{"ID": "PMID:19829295", "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "status": "current", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/19829295", "award": {"center_title": "DCIC - Park", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "@id": "/awards/2U01CA200059-06/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "project": "4DN", "name": "2U01CA200059-06", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Human DNA methylomes at base resolution show widespread epigenomic differences.", "status": "current", "aliases": ["4dn-dcic-lab:wgbs_ref_PMID_19829295"], "authors": ["Lister R", "Pelizzola M", "Dowen RH", "Hawkins RD", "Hon G", "Tonti-Filippini J", "Nery JR", "Lee L", "Ye Z", "Ngo QM", "Edsall L", "Antosiewicz-Bourget J", "Stewart R", "Ruotti V", "Millar AH", "Thomson JA", "Ren B", "Ecker JR"], "journal": "Nature", "abstract": "DNA cytosine methylation is a central epigenetic modification that has essential  roles in cellular processes including genome regulation, development and disease.  Here we present the first genome-wide, single-base-resolution maps of methylated  cytosines in a mammalian genome, from both human embryonic stem cells and fetal  fibroblasts, along with comparative analysis of messenger RNA and small RNA  components of the transcriptome, several histone modifications, and sites of  DNA-protein interaction for several key regulatory factors. Widespread  differences were identified in the composition and patterning of cytosine  methylation between the two genomes. Nearly one-quarter of all methylation  identified in embryonic stem cells was in a non-CG context, suggesting that  embryonic stem cells may use different methylation mechanisms to affect gene  regulation. Methylation in non-CG contexts showed enrichment in gene bodies and  depletion in protein binding sites and enhancers. Non-CG methylation disappeared  upon induced differentiation of the embryonic stem cells, and was restored in  induced pluripotent stem cells. We identified hundreds of differentially  methylated regions proximal to genes involved in pluripotency and  differentiation, and widespread reduced methylation levels in fibroblasts  associated with lower transcriptional activity. These reference epigenomes  provide a foundation for future studies exploring this key epigenetic  modification in human disease and development.", "categories": ["key publication", "methods paper"], "date_created": "2025-05-13T20:14:40.796745+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-05-13T20:14:41.034831+00:00"}, "date_published": "2009-11-19", "public_release": "2025-05-13", "schema_version": "2", "project_release": "2025-05-13", "@id": "/publications/ce597f38-f68b-4af7-afdc-be2cbac2afe8/", "@type": ["Publication", "Item"], "uuid": "ce597f38-f68b-4af7-afdc-be2cbac2afe8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Lister R et al. (2009) PMID:19829295", "external_references": [], "short_attribution": "Lister R et al. (2009)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}