PUBLICATION

Chromatin architecture transitions from zebrafish sperm through early embryogenesis

Authors
Wike, C.L., Guo, Y., Tan, M., Nakamura, R., Shaw, D.K., Díaz, N., Whittaker-Tademy, A.F., Durand, N.C., Lieberman Aiden, E., Vaquerizas, J.M., Grunwald, D., Takeda, H., Cairns, B.R.
ID
ZDB-PUB-210520-2
Date
2021
Source
Genome research   31(6): 981-994 (Journal)
Registered Authors
Grunwald, David
Keywords
none
Datasets
GEO:GSE167125, GEO:GSE152743, GEO:GSE152742, GEO:GSE152741, GEO:GSE152744
MeSH Terms
  • Animals
  • Chromatin*/genetics
  • Chromatin*/metabolism
  • Chromosomes/genetics
  • Embryonic Development/genetics
  • Gene Expression Regulation, Developmental
  • Male
  • Spermatozoa/metabolism
  • Zebrafish*/genetics
  • Zygote
PubMed
34006569 Full text @ Genome Res.
Abstract
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.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes