Public Release: 

NIH grants $3.7 million to develop new system for understanding the 3-D genome

Jackson Laboratory

Farmington, Conn. - A five-year, $3.7 million grant was awarded to a team led by Professor Yijun Ruan, Ph.D., of The Jackson Laboratory (JAX) for Genomic Medicine to fund research into how the human genome is organized in the nucleus of the cell.

Composed of DNA, the genome in a single cell would stretch to more than six feet in length if extended. Instead it is intricately looped and physically packed into microscopic nuclei. This three-dimensional (3D) structure is thought to play many important roles in genome regulation and function.

Ruan is the Florine Deschenes Roux Chair Professor and director of genomic sciences at The Jackson Laboratory. An international leader in genome structure research, he is developing a new system for understanding 3D genome organization and regulation.

The grant is part of the 4D Nucleome program, supported by the National Institutes of Health's Common Fund to investigate nuclear organization in space and over time (the fourth dimension, or 4D).

Ruan says. "We know now that there are complex interplays between DNA, protein factors and RNA species, together shaping the precise but ever-changing 3D genome conformation within the tiny nuclear space. We have a great deal to learn about how such structure is organized and how it affects gene expression in normal development and disease."

Ruan's team includes co-investigators Chia-Lin Wei, Ph.D., of Lawrence Berkeley National Laboratory, Paul Blainey, Ph.D., of the Broad Institute and Rafael Casellas, Ph.D., of the National Institute of Arthritis and Musculoskeletal and Skin Diseases. Together they will develop a comprehensive, high-resolution mapping program that will deliver complex interaction network maps that can provide insight into the dynamics of individual genomic elements in the context of 3D genome structures.

Called the Nucleome Positioning System (NPS), the program will comprise a genome-wide mapping technology platform, integrated computational modeling algorithms, cutting-edge nuclear imaging methods and advanced functional validation approaches. The resulting tools and mapping data will be made available to the larger research community and help establish the standards for future 3D/4D nucleome studies.

The grant provides $749,775 for the first year of research, and provisional funding for an addiitonal four years.


The Jackson Laboratory is an independent, nonprofit biomedical research institution and National Cancer Institute-designated Cancer Center based in Bar Harbor, Maine, with a facility in Sacramento, Calif., and The Jackson Laboratory for Genomic Medicine in Farmington, Conn. It employs 1,700 staff, and its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.

Research reported in this publication was supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under Award Number U54DK107967. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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