{"ID": "PMID:35551308", "lab": {"uuid": "d3412190-317a-4837-823f-3892b9f641a4", "status": "current", "@id": "/labs/external-lab/", "title": "External Lab", "display_title": "External Lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d3412190-317a-4837-823f-3892b9f641a4"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/35551308", "tags": ["4dn-external-reuse"], "award": {"display_title": "EXTERNAL AWARD", "name": "external-award", "status": "current", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "center_title": "External", "center": "External", "description": "Funding source is from outside 4DN.", "project": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Sequence-based modeling of three-dimensional genome architecture from kilobase to  chromosome scale.", "status": "current", "aliases": ["4dn-dcic-lab:PMID:35551308"], "authors": ["Zhou J"], "journal": "Nature genetics", "abstract": "To learn how genomic sequence influences multiscale three-dimensional (3D) genome  architecture, this manuscript presents a sequence-based deep-learning approach,  Orca, that predicts directly from sequence the 3D genome architecture from  kilobase to whole-chromosome scale. Orca captures the sequence dependencies of  structures including chromatin compartments and topologically associating  domains, as well as diverse types of interactions from CTCF-mediated to  enhancer-promoter interactions and Polycomb-mediated interactions with cell-type  specificity. Orca enables various applications including predicting structural  variant effects on multiscale genome organization and it recapitulated effects of  experimentally studied variants at varying sizes (300 bp to 90 Mb). Moreover,  Orca enables in silico virtual screens to probe the sequence basis of 3D genome  organization at different scales. At the submegabase scale, it predicted specific  transcription factor motifs underlying cell-type-specific genome interactions. At  the compartment scale, virtual screens of sequence activities suggest a model for  the sequence basis of chromatin compartments with a prominent role of  transcription start sites.", "date_created": "2024-02-13T22:04:45.589569+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-15T15:43:01.598314+00:00"}, "date_published": "2022-05", "public_release": "2024-03-15", "schema_version": "2", "project_release": "2024-03-15", "exp_sets_used_in_pub": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES21D8SP8/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES21D8SP8", "uuid": "a9007b58-6a8c-4d22-8f6f-f9f347e58165", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/9095d07f-54e7-439c-9e56-9b1487cf9489/", "@type": ["Publication", "Item"], "uuid": "9095d07f-54e7-439c-9e56-9b1487cf9489", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Zhou J (2022) PMID:35551308", "external_references": [], "short_attribution": "Zhou J (2022)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}