Wike, Candice L.Guo, YixuanTan, MengyaoNakamura, RyoheiShaw, Dana KlattDíaz, NoeliaWhittaker-Tademy, Aneasha F.Durand, Neva C.Aiden, Erez LiebermanVaquerizas, Juan M.Grunwald, DavidTakeda, HiroyukiCairns, Bradley R.2021-06-252021-06-252021Wike, Candice L., Guo, Yixuan, Tan, Mengyao, et al.. "Chromatin architecture transitions from zebrafish sperm through early embryogenesis." <i>Genome Research,</i> 31, no. 6 (2021) Cold Spring Harbor Laboratory Press: 981-994. https://doi.org/10.1101/gr.269860.120.https://hdl.handle.net/1911/110835Chromatin 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.engThis article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.Journal articleGenomeRes-2021-Wike-981-94https://doi.org/10.1101/gr.269860.120