The zebrafish ( Danio rerio ) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species 1 . However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis -regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization. A comprehensive map of transcriptomes, cis -regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish ( Danio rerio ) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development.

中文翻译：

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斑马鱼顺式调控元件和 3D 基因组结构图

斑马鱼 (Danio rerio) 已广泛用于人类疾病和发育的研究，两个物种之间约有 70% 的蛋白质编码基因是保守的 1 。然而，斑马鱼的研究仍然受到斑马鱼基因组中功能控制元件的稀疏注释的限制。在这里，我们进行了 RNA 测序、使用测序 (ATAC-seq) 检测转座酶可及染色质、测序染色质免疫沉淀、全基因组亚硫酸氢盐测序和染色体构象捕获 (Hi-C) 实验，在多达 11 个成人和两个胚胎组织中进行在斑马鱼图宾根参考品系中生成转录组、顺式调控元件、异染色质、甲基化组和 3D 基因组组织的综合图谱。斑马鱼的比较，人和小鼠的调控元件能够识别进化上保守的和物种特异性的调控序列和网络。我们观察到拓扑相关域边界处进化断点的富集，这与强组蛋白 H3 赖氨酸 4 三甲基化 (H3K4me3) 和 CCCTC 结合因子 (CTCF) 信号相关。我们在斑马鱼大脑中进行了单细胞 ATAC-seq，它描绘了 25 种不同的细胞类型簇。通过结合长读长 DNA 测序和 Hi-C，我们从头组装了决定性别的 4 号染色体。总的来说，我们的工作为脊椎动物基因组的功能注释和 3D 基因组组织的进化保守元素研究提供了一个额外的表观基因组锚。转录组、顺式调控元件的综合图谱，