Obtaining High-Resolution Maps of DNA Organization

Researchers at Karolinska Institutet in Sweden have developed a new sequencing method that makes it possible to map how DNA is spatially organized in the cell nucleus, revealing which genomic regions are at higher risk of mutation and DNA damage. The technique was published today in Nature Biotechnology.

The spatial arrangement of the genome in the nucleus strongly affects how the genome is read by the cell’s transcriptional apparatus. However, the spatial arrangement of individual genes in the three-dimensional space of the nucleus has remained largely unexplored. Now, researchers have developed a new genomic method—Genomic loci Positioning by Sequencing, or GPSeq—that can be used to obtain high-resolution maps of DNA organization in the nucleus.

The method works by gradually cutting the DNA from the nuclear periphery towards the center, followed by reading the DNA sequence around each cut. Mathematical modeling can then be used to reconstruct the 3D genome structure and find where individual genes and regions between genes are located along the nuclear radius as well as in relation to each other.

“We found that the spatial distribution of different types of chromatin (composed of DNA, RNA, and protein complexes) often differed from what we expected to find,” says senior author Magda Bienko. “To our surprise, we found that the picture is not as simple as having all the inactive chromatin sitting at the nuclear periphery and the active chromatin amassed in the center. Instead, there is a continuum, a gradient of increasing activity from the nuclear periphery towards the interior, even though the inactive chromatin can be found in the very center of the nucleus too.”

An important aspect of knowing where different genomic regions are located in the nucleus is that it is now possible to map where DNA damage and mutations are most likely to occur. “We discovered that DNA mutations that are often encountered in different cancer types are enriched in the inactive chromatin located at the nuclear periphery, which might have to do with the fact that many mutagens originate from outside the cell,” says senior author Nicola Crosetto. “On the other hand, DNA breaks and gene fusions are much more likely to be found in the nuclear center, which might be due to the high levels of transcription that we find in the center.”