PUBLICATION

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

Authors
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C., Daub, C.O., Lenhard, B., Müller, F.
ID
ZDB-PUB-220706-21
Date
2022
Source
Nature Genetics   54(7): 1037-1050 (Journal)
Registered Authors
Bogdanovic, Ozren, Gómez-Skarmeta, José Luis, Müller, Ferenc, Onichtchouk, Daria, van Eeden, Freek, Wardle, Fiona, Westerfield, Monte, Winata, Cecilia Lanny
Keywords
none
MeSH Terms
  • Animals
  • Chromatin/genetics
  • Databases, Genetic*
  • Gene Expression Regulation, Developmental*
  • Genome*/genetics
  • Genomics*
  • Humans
  • Mice
  • Molecular Sequence Annotation
  • Organogenesis/genetics
  • Regulatory Sequences, Nucleic Acid*/genetics
  • Zebrafish*/embryology
  • Zebrafish*/genetics
  • Zebrafish Proteins*/genetics
PubMed
35789323 Full text @ Nat. Genet.
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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes