{"ID": "PMID:30778195", "lab": {"@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "correspondence": [{"contact_email": "eWlqdW4ucnVhbkBqYXgub3Jn", "@id": "/users/d8ac229e-ec08-4411-be38-dc779520ea62/", "display_title": "Yijun Ruan"}], "status": "current", "title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/30778195", "award": {"@id": "/awards/1U54DK107967-01/", "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "status": "current", "center_title": "NOFIC - Ruan", "@type": ["Award", "Item"], "name": "1U54DK107967-01", "project": "4DN", "description": "NOFIC: This proposal seeks to fulfill a community need for a comprehensive, high-resolution genome-mapping platform that will enable investigation of the structural, functional and spatiotemporal organization of the human genome. Our ultimate goal is to deliver complex chromatin interaction network maps in the context of 3D genome structures from which the dynamics of individual genomic elements can be monitored and referenced. Here, we propose to develop a Nucleome Positioning System (NPS)-comprised of 1) a robust genome- wide mapping technology platform, 2) advanced computational modeling algorithms and 3) state-of-the-art nuclear imaging methods-that will allow users community-wide to uncover the regulatory functions of 3D genome organization in human cells. NPS will be based upon the established ChIA-PET method (1,2), enhanced by process optimizations-i.e., microfluidic-based miniaturization and Tn5-transposase-based library preparation-to facilitate the study of chromatin interactions mediated by protein factors across a broader range of human cell types (Aim 1, see also Mapping Technology Development Component). We will also optimize RICh-PET for the comprehensive mapping of chromatin interactions mediated by non-coding RNAs (Aim 1). The high-quality mapping data generated through these optimization efforts will be analyzed by a new computational platform (Three-Dimensional Nucleome Modeling Engine, or 3D-NOME) that makes use of hierarchical multi-scaling to model 3D genome structures (Aim 2, Data Analysis and Modeling component). We will also complement the 3D modeling with transcriptome, epigenome and SNP data associated with genetic diseases (GWAS) to provide functional annotation to structural units (Aim 2). We will continue by developing strategies to validate the nucleome geometry predicted by 3D-NOME both structurally, using new nuclear imaging technologies, and functionally, using cutting-edge genome- and epigenome-editing approaches, in both human cell lines and mouse models (Aim 3, Biological Validation Component). Finally, we will implement NPS to generate pilot 3D genome maps from a wide range of human cell lines and primary immune cells sorted from whole blood, to elucidate the spatiotemporal dynamics of human genome organization over major developmental and hematopoietic cell lineages, as well as among differentiating lymphocytes involved in the immune response (Aim 4, Data Generation Component). Together, these efforts will yield a powerful set of sophisticated, high-quality tools and mapping data for the larger research community, and will help establish the standards for future 3D/4D nucleome studies. They will also provide insights into the broad mechanisms that organize the structure and regulate the function of the human genome, as well as the specific mechanisms by which immune responses are regulated at the nuclear level.", "uuid": "029a2578-43dc-4343-8f41-694518cce304", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Multiplex chromatin interactions with single-molecule precision.", "status": "current", "aliases": ["4dn-dcic-lab:chia-drop-method"], "authors": ["Zheng M", "Tian SZ", "Capurso D", "Kim M", "Maurya R", "Lee B", "Piecuch E", "Gong L", "Zhu JJ", "Li Z", "Wong CH", "Ngan CY", "Wang P", "Ruan X", "Wei CL", "Ruan Y"], "journal": "Nature", "abstract": "The genomes of multicellular organisms are extensively folded into 3D chromosome  territories within the nucleus(1). Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation capture, Hi-C)(2), and chromatin immunoprecipitation techniques (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET)(3), have revealed topologically associating domains(4) with frequent chromatin contacts, and have identified chromatin loops mediated by specific protein factors for insulation and regulation of transcription(5-7). However, these methods rely on pairwise proximity ligation and reflect population-level views, and thus cannot reveal the detailed nature of chromatin interactions. Although single-cell Hi-C(8) potentially overcomes this issue, this method may be limited by the sparsity of data that is inherent to current single-cell assays. Recent advances in microfluidics have opened opportunities for droplet-based genomic analysis(9) but this approach has not yet been adapted for chromatin interaction analysis. Here we describe a strategy for multiplex chromatin-interaction analysis via droplet-based and barcode-linked sequencing, which we name ChIA-Drop. We demonstrate the robustness of ChIA-Drop in capturing  complex chromatin interactions with single-molecule precision, which has not been possible using methods based on population-level pairwise contacts. By applying ChIA-Drop to Drosophila cells, we show that chromatin topological structures predominantly consist of multiplex chromatin interactions with high heterogeneity; ChIA-Drop also reveals promoter-centred multivalent interactions,  which provide topological insights into transcription.", "date_created": "2019-11-25T20:41:18.270080+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-11-25T20:46:53.373833+00:00"}, "date_published": "2019-02", "public_release": "2019-11-25", "schema_version": "2", "project_release": "2019-11-25", "@id": "/publications/f325359a-8629-4b0c-9b9f-4bdace40212e/", "@type": ["Publication", "Item"], "uuid": "f325359a-8629-4b0c-9b9f-4bdace40212e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Zheng M et al. (2019) PMID:30778195", "external_references": [], "short_attribution": "Zheng M et al. (2019)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}