Decoding DNA folding patterns

April 12, 2012

Schematic illustrating topological domains and resulting directional bias. A: Interactions upstreamp; B: Interactions downstream (credit: Jesse R. Dixon et al./Nature)

Using a powerful DNA sequencing methodology, researchers at the Ludwig Institute for Cancer Research have investigated the three-dimensional structure of DNA folds in the nucleus of a chromosome.

“With the knowledge of how DNA folds inside the nucleus, we now have a more complete picture of the regulatory process of genes,”said Dr. Bing Ren, Member of the Ludwig Institute for Cancer Research and Professor of Cellular and Molecular Medicine at the University of California, San Diego.

“That is the primary reason we sought to tackle this problem.”

The spatial organization is intimately linked to its role in the body. The findings provide scientists with a greater understanding about the basic principles of DNA folding and its role in gene regulation.


The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete.

Chromosomes are strands of DNA that contain the blueprint of all living organisms. Humans have 23 pairs of chromosomes that instruct how genes are regulated during development of the human body. While scientists have developed an understanding of the one-dimensional structure of DNA, until today, little was known about how different parts of DNA are folded next to each other inside the nucleus.

“In any biology textbook, when you look at a diagram of how genes are depicted, it is invariably a one-dimensional line. In reality, genes are arranged in such a way that two parts of the gene may be distal to each other linearly, but very close in 3-D,” said Ren.

Topological domains: basic unit of folding


Topological domains in the mouse ES cell genome (credit: Jesse R. Dixon et al./Nature)

Ludwig researchers used a sequencing-based method called Hi-C to examine the 3-D structure of chromosomes. “With this technology, we were able to build a map of pair-wise interactions from each chromosome, and from that, extrapolate the basic folding pattern of the DNA.

What we learned is that they fold into many local domains termed topological domains, which are on average one million base pairs in size. By way of comparison, the whole human genome is just over three billion base pairs in size,” explained lead researcher, Jesse Dixon, a graduate student in Dr. Ren’s lab.

In examining the interaction map, Dr. Ren’s team discovered that topological domains are the basic unit of folding. The team confirmed their findings by comparing it among different cell types. In each type, the folding of DNA into topological domains was constant.

A parallel study by researchers at Institut Curie and the University of Massachusetts Medical School support Ludwig researchers’ findings. By focusing on the mouse X chromosome segment in embryonic stem cells, as well as neuronal cells and fibroblasts, researchers showed that this segment adhered to similar folding patterns as the ones found by Ren’s team. They further showed that this organization could be linked to gene regulation.

Clues for diagnosis of cancers

“This is just the beginning of a very exciting area of research focused on the understanding of nuclear processes from a three-dimensional point of view,” said Ren. “We know that some cancers, including many leukemias, are caused by the translocation of two genes.

“It’s not clear how these translocations are regulated or whether they result from random events. It’s possible that the spatial structure of the chromosome can provide clues about how these translocations occur and, more importantly, how we can prevent them or at least mitigate their effect.”

Ref.: Jesse R. Dixon et al., Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 2012 [DOI: 10.1038/nature11082]