2020年11月25日出版的《自然》杂志在线发表了美国西北大学岳峰课题组的最新研究成果。他们的研究揭示了斑马鱼（Danio rerio）的顺式调控元件和3D基因组结构图。

在本研究中，研究人员进行了RNA测序、利用测序（ATAC-seq）对转座酶染色质的可及性进行了测定，并通过染色质免疫沉淀、全基因组亚硫酸氢盐测序和染色体构象捕获（Hi-C）实验生成了Tu?bingen 品系斑马鱼11个成年组织和2个胚胎组织的组织特异性转录组、顺式调控元件、异染色质、甲基化和3D基因组的综合图谱。通过比较斑马鱼、人和小鼠的调控元件，研究人员鉴定了进化上保守的物种特异性调控序列和网络。研究人员观察到进化断点在拓扑关联域边界的富集，这与组蛋白H3赖氨酸4三甲基化（H3K4me3）和CCCTC结合因子（CTCF）信号强度相关。

研究人员对斑马鱼的大脑进行了单细胞ATAC-seq，揭示了25种不同的细胞类型簇。通过结合长时间阅读DNA测序和Hi-C，研究人员重构了决定性别的4条从头合成染色体。总体而言，该工作为脊椎动物基因组的功能注释和3D基因组保守进化元素的研究提供了附加的表观基因组图。

据介绍，斑马鱼已被广泛用于研究人类发育和疾病进展，并且约有70％的蛋白质编码基因在两个物种之间是保守的。然而，对斑马鱼的研究仍然受到对斑马鱼基因组中功能调控元件理解的限制。

附：英文原文

Title: A map of cis -regulatory elements and 3D genome structures in zebrafish

Author: Hongbo Yang, Yu Luan, Tingting Liu, Hyung Joo Lee, Li Fang, Yanli Wang, Xiaotao Wang, Bo Zhang, Qiushi Jin, Khai Chung Ang, Xiaoyun Xing, Juan Wang, Jie Xu, Fan Song, Iyyanki Sriranga, Chachrit Khunsriraksakul, Tarik Salameh, Daofeng Li, Mayank N. K. Choudhary, Jacek Topczewski, Kai Wang, Glenn S. Gerhard, Ross C. Hardison, Ting Wang, Keith C. Cheng, Feng Yue

Issue&Volume: 2020-11-25

Abstract: 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 species1. 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.

DOI: 10.1038/s41586-020-2962-9

Source: https://www.nature.com/articles/s41586-020-2962-9