To function properly, each cell in our body requires a set of genes to be translated into proteins in the correct amount. To achieve this task, our cells utilize a complex network of regulatory sequences – short fragments embedded in our genome that do not code for proteins. These regions recruit a subset of proteins called transcription factors, which in turn establish communication between regulatory sequences and the downstream genes whose synthesis they control. How exactly the communication between different regulatory parts of the genome is coordinated by transcription factors, however, remains unknown.
The project addresses this question in two ways: The first approach used a large dataset summarizing the regulatory activity of all transcription factors found at a given genomic region, and compared this activity across a set of genetically diverse individuals. Since each human harbors a specific set of DNA mutations that make their genomes unique, regulatory activities can vary from individual to individual as a function of these mutations. Leveraging this information, the project investigated what composition of transcription factors predisposes a regulatory region to become sensitive to mutations.
An important finding is the discovery of a subset of ‘cooperativity-enhancing’ transcription factors that boost the activity of many others, thus turbo-charging effects introduced by DNA mutations. The same set of cooperativity-drivers are also important for the establishment of communication between two or more regulatory regions.
As certain DNA mutations can predispose individuals to diseases, or initiate malignancies such as cancer, the insights gained by the first part of the project may help researchers to not only identify malignant mutations faster, but to also interpret their mode of action. The latter is an essential first step to personalize treatment plans.
The second part of the project is devoted to the development of a new methodology that can detect communication of distant regulatory regions with their target genes, while simultaneously measuring gene output. The approach allows researchers to test what effect DNA mutations in regulatory regions, for example those found in certain cancers, have on gene synthesis. As the method can test many different conditions at once, it provides mechanistic insights into which regulatory networks are involved in the process. The insights obtained from such experiments will improve our understanding of why and how mutations in the regulatory parts of our genome trigger disease. Once mechanisms are understood, they can be targeted by therapeutics.
As such, the overall objective of this proposal was to develop the necessary molecular tools that will allow us to better understand how DNA mutations ultimately lead to disease and what vulnerabilities in disease-linked regulatory networks can be exploited for the development of targeted therapies.
The developed method was applied to a disease-linked genomic region, the AXIN2 gene, that harboured a small mutation, which is linked to the progression of chronic lymphocytic leukaemia. By systematically probing which transcription factors lead to communication between the mutated and the gene synthesis region, the method revealed that a combination of transcription factors is required to activate AXIN2 synthesis. In conclusion, the approach was applied to investigate the mechanism underlying a distinct disease-linked genomic region and provided further insights into how communication between regulatory regions and their target genes is mediated by transcription factors.
