{"ID": "PMID:39681766", "aka": "http://biorxiv.org/lookup/doi/10.1101/2022.04.25.489471", "lab": {"title": "Bing Ren, UCSD", "display_title": "Bing Ren, UCSD", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "@id": "/labs/bing-ren-lab/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/39681766", "award": {"name": "1U54DK107977-01", "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "center_title": "NOFIC - Ren", "project": "4DN", "description": "NOFIC: The complete sequencing of the human genome has provided an unprecedented opportunity for the study of the structure and function of the human genome. While our genome has historically been viewed as a linear sequence of bases, it has progressively become clear that this is an inadequate way to represent our genetic information. Notably, research over the last 30 years has begun to shed light on the fact that the higher-order, 3-dimensional organization of our genome plays a critical role in the interpretation of the genetic information encoded in our genome. The structure of our genome in the nucleus has been clearly demonstrated to play influential roles in diverse nuclear processes including DNA replication and gene expression. Despite this, our understanding of the structure of our genome within the nucleus remains incomplete. The reasons for this include limitations in the resolution and throughput of existing tools in chromatin topology mapping, a scarcity of the analytical tools for studying genome structure datasets, and the difficulty to relate the nuclear structure to function. Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. We expect that the tools and datasets generated through the proposed research will dramatically advance our understanding of the chromatin structure and function in human cells.", "status": "current", "display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "@id": "/awards/1U54DK107977-01/", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.", "status": "current", "authors": ["Yu M", "Zemke NR", "Chen Z", "Juric I", "Hu R", "Raviram R", "Abnousi A", "Fang R", "Zhang Y", "Gorkin DU", "Li YE", "Zhao Y", "Lee L", "Mishra S", "Schmitt AD", "Qiu Y", "Dickel DE", "Visel A", "Pennacchio LA", "Hu M", "Ren B"], "journal": "Nature structural & molecular biology", "abstract": "While a rich set of putative cis-regulatory sequences involved in mouse fetal  development have been annotated recently on the basis of chromatin accessibility  and histone modification patterns, delineating their role in developmentally  regulated gene expression continues to be challenging. To fill this gap, here we  mapped chromatin contacts between gene promoters and distal sequences across the  genome in seven mouse fetal tissues and across six developmental stages of the  forebrain. We identified 248,620 long-range chromatin interactions centered at  14,138 protein-coding genes and characterized their tissue-to-tissue variations  and developmental dynamics. Integrative analysis of the interactome with previous  epigenome and transcriptome datasets from the same tissues revealed a strong  correlation between the chromatin contacts and chromatin state at distal  enhancers, as well as gene expression patterns at predicted target genes. We  predicted target genes of 15,098 candidate enhancers and used them to annotate  target genes of homologous candidate enhancers in the human genome that harbor  risk variants of human diseases. We present evidence that schizophrenia and other  adult disease risk variants are frequently found in fetal enhancers, providing  support for the hypothesis of fetal origins of adult diseases.", "categories": ["model organism biology"], "date_created": "2024-12-19T21:53:08.672747+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-12-19T21:53:08.947974+00:00"}, "date_published": "2024-12-16", "public_release": "2024-12-19", "schema_version": "2", "project_release": "2024-12-19", "exp_sets_prod_in_pub": [{"experimentset_type": "replicate", "display_title": "4DNESG7Q6HPT", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "0b38c2ff-136f-44f1-b472-8dddf6772096", "status": "released", "@id": "/experiment-set-replicates/4DNESG7Q6HPT/", "accession": "4DNESG7Q6HPT", "experiments_in_set": [{"@type": ["ExperimentChiapet", "Experiment", "Item"], "@id": "/experiments-chiapet/4DNEX6S3ZPB8/", "display_title": "PLAC-seq against H3K4me3 (mouse) on forebrain - 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