{"ID": "PMID:36629266", "lab": {"@type": ["Lab", "Item"], "uuid": "d3412190-317a-4837-823f-3892b9f641a4", "display_title": "External Lab", "status": "current", "title": "External Lab", "@id": "/labs/external-lab/", "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/36629266", "tags": ["4dn-external-reuse"], "award": {"project": "External", "center_title": "External", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "center": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "status": "current", "name": "external-award", "description": "Funding source is from outside 4DN.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Hypothesis-driven probabilistic modelling enables a principled perspective of  genomic compartments.", "status": "current", "aliases": ["4dn-dcic-lab:PMID:36629266"], "authors": ["Kariti H", "Feld T", "Kaplan N"], "journal": "Nucleic acids research", "abstract": "The Hi-C method has revolutionized the study of genome organization, yet  interpretation of Hi-C interaction frequency maps remains a major challenge.  Genomic compartments are a checkered Hi-C interaction pattern suggested to  represent the partitioning of the genome into two self-interacting states  associated with active and inactive chromatin. Based on a few elementary  mechanistic assumptions, we derive a generative probabilistic model of genomic  compartments, called deGeco. Testing our model, we find it can explain observed  Hi-C interaction maps in a highly robust manner, allowing accurate inference of  interaction probability maps from extremely sparse data without any training of  parameters. Taking advantage of the interpretability of the model parameters, we  then test hypotheses regarding the nature of genomic compartments. We find clear  evidence of multiple states, and that these states self-interact with different  affinities. We also find that the interaction rules of chromatin states differ  considerably within and between chromosomes. Inspecting the molecular  underpinnings of a four-state model, we show that a simple classifier can use  histone marks to predict the underlying states with 87% accuracy. Finally, we  observe instances of mixed-state loci and analyze these loci in single-cell Hi-C  maps, finding that mixing of states occurs mainly at the cell level.", "date_created": "2024-02-13T22:04:46.954436+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-15T16:02:50.513389+00:00"}, "date_published": "2023-02-22", "public_release": "2024-03-15", "schema_version": "2", "project_release": "2024-03-15", "exp_sets_used_in_pub": [{"uuid": "ec888986-1cca-4931-80e3-a0c9a031678f", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES21VTCK2", "@id": "/experiment-set-replicates/4DNES21VTCK2/", "status": "released", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "aa6f0d82-16c9-4109-a1f8-3fa0636a3560", "@type": ["ExperimentSetReplicate", "ExperimentSet", 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