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Program Snapshot

The goal of the Common Fund’s 4D Nucleome (4DN) program is to study the three-dimensional organization of the nucleus in space and time (the 4th dimension). The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions. Scientists know that how the information in the nucleus organized, stored, and unpackaged are all important to basic human health and we are only starting to learn how changes in this organization can lead to the development of different diseases, such as cancer or our response to infectious agents like viruses.

Under different conditions, such as disease, regions of our DNA (different colored ovals) may change shape or location inside the nucleus of a cell (large circles). These movements may start or stop the production of certain proteins at the wrong time.

Being Developed by 4DN Network Investigators

The 4DN program has generated a variety of tools and resources so scientists can continue to learn about the importance of nuclear organization. Program deliverables currently available through the public 4DN Portal include nearly 2000 datasets from hundreds of experiments, 52 software packages and 23 protocols and reagents for researchers to use.

Program deliverables currently available through the public 4DN Portal include nearly 2000 datasets from hundreds of experiments, 52 software packages and 23 protocols and reagents for researchers to use. To find more, go to

Next Initiatives

The first phase of the 4DN program was very successful but there is still a need to deliver data and tools to the broader biomedical research community to address the role of nuclear organization in health and disease. A second stage of funding for the 4DN program has recently started and will focus on the following initiatives:

  • Real Time Chromatin Dynamics and Function
  • 4DN Centers for Data Integration, Modeling, and Visualization
  • 4DN Organization and Function in Human Health and Disease
  • New Investigator Projects on 4DN Organization and Function in Human Health and Disease

Check back regularly for more information on stage 2 of the 4DN program!

In Detail

The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions. It is estimated that each human cell contains approximately 2 meters (6.5 feet) of DNA, squeezed inside the cell’s microscopic nucleus. We now know that DNA is not randomly arranged within the nucleus; instead, the organization of the nucleus is tightly controlled. However, the functional consequences of this organization are not well understood. What are the principles that govern the three-dimensional architecture of the nucleus, and how does this architecture contribute to gene expression regulation? How does nuclear architecture change over time (the 4th dimension) in the course of normal development? Do dysfunctional alterations in nuclear organization lead to disease, and/or could they be used to diagnose diseases?

The Common Fund’s 4D Nucleome program aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. This program is developing technologies, resources and data to enable the study of the 4D Nucleome, including novel tools to explore the dynamic nuclear architecture and its role in gene expression programs, models to examine the relationship between nuclear organization and function in both normal development and disease, and reference maps of nuclear architecture in a variety of cells and tissues.

This program includes six initiatives:

  • Nuclear Organization and Function Interdisciplinary Consortium (NOFIC): NOFIC
    is composed of multidisciplinary teams that are developing and validating novel approaches and genome-wide mapping technologies that will lead to a deeper understanding of nuclear organization in time and space, and the role of this organization in regulating gene expression programs.
  • Nucleomics Tools:
    This initiative is stimulating the development and validation of chemical and biochemical technologies for measuring three dimensional interactions between specific places in the genome (genomic loci), or between genomic loci and regulators of genome organization and function, in mammalian cells.
  • Study of Nuclear Bodies and Compartments:
    Nuclear bodies (structural and functional subunits within the nucleus) and nuclear compartments (specific subregions within the nucleus) set up distinct local environments that facilitate many important nuclear processes. This initiative supports the development of tools and strategies to study the three dimensional architecture of the nucleus in relationship to the spatial arrangement of nuclear bodies and molecular machinery regulating gene expression, the structure and function of poorly characterized nuclear structures and compartments, and the role of specialized proteins and RNAs in nuclear organization and function.
  • Imaging Tools:
    This initiative stimulates the development of higher throughput, higher resolution and higher content imaging approaches that can measure changes in nuclear organization in live single cells.
  • Organizational Hub (4DN-OH) and Opportunity Pool:
    The 4DN-OH developed a community website to facilitate sharing of data, reagents, standards, and protocols between 4D Nucleome investigators, and with the larger scientific community. 4DN-OH helps foster collaborations between 4D Nucleome investigators, organize yearly scientific meetings, and oversee administrative aspects of the program. 4DN-OH also administers the Opportunity Pool, a fund to support new projects and initiatives that address identified needs arising throughout the lifetime of the program.
  • Data Coordination and Integration Center (4DN-DCIC):
    4DN-DCIC tracks, stores, and displays all data generated by 4D Nucleome investigators. It provides a Data Analysis Center to assist with integrated analyses, develops metrics and standards to be adopted by the community at large, and provides visualization tools to facilitate access and understanding of complex datasets.


Become a 4DN Associate Member!

4DN joins International Human Epigenome Consortium

New Science Highlights

Zooming in on Genome Structure

SARS-CoV-2 Reorganizes the Genome to Gain an Immune Advantage

4DN News

Article Features 4DN Program

Read here about how NIH-supported research is advancing what we know about genome organization.

4DN Portal

Find information about the data, protocols, reagents, resources, and methods that are currently being developed by 4DN Network investigators.


4DN Tutorial Series

Data, Resources and Tools to Help Elucidate Nuclear Organization in Space and Time

Multimodal Visualization for 4DN Data Using Nucleome Browser and OME

This page last reviewed on October 31, 2023