Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
Genome Res. 2021 Jun;31(6):981-994. doi: 10.1101/gr.269860.120. Epub 2021 May 18.
Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated domains and instead displays "hinge-like" domains of ∼150 kb that repeat every 1-2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of ∼90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. Together, this study reveals hinge-like domains in histone-packaged zebrafish sperm chromatin and determines that the initial formation of high-order chromatin architecture in zebrafish embryos occurs after ZGA primarily at enhancers bearing high H3K27ac.
染色质构象在 3D 结构中的图谱绘制增加了我们对调节序列和基因表达在基因组中如何连接和调控的理解。3D 染色质基因组在胚胎发育过程中经历了广泛的重塑，尽管大多数物种的卵裂期胚胎在合子基因组激活（pre-ZGA）之前缺乏结构，但已报道斑马鱼具有结构。在这里，我们旨在确定父本/精子斑马鱼配子细胞中的染色体结构，以确定其是否类似于或告知早期 pre-ZGA 斑马鱼胚胎染色质结构。首先，我们通过高级低细胞原位 Hi-C 评估了高级结构。组蛋白包装的斑马鱼精子的结构缺乏拓扑相关结构域，而是显示出重复频率为 1-2 Mbs 的约 150 kb 的“铰链样”结构域，表明其具有类似于有丝分裂染色体的浓缩重复结构。与之前的工作相反，pre-ZGA 胚胎缺乏染色体结构，并且仅在 post-ZGA 后才发育出结构。在 post-ZGA 期间，我们发现染色质结构开始在长度约为 90 kb 的小接触域中形成。这些小接触域在增强子（包括超级增强子）处建立，化学抑制 Ep300a（p300）和 Crebbpa（CBP）的活性，降低组蛋白 H3K27ac，但不抑制转录，会减少这些接触。总之，这项研究揭示了组蛋白包装的斑马鱼精子染色质中的铰链样结构域，并确定了斑马鱼胚胎中高级染色质结构的初始形成主要发生在 ZGA 之后，主要发生在具有高 H3K27ac 的增强子上。
