New method reveals where in the cell DNA are at increased risk
Credit: Karolinska Institutet

Researchers at Karolinska Institutet have developed a new sequencing method that makes it possible to map how DNA is organized in the cell nucleus – which reveals which regions of the genetic material are at increased risk of DNA damage and mutations. The technique is described in an article published in the scientific journal Nature Biotechnology.

Most cells in the human body contain about two meters of DNA. The long strand of DNA is divided into 46 large pieces – the chromosomes – that occupy distinct regions, so-called chromosome territories, in the cell nucleus.

How individual parts of the genetic material are arranged spatially in the cell nucleus significantly affects how the cell’s transcription machinery reads the genes. However, the spatial arrangement of individual genes in the three-dimensional space in the cell nucleus has largely remained unexplored.

High resolution maps

Now a research team led by Magda Bienko at the Science for Life Laboratory (SciLifeLab) and the Department of Medical Biochemistry and Biophysics , Karolinska Institutet, has developed a new method, called Genomic loci Positioning by Sequencing or GPSeq, which can be used to obtain high-resolution maps about how DNA is organized spatially in the cell nucleus.

The method works by gradually cutting the DNA from the periphery of the cell nucleus towards the middle, and then reading the DNA sequence around each incision. Mathematical modeling can then be used to reconstruct the three-dimensional structure and find where the individual genes and regions between the genes are located along the radius of the cell nucleus and in relation to each other.

– We discovered that the spatial distribution of different types of chromatin (consisting of DNA, RNA and protein complexes) often differed from what we expected to find. To our surprise, we found that the image is not as simple as all the inactive chromatin located at the periphery of the cell nucleus and that the active chromatin is collected in the center of the cell nucleus. Instead, there is a continuum, a gradually increasing activity from the periphery of the cell nucleus toward the interior, although inactive chromatin can also be found in the center of the cell nucleus, says Magda Bienko, one of the study’s lead authors.

Reveals where the risk of injury is greatest

An important aspect of knowing where different regions of the genetic material are located in the cell nucleus is that it is now possible to map where DNA damage and mutations are most likely to occur, explains Nicola Crosetto , a researcher at the same institution at Karolinska Institutet and the second of the study’s lead authors.

– We discovered that DNA mutations that are often found in different cancers accumulate in the inactive chromatin found at the periphery of the cell nucleus, which may be related to the fact that many mutagens originate outside the cell. On the other hand, DNA breaks and gene fusions are much more likely to be found in the center of the cell nucleus, which may be due to the high levels of transcription that occurs in the center of the cell nucleus, says Nicola Crosetto.

The research has been supported by the Swedish Society for Medical Research (SSMF), the Science for Life Laboratory, the Swedish Research Council, the Ragnar Söderberg Foundation, the Cancer Foundation, the Strategic Research Program in Cancer (StratCan) at Karolinska Institutet and the European Research Council.

Publication

GPSeq reveals the radial organization of chromatin in the cell nucleus“. Gabriele Girelli, Joaquin Custodio, Tomasz Kallas, Federico Agostini, Erik Wernersson, Bastiaan Spanjaard, Ana Mota, Solrun Kolbeinsdottir, Eleni Gelali, Nicola Crosetto & Magda Bienko. Nature Biotechnology , online May 25, 2020, doi: 10.1038 / s41587-020-0519-y