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.

Public Health Relevance

It is becoming increasingly recognized that higher-order genome organization crucially influences gene regulation, cell function and ultimately human health. However, the ability to investigate these relationships will depend on technological advances that enable a more precise, integrated view of genome structure and function. This proposal seeks to address this challenge through the development of a Nucleome Positioning System that will provide a powerful platform for studying genomic structure in space (3D) and time (4D).

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZRG1)
Program Officer
Blondel, Olivier
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Jackson Laboratory
Bar Harbor
United States
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Basu, Subhadip; Saha, Punam Kumar; Roszkowska, Matylda et al. (2018) Quantitative 3-D morphometric analysis of individual dendritic spines. Sci Rep 8:3545
Szalaj, Przemyslaw; Plewczynski, Dariusz (2018) Three-dimensional organization and dynamics of the genome. Cell Biol Toxicol 34:381-404
Al Bkhetan, Ziad; Plewczynski, Dariusz (2018) Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. Sci Rep 8:5217
Vian, Laura; P?kowska, Aleksandra; Rao, Suhas S P et al. (2018) The Energetics and Physiological Impact of Cohesin Extrusion. Cell 173:1165-1178.e20
Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian et al. (2017) Cohesin Loss Eliminates All Loop Domains. Cell 171:305-320.e24
Li, Xingwang; Luo, Oscar Junhong; Wang, Ping et al. (2017) Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Nat Protoc 12:899-915
Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P et al. (2017) Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 67:566-578.e10
Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B et al. (2017) High-throughput automated microfluidic sample preparation for accurate microbial genomics. Nat Commun 8:13919
Canela, Andres; Maman, Yaakov; Jung, Seolkyoung et al. (2017) Genome Organization Drives Chromosome Fragility. Cell 170:507-521.e18
Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul et al. (2016) An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Genome Res 26:1697-1709

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