Feng Yue, PhD, the Duane and Susan Burnham Professor of Molecular Medicine in the Department of Biochemistry and Molecular Genetics, was a co-corresponding author of the study published in Nature.

In a landmark effort to understand how the physical structure of our DNA influences human biology, Northwestern investigators and the 4D Nucleome Project have unveiled the most detailed maps to date of the genome’s three‑dimensional organization across time and space, according to a new study published in Nature.

The findings, generated using human embryonic stem cells and fibroblasts, offer a sweeping view of how genes interact, fold and reposition themselves as cells function and divide, said Feng Yue, PhD, the Duane and Susan Burnham Professor of Molecular Medicine in the Department of Biochemistry and Molecular Genetics, who was a co-corresponding author of the study.

“Understanding how the genome folds and reorganizes in three dimensions is essential to understanding how cells function,” said Yue, who is also director of the Center for Advanced Molecular Analysis and founding director of the Center for Cancer Genomics at the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. “These maps give us an unprecedented view of how genome structure helps regulate gene activity in space and time.”

Rather than existing as a straight ladder of code, the human genome folds into looping structures and compartments within the nucleus. These physical interactions can determine which genes turn on or off, influencing everything from development to cell identity and disease.

To study this complexity, Yue and his international collaborators employed a wide array of genomic technologies on fibroblasts and human embryonic stem cells to produce a unified dataset.

This effort identified:

• More than 140,000 chromatin loops per cell type, identifying the underlying elements at the different types of loop anchors and how they contribute to gene regulation.
• Comprehensive classifications of chromosomal domains, including where they reside inside the nucleus.
• High‑resolution 3D models of entire genomes at the single‑cell level, showing how each gene is positioned relative to its neighbors and regulatory elements.

These maps reveal how the genome’s architecture varies from cell to cell and how these variations relate to essential processes, including transcription and DNA replication.

Because no single technology can fully capture the genome’s 4D structure, the study also assessed the capabilities and limitations of the methods involved. Through extensive benchmarking, the investigators identified which assays are best suited to detect loops, domain boundaries, or nuanced differences in nuclear positioning — providing a roadmap for scientists pursuing similar questions in the future.

Additionally, by developing computational tools capable of predicting how the genome will fold purely from its sequence, the study authors have set the stage for future scientists to estimate how genetic variants — including those linked to disease — might alter 3D genome architecture, all without needing to run complex experiments.

This advance could accelerate the discovery of pathogenic mutations and reveal previously hidden mechanisms behind inherited disorders, Yue said.

“Since the majority of variants associated with human diseases are located in the non-coding regions of the genome, it is critical to understand how these variants influence essential gene expression and contribute to disease. The 3D genome organization provides a powerful framework for predicting which genes are likely to be affected by these pathogenic variants,” Yue said.

The work underscores a growing recognition that the genome’s function cannot be understood only by reading its sequence and that it’s shape matters, too. By revealing the connections between DNA folding, chromatin loops, gene activity and cell behavior, the study moves the field closer to a holistic view of how genetic instructions operate inside living cells.

Moving forward, Yue said he hopes these tools will eventually help decode how genome misfolding contributes to cancers, developmental disorders and other conditions, opening the door to structural genomics–based diagnostics and therapies.

“Having observed 3D genome alterations across cancers, including leukemia and brain tumors, our next aim is to explore how these structures can be precisely targeted and modulated using drugs such as epigenetic inhibitors,” Yue said.

The study was supported by grants from the National Institutes of Health Common Fund (The 4D Nucleome Project).