{"ID": "doi:10.1101/2021.06.10.447969", "lab": {"title": "Sheng Zhong, UCSD", "status": "current", "correspondence": [{"contact_email": "c3pob25nQHVjc2QuZWR1", "@id": "/users/5549e16d-fa63-477c-a1ed-6189cecc1304/", "display_title": "Sheng Zhong"}], "@type": ["Lab", "Item"], "display_title": "Sheng Zhong, UCSD", "@id": "/labs/sheng-zhong-lab/", "uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}, "pi": {"error": "no view permissions"}}, "url": "http://biorxiv.org/lookup/doi/10.1101/2021.06.10.447969", "award": {"@id": "/awards/1U01CA200147-01/", "center_title": "OH - Zhong", "@type": ["Award", "Item"], "description": "OH: Recent technological developments have significantly advanced our understanding of the three-dimensional organization of the nucleus. It has also become increasingly clear that the 3D nucleome plays an important role in regulating gene expression. Large cohorts of data are being generated to investigate the impact of the temporal changes of nuclear organization (the 4D nucleome) to normal development and disease processes. The primary goal of this proposal is the creation of an effective organizational hub and web portal for the 4D nucleome. We also propose to develop an effective coordination structure for the 4D nucleome activities. First, we will develop and organize effective networking methods and consortium meetings for establishing protocols and standards. We will develop a framework for coordination of the funded 4D nucleome projects. We will organize annual consortium-wide grantees meeting. We will utilize the professional organizers who have previously worked with the PIs and the premium conference venues at Atkinson Hall in UCSD (http://www.calit2.net). Two major activities will be organized during the annual meeting. Second, we will develop an adaptable, scalable, and user-friendly 4DN web portal. We will build the 4DN Network community web portal and a Virtual Resource Repository. This portal will be an integrated, versatile, and inter-operable data management, retrieval, analysis, and visualization system. We will leverage the ENCODE Comparative Browser (http://encode.cepbrowser.org) for developing the 4D network portal. In addition, the portal will incorporate data generated from outside the consortium, publish E-manuals for the consortium-agreed protocols, and provide the most up-to-date information on the data clearance. Third, we will coordinate and manage the 4DN Network Opportunity Pool. The opportunity pool of funds will be distributed and managed with 100% transparency. Competitive distribution with the funds will be coordinated by a professional manager with extensive experience in managing Center and Training Grants. Fourth, we will develop a comprehensive strategy for training and outreach. The proposed unit will aim to regularly train and update 4DN research network members and collaborators in several key areas including: 1) new technologies; 2) data/sample collection protocols; 3) data analysis methods; 4) data submission protocols; 5) data retrieval methods; 6) data QA/QC; 7) data exchange standards and data ontologies; 8) the contents of different 4DN and public databases; 9) data privacy and 10) data dissemination.", "display_title": "THE ORGANIZATIONAL HUB AND WEB PORTAL FOR THE 4D NUCLEOME NETWORK", "status": "current", "uuid": "c55dd1f0-433b-4714-bfce-8b3ae09f071c", "name": "1U01CA200147-01", "project": "4DN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "title": "Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells", "status": "current", "aliases": ["4dn-dcic-lab:calendrelli_et_al_zhong_lab_biorxiv_2021"], "authors": ["Calandrelli R", "Wen X", "Nguyen TC", "Chen C-J", "Qi Z", "Chen W", "Yan Z", "Wu W", "Zaleta-Rivera K", "Hu R", "Yu M", "Wang Y", "Ma J", "Ren B", "Zhong S"], "journal": "bioRxiv", "version": "2", "abstract": "Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the three-dimensional (3D) genome organization and function remain poorly understood. Here, we map caRNAs spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. We find that the relative abundance of trans-acting caRNA reflects the functional nuclear compartmentalization of the 3D genome, and the caRNAs sequence features are predictive of its spatial localization. We observe extensive caRNA-genome interactions that span several hundred kilobases to several megabases. These caRNA domains correlate with chromatin loops and enhancer-promoter interactions. We report a tradeoff of caRNAs promotive and suppressive roles to chromatin interactions. As a result, caRNA promotes chromatin interactions outside the anchors of chromatin loops, whereas caRNA exhibits an overall suppressive impact to chromatin interactions between loop anchors. Furthermore, caRNA suppresses chromatin loops number and strengths genome-wide, and this suppression depends on electric charge-mediated RNA interactions. These results reveal caRNAs multifaced role in regulating 3D chromatin organization and highlight caRNAs ability to modulate chromatin looping.", "date_created": "2021-06-14T17:34:59.403265+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-02-27T09:53:29.614142+00:00"}, "date_published": "2021-07-14", "public_release": "2021-06-14", "schema_version": "2", "static_content": [{"content": {"lab": {"@id": "/labs/sheng-zhong-lab/", "uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "status": "current", "display_title": "Sheng Zhong, UCSD", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "display_title": "zhong-ext-grant-note", "name": "zhong-ext-grant-note", "content": "Grant DP1DK126138 to Dr. Sheng Zhong provided additional support for this work.", "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "@type": ["StaticSection", "UserContent", "Item"], "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "status": "current", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - 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