{"ID": "PMID:37336949", "aka": "http://biorxiv.org/lookup/doi/10.1101/2020.07.31.230284", "lab": {"display_title": "Ana Pombo, MDC", "status": "current", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "title": "Ana Pombo, MDC", "@type": ["Lab", "Item"], "@id": "/labs/ana-pombo-lab/", "correspondence": [{"contact_email": "YW5hLnBvbWJvQG1kYy1iZXJsaW4uZGU=", "@id": "/users/bce4f2b5-9a2a-4db2-9dd6-7d61f19025c1/", "display_title": "Ana Pombo"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/37336949", "award": {"uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "project": "4DN", "@type": ["Award", "Item"], "display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "status": "current", "name": "1U54DK107977-01", "@id": "/awards/1U54DK107977-01/", "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.", "center_title": "NOFIC - Ren", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Multiplex-GAM: genome-wide identification of chromatin contacts yields insights  overlooked by Hi-C.", "status": "current", "authors": ["Beagrie RA", "Thieme CJ", "Annunziatella C", "Baugher C", "Zhang Y", "Schueler M", "Kukalev A", "Kempfer R", "Chiariello AM", "Bianco S", "Li Y", "Davis T", "Scialdone A", "Welch LR", "Nicodemi M", "Pombo A"], "journal": "Nature methods", "abstract": "Technology for measuring 3D genome topology is increasingly important for  studying gene regulation, for genome assembly and for mapping of genome  rearrangements. Hi-C and other ligation-based methods have become routine but  have specific biases. Here, we develop multiplex-GAM, a faster and more  affordable version of genome architecture mapping (GAM), a ligation-free  technique that maps chromatin contacts genome-wide. We perform a detailed  comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When  examining the strongest contacts detected by either method, we find that only  one-third of these are shared. The strongest contacts specifically found in GAM  often involve 'active' regions, including many transcribed genes and  super-enhancers, whereas in Hi-C they more often contain 'inactive' regions. Our  work shows that active genomic regions are involved in extensive complex contacts  that are currently underestimated in ligation-based approaches, and highlights  the need for orthogonal advances in genome-wide contact mapping technologies.", "date_created": "2023-06-21T16:22:48.042136+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-06-21T16:22:48.438609+00:00"}, "date_published": "2023-06-19", "public_release": "2023-06-21", "schema_version": "2", "project_release": "2023-06-21", "exp_sets_prod_in_pub": [{"accession": "4DNESALAVZ67", "status": "released", "@id": "/experiment-set-replicates/4DNESALAVZ67/", "uuid": "c5096cd4-0e78-4a8a-90c5-1206a0003ac5", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESALAVZ67", "experimentset_type": "replicate", "experiments_in_set": [{"@id": "/experiments-seq/4DNEXTQ35QAS/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "6d4f064d-76ea-4492-bfa7-62a9ce633116", "display_title": "GAM on 46C with Sox1-GFP - 4DNEXTQ35QAS", "status": "released", "experiment_type": {"@id": "/experiment-types/gam/", "display_title": "GAM", "title": "GAM", "@type": ["ExperimentType", "Item"], "status": "released", "uuid": "1c41d7cc-8bfb-402f-b752-9db223de86f4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/5946fa1d-a501-4676-a602-cc28cad65a8b/", "@type": ["Publication", "Item"], "uuid": "5946fa1d-a501-4676-a602-cc28cad65a8b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Beagrie RA et al. (2023) PMID:37336949", "external_references": [], "short_attribution": "Beagrie RA et al. (2023)", "number_of_experiment_sets": 1, "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}