Similar Datasets
Project description: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.
| S-EPMC8168589 | biostudies-literature
Project description:Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps. Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control. We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable. Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.
2021-04-05 | GSE152743 | GEO
Project description:Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps. Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control. We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable. Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.
2021-04-05 | GSE152742 | GEO
Project description:Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps. Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control. We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable. Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.
2021-04-05 | GSE152741 | GEO
Project description:Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps. Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control. We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable. Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.
2021-04-05 | GSE167125 | GEO
Project description:Chromatin architecture transitions from zebrafish sperm through early embryogenesis
| PRJNA640309 | ENA
Project description:Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ATAC-seq]
| PRJNA640315 | ENA
Project description:Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ChIP-seq]
| PRJNA640314 | ENA
Project description:Chromatin architecture transitions from zebrafish sperm through early embryogenesis [Hi-C]
| PRJNA640313 | ENA
Project description:Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ChIP-seq II]
| PRJNA703030 | ENA