. and Kopp, W. and Chambers, E. and Wang, D. and Kim, H.R. and Acemel, R.D. and Naranjo, S. and Łapiński, M. and Chong, V. and Mathavan, S. and Peers, B. and Sauka-Spengler, T. and Vingron, M. and Carninci, P. and Ohler, U. and Lacadie, S.A. and Burgess, S.M. and Winata, C. and van Eeden, F. and Vaquerizas, J.M. and Gómez-Skarmeta, J.L. and Onichtchouk, D. and Brown, B.J. and Bogdanovic, O. and van Nimwegen, E. and Westerfield, M. and Wardle, F.C and Daub, C.O. and Lenhard, B. and Müller, F. |
| 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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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. |
| Keywords: | Genetic Databases, Genome, Genomics, Mammals, Zebrafish Proteins, Animals, Mice, Zebrafish |
| Source: | Nature Genetics |
| ISSN: | 1061-4036 |
| Publisher: | Nature Publishing Group |
| Volume: | 54 |
| Number: | 7 |
| Page Range: | 1037-1050 |
| Date: | July 2022 |
| Official Publication: | https://doi.org/10.1038/s41588-022-01089-w |
| PubMed: | View item in PubMed |
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