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Recent years have seen a rapid expansion of the understanding of many of the basic features that define how genomes are organized in space inside of cells, including the identification of features such as A/B compartments, Topologically Associated Domains, and chromatin loops. Furthermore, there is evidence that mutations that alter 3D genome organization can contribute to human disease. This is most evident for a class of mutations known as structural variants, which includes translocations, inversions, tandem duplications, and deletions. When these mutations disrupt sequence features that are critical for 3D genome structure, such as the boundaries between Topologically Associating Domains, this can lead to enhancer-promoter rewiring, changes in gene expression, and phenotypic consequences. Such effects have been observed both in the context of germline structural variants that contribute to syndromic disorders of development as well as somatic structural variants that can lead to cancer. While it has become clear that structural variants can alter 3D genome organization and gene expression, more recent studies that comprehensively examined structural variants and gene expression indicate their relationship is considerably more complex. Specifically, in only a minority of instances do structural variants lead to changes in expression of neighboring genes. Therefore, why structural variants can have dramatic consequences on 3D genome structure and gene expression in some contexts but not others is currently unclear. This proposal will investigate the relationship between structural variants, 3D genome organization, and gene expression in cancer genomes with the goal of understanding where and when structural variants will actually lead to changes in gene expression that may contribute to oncogenesis. Specific aim 1 will test whether only specific sets genes are sensitive to structural variant induced changes in enhancer-promoter communication by examining changes in 3D genome structure and gene expression in haplotype resolved human tumor samples. Specific aim 2 will use CRISPR/Cas9 genome engineering to evaluate the effects of structural variant partner regions on induction of oncogene expression. Specific aim 3 will assess the role of intra-tumor heterogeneity on the effects of structural variants on 3D genome structure by using novel multi-omic methods for profiling DNA methylation and 3D genome structure simultaneously within single cells derived from patient tumor samples. Successful completion of these aims will result in a deeper understanding of the relationship between structural variation, 3D genome organization, and gene regulation in the context of cancer genomes. 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"experiment_sets": [{"accession": "4DNESCCOW4O6", "@id": "/experiment-set-replicates/4DNESCCOW4O6/", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "uuid": "7efccb4e-b9d9-4058-9348-791b3796440f", "display_title": "4DNESCCOW4O6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Liu Z et al. (2023) PMID:37932264", "@id": "/publications/19089239-6a7a-4454-8380-71fbae6f4280/", "status": "current", "uuid": "19089239-6a7a-4454-8380-71fbae6f4280", "journal": "Nature communications", "abstract": "Chromatin conformation reorganization is emerging as an important layer of  regulation for gene expression and lineage specification. Yet, how  lineage-specific transcription factors contribute to the establishment of cell  type-specific 3D chromatin architecture in the immune cells remains unclear,  especially for the late stages of T cell subset differentiation and maturation.  Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation  of T cells specializing in suppressing excessive immune responses. Here, by  comprehensively mapping 3D chromatin organization during Treg cell  differentiation, we show that Treg-specific chromatin structures were  progressively established during its lineage specification, and highly associated  with Treg signature gene expression. Additionally, the binding sites of Foxp3, a  Treg lineage specifying transcription factor, were highly enriched at  Treg-specific chromatin loop anchors. Further comparison of the chromatin  interactions between wide-type Tregs versus Treg cells from Foxp3  knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that  Foxp3 was essential for the establishment of Treg-specific 3D chromatin  architecture, although it was not dependent on the formation of the Foxp3  domain-swapped dimer. These results highlighted an underappreciated role of Foxp3  in modulating Treg-specific 3D chromatin structure formation.", "short_attribution": "Liu Z et al. (2023)", "ID": "PMID:37932264", "date_published": "2023-11-06", "authors": ["Liu Z", "Lee DS", "Liang Y", "Zheng Y", "Dixon JR"], "title": "Foxp3 orchestrates reorganization of chromatin architecture to establish  regulatory T cell identity.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"uuid": "19089239-6a7a-4454-8380-71fbae6f4280", "@id": "/publications/19089239-6a7a-4454-8380-71fbae6f4280/", "ID": "PMID:37932264", "display_title": "Liu Z et al. (2023) PMID:37932264", "journal": "Nature communications", "@type": ["Publication", "Item"], "short_attribution": "Liu Z et al. (2023)", "date_published": "2023-11-06", "title": "Foxp3 orchestrates reorganization of chromatin architecture to establish  regulatory T cell identity.", "abstract": "Chromatin conformation reorganization is emerging as an important layer of  regulation for gene expression and lineage specification. Yet, how  lineage-specific transcription factors contribute to the establishment of cell  type-specific 3D chromatin architecture in the immune cells remains unclear,  especially for the late stages of T cell subset differentiation and maturation.  Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation  of T cells specializing in suppressing excessive immune responses. Here, by  comprehensively mapping 3D chromatin organization during Treg cell  differentiation, we show that Treg-specific chromatin structures were  progressively established during its lineage specification, and highly associated  with Treg signature gene expression. Additionally, the binding sites of Foxp3, a  Treg lineage specifying transcription factor, were highly enriched at  Treg-specific chromatin loop anchors. Further comparison of the chromatin  interactions between wide-type Tregs versus Treg cells from Foxp3  knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that  Foxp3 was essential for the establishment of Treg-specific 3D chromatin  architecture, although it was not dependent on the formation of the Foxp3  domain-swapped dimer. These results highlighted an underappreciated role of Foxp3  in modulating Treg-specific 3D chromatin structure formation.", "authors": ["Liu Z", "Lee DS", "Liang Y", "Zheng Y", "Dixon JR"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "IgG protein (mouse)", "combined": "Target: IgG protein (mouse)"}, "experiment_summary": "CUT&RUN against IgG protein (mouse) on Treg - thymus - Foxp3-Thy1.1 WT", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}