New method makes spatial organization of DNA visible at high resolution
Whether a cell develops into a liver-, skin-, or nerve cell is controlled by the genes in our DNA. Their activity is regulated extremely precisely. How the DNA folds in the cell nucleus plays an important role in this regulation. Researchers in Göttingen have now developed a new method that allows to investigate the spatial organization of DNA at very high resolution. With this technique, they can study the regulation of DNA and its activity in more detail than was previously possible. Ultimately, this can contribute to a better understanding of the genetic underpinnings of human diseases.
Our body consists of hundreds of different cell types that perform very different tasks: They fight pathogens, make our muscles work, or contract our heart rhythmically. Yet, they all contain the same blueprint, which is encoded in the genes in our DNA. Cells become specialists by activating only those genes that are needed for their respective function. How this process, called gene expression, takes place is an intensively researched field with many unanswered questions.
The DNA of a single human cell, stretched to its full length, would be about two meters long and contains several billion individual DNA base pairs. In order to fit into the tiny cell nucleus, it must fold into specific three-dimensional structures. “Genome folding not only makes the DNA more compact, but also influences whether genes in the DNA can be activated at all,” says Marieke Oudelaar, who heads the Lise Meitner Group Genome Organization and Regulation at the institute. Her team has now achieved a methodological breakthrough: making the spatial organization of DNA regions visible with a resolution of up to 20 base pairs.
“We already know that genes are activated or inhibited very precisely as needed, through different mechanisms. For example, there are certain DNA segments called promoters and enhancers that enable the regulated expression of a gene,” explains Abrar Aljahani, a PhD student in Oudelaar's team and first author of the paper now published in the journal Nature Communications.
3D DNA structures at very high resolution
Gene promoters are bound by regulatory proteins, which can amplify and switch off expression. Upon contact with protein-bound promoters, enhancers cause a gene to be activated more strongly. However, enhancer and promoter regions can be hundreds of thousands of base pairs apart from each other on a DNA strand. So how does this work? To bring the enhancer close to its promotor, the DNA strand forms loops with the help of architectural proteins. If the contacts between promoters and enhancers are disrupted, diseases such as cancer can result. “Our technique makes it possible to visualize the 3D DNA structures in which promoters and enhancers interact at extremely high resolution. This gives us an important tool to study how disrupted contacts between these DNA segments affect gene expression,” Oudelaar reports.
Oudelaar's team has already successfully used the method to investigate the mechanisms that regulate DNA folding and gene activation. By selectively removing architectural proteins the scientists could precisely map how loss of these proteins disrupts the specific 3D interactions between promoters and enhancers. As a result, gene expression levels were lower and less precisely regulated. “We can now use the method to further decipher the fundamental principles underlying gene regulation. In the future, we hope that we can also use the technique to map how genetic variation and mutations in human individuals influence the organization and regulation of our DNA,” the research group leader says. (cr/mo)