GSE134055
A map of cis-regulatory elements and 3D genome structures in zebrafish
The zebrafish has been widely used for the study of human disease and development, as ~70% of the protein-coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome, however, has lagged behind that of other model systems such as mouse and Drosophila. Based on multi-omics approaches taken in the ENCODE and Roadmap Epigenomics projects, we performed RNA-seq, ATAC-seq, ChIP-seq and Hi-C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall, we have identified 235,596 cis-regulatory elements, which potentially shape the tissue-specific and developmental-stage-specific gene expression in zebrafish. A comparison of zebrafish, human, and mouse regulatory elements allowed us to identify both evolutionarily conserved and species-specific regulatory sequences. Furthermore, through the analysis of Hi-C data in zebrafish brain and muscle, we observed different levels of 3D genome organization, including compartment, topological associating domains (TADs), and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP-Seq (H3K27ac and H3K4me3), RNA-Seq, 11 of them were examined using ATAC-seq ,WGBS and ChIP-seq (H3K9me3 and H3K9me2), and one scATAC-seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that, for the samples GSM4661977-GSM4662088, [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.