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Topological Associating Domains (TADs) comprise the basic unit of organization within the genome, with sharp boundaries characterized by highly transcribed housekeeping genes, short interspersed nuclear elements (SINE) or sites for the DNA-binding protein CCCTC-binding factor (CTCF) \nwhich interacts with Cohesin. This proposal addresses several major unanswered questions and explores new opportunities in the field, including: i) When does 3D genome architecture (TADs and their boundaries) begin to form during early vertebrate embryogenesis? ii) Is genome-wide transcriptional activation in the developing embryo required for the establishment of TADs? iii) How dynamic are individual TADs at the single cell level and what is their effect on gene expression and nuclear architecture? Importantly, our combination of genomics with super-resolution imaging bridges and connects two major disciplines in the 4D Nucleome community. \nOur central goal is to determine when and how higher-order 3D chromatin architecture is first established in early embryos, how is it remodeled during developmental reprograming and what is their impact on transcription. This proposal is significant for several reasons. First, from a standpoint of nuclear architecture, it addresses how TADs are formed over time and what is their effect on genome \nactivation and nuclear architecture. Second, it addresses how positional information in the nucleus plays a role in the fundamental step of transcription in vivo. Third, within the context of the 4D Nucleome initiative and a technological standpoint, the zebrafish embryo is a powerful system for probing different technologies that \nthat can be further applied across the 4D Nucleome initiatives directly relevant to ES cells, mouse embryos and differentiated tissues to understand how nuclear architecture is established in vivo. From a developmental biology and fertility standpoint, we address fundamental mechanisms of initiation of gene expression after fertilization - a universal transition across animals. \nIn our proposal, we provide preliminary evidence supporting the following hypothesis: TADs and their boundary elements are fully established only after the onset of genome-wide transcriptional activation, to refine embryonic transcription. The experiments described below will define the true relationship of TADs \nto transcription, illuminating the fundamental mechanisms responsible for assembling the 4D nuclear architecture during embryogenesis when cells become totipotent. 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updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "embryos", "crosslinking_temperature": 22.0, "library_preparation_date": "2019-01-14", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEX5BHUL5I/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "a62dc1cd-6203-4544-b1fb-22a90d9f098a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on Zebrafish Embryo with MboI - 4DNEX5BHUL5I", "external_references": [{"ref": "GEO:GSM4625567", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4625567"}, {"ref": "SRA:SRX8573308", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX8573308"}], "experiment_sets": [{"uuid": "b99d8dde-e712-430e-af58-d13309c7c376", "display_title": "4DNESVZFWQZX", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESVZFWQZX", "status": "released", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESVZFWQZX/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"journal": "Genome research", "authors": ["Wike CL", "Guo Y", "Tan M", "Nakamura R", "Shaw DK", "Diaz N", "Whittaker-Tademy AF", "Durand NC", "Aiden EL", "Vaquerizas JM", "Grunwald D", "Takeda H", "Cairns BR"], "@type": ["Publication", "Item"], "short_attribution": "Wike CL et al. (2021)", "date_published": "2021-06", "uuid": "75fc85cf-66ba-4d08-b50e-e7122482810c", "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 approximately 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 approximately 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.", "status": "current", "@id": "/publications/75fc85cf-66ba-4d08-b50e-e7122482810c/", "title": "Chromatin architecture transitions from zebrafish sperm through early embryogenesis.", "display_title": "Wike CL et al. (2021) PMID:34006569", "ID": "PMID:34006569", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"ID": "PMID:34006569", "@type": ["Publication", "Item"], "status": "current", "@id": "/publications/75fc85cf-66ba-4d08-b50e-e7122482810c/", "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 approximately 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 approximately 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.", "date_published": "2021-06", "title": "Chromatin architecture transitions from zebrafish sperm through early embryogenesis.", "short_attribution": "Wike CL et al. (2021)", "display_title": "Wike CL et al. (2021) PMID:34006569", "uuid": "75fc85cf-66ba-4d08-b50e-e7122482810c", "authors": ["Wike CL", "Guo Y", "Tan M", "Nakamura R", "Shaw DK", "Diaz N", "Whittaker-Tademy AF", "Durand NC", "Aiden EL", "Vaquerizas JM", "Grunwald D", "Takeda H", "Cairns BR"], "journal": "Genome research", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MboI", "combined": "Enzyme: MboI"}, "experiment_summary": "in situ Hi-C on Zebrafish Embryo with MboI", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}