@article {125, title = {Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.}, journal = {Nat Genet}, volume = {54}, year = {2022}, month = {2022 Jul}, pages = {1037-1050}, 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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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 = {Animals, Chromatin, Databases, Genetic, Gene Expression Regulation, Developmental, Genome, Genomics, Humans, Mice, Molecular Sequence Annotation, Organogenesis, Regulatory Sequences, Nucleic Acid, Zebrafish, Zebrafish Proteins}, issn = {1546-1718}, doi = {10.1038/s41588-022-01089-w}, author = {Baranasic, Damir and H{\"o}rtenhuber, Matthias and Balwierz, Piotr J and Zehnder, Tobias and Mukarram, Abdul Kadir and Nepal, Chirag and V{\'a}rnai, Csilla and Hadzhiev, Yavor and Jimenez-Gonzalez, Ada and Li, Nan and Wragg, Joseph and D{\textquoteright}Orazio, Fabio M and Relic, Dorde and Pachkov, Mikhail and D{\'\i}az, Noelia and Hern{\'a}ndez-Rodr{\'\i}guez, Benjam{\'\i}n and Chen, Zelin and Stoiber, Marcus and Dong, Micha{\"e}l and Stevens, Irene and Ross, Samuel E and Eagle, Anne and Martin, Ryan and Obasaju, Oluwapelumi and Rastegar, Sepand and McGarvey, Alison C and Kopp, Wolfgang and Chambers, Emily and Wang, Dennis and Kim, Hyejeong R and Acemel, Rafael D and Naranjo, Silvia and {\L}api{\'n}ski, Maciej and Chong, Vanessa and Mathavan, Sinnakaruppan and Peers, Bernard and Sauka-Spengler, Tatjana and Vingron, Martin and Carninci, Piero and Ohler, Uwe and Lacadie, Scott Allen and Burgess, Shawn M and Winata, Cecilia and van Eeden, Freek and Vaquerizas, Juan M and G{\'o}mez-Skarmeta, Jos{\'e} Luis and Onichtchouk, Daria and Brown, Ben James and Bogdanovic, Ozren and van Nimwegen, Erik and Westerfield, Monte and Wardle, Fiona C and Daub, Carsten O and Lenhard, Boris and M{\"u}ller, Ferenc} } @article {34, title = {Prepatterning of developmental gene expression by modified histones before zygotic genome activation.}, journal = {Dev Cell}, volume = {21}, year = {2011}, month = {2011 Dec 13}, pages = {993-1004}, abstract = {

A hallmark of anamniote vertebrate development is a window of embryonic transcription-independent cell divisions before onset of zygotic genome activation (ZGA). Chromatin determinants of ZGA are unexplored; however, marking of developmental genes by modified histones in sperm suggests a predictive role of histone marks for ZGA. In zebrafish, pre-ZGA development for ten cell cycles provides an opportunity to examine whether genomic enrichment in modified histones is present before initiation of transcription. By profiling histone H3 trimethylation on all zebrafish promoters before and after ZGA, we demonstrate here an epigenetic prepatterning of developmental gene expression. This involves pre-ZGA marking of transcriptionally inactive genes involved in homeostatic and developmental regulation by permissive H3K4me3 with or without repressive H3K9me3 or H3K27me3. Our data suggest that histone modifications are instructive for the developmental gene expression program.

}, keywords = {Animals, Body Patterning, Chromatin, Epigenesis, Genetic, Female, Gene Expression Regulation, Developmental, Histones, Male, Methylation, Multigene Family, Promoter Regions, Genetic, Spermatozoa, Zebrafish, Zebrafish Proteins}, issn = {1878-1551}, doi = {10.1016/j.devcel.2011.10.008}, author = {Lindeman, Leif C and Andersen, Ingrid S and Reiner, Andrew H and Li, Nan and Aanes, H{\r a}vard and {\O}strup, Olga and Winata, Cecilia L and Mathavan, Sinnakaruppan and M{\"u}ller, Ferenc and Alestr{\"o}m, Peter and Collas, Philippe} } @article {69, title = {Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos.}, journal = {Int J Dev Biol}, volume = {54}, year = {2010}, month = {2010}, pages = {803-13}, abstract = {

Embryo development proceeds from a cascade of gene activation and repression events controlled by epigenetic modifications of DNA and histones. Little is known about epigenetic states in the developing zebrafish, despite its importance as a model organism. We report here DNA methylation and histone modification profiles of promoters of developmentally-regulated genes (pou5f1, sox2, sox3, klf4, nnr, otx1b, nes, vasa), as well as tert and bactin2, in zebrafish embryos at the mid-late blastula transition, shortly after embryonic genome activation. We identify four classes of promoters based on the following profiles: (i) those enriched in marks of active genes (H3K9ac, H4ac, H3K4me3) without transcriptionally repressing H3K9me3 or H3K27me3; (ii) those enriched in H3K9ac, H4ac and H3K27me3, without H3K9me3; one such gene was klf4, shown by in situ hybridization to be mosaically expressed, likely accounting for the detection of both activating and repressive marks on its promoter; (iii) those enriched in H3K4me3 and H3K27me3 without acetylation; and (iv) those enriched in all histone modifications examined. Culture of embryo-derived cells under differentiation conditions leads to H3K9 and H4 deacetylation and H3K9 and H3K27 trimethylation on genes that are inactivated, yielding an epigenetic profile similar to those of fibroblasts or muscle. All promoters however retain H3K4me3, indicating an uncoupling of H3K4me3 occupancy and gene expression. All non-CpG island developmentally-regulated promoters are DNA unmethylated in embryos, but hypermethylated in fibroblasts. Our results suggest that differentially expressed embryonic genes are regulated by various patterns of histone modifications on unmethylated DNA, which create a developmentally permissive chromatin state.

}, keywords = {Animals, Blastula, Cell Line, Chromatin, Chromatin Immunoprecipitation, CpG Islands, DNA Methylation, Embryo, Nonmammalian, Fibroblasts, Gene Expression Profiling, Gene Expression Regulation, Developmental, Histones, In Situ Hybridization, Lysine, Methylation, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Reverse Transcriptase Polymerase Chain Reaction, Zebrafish, Zebrafish Proteins}, issn = {1696-3547}, doi = {10.1387/ijdb.103081ll}, author = {Lindeman, Leif C and Winata, Cecilia L and Aanes, Hvard and Mathavan, Sinnakaruppan and Alestrom, Peter and Collas, Philippe} }