The doctoral dissertation in the fields of Biomedicine and Molecular Medicine will be examined at the Faculty of Health Sciences at Kuopio campus.
What is the topic of your doctoral research? Why is it important to study the topic?
The focus of my doctoral research was to identify how genetic variation, chromatin remodelling, and transcription factor (TF) binding are interconnected and how this could be used to identify regulatory variation that affects gene expression by using a mouse model for polygenic obesity. Most of the risk variants identified by genome-wide association studies for polygenic diseases are located outside the protein coding regions of the genome. Despite their prevalence, the functional mechanisms by which these non-coding variants influence disease risk remain largely unknown. One proposed mechanism is the alteration of TF binding, which can have downstream effects on gene regulation. Mouse models for polygenic diseases offer a valuable platform for investigating how genetic variation affects the regulatory landscape. These models can provide important information on how altered TF binding events may be predicted using non-targeted sequencing methods and used to identify novel targets for future research. The research also included an in-depth examination of TCF7L2, an important regulator of metabolism in both liver and white adipose tissue.
What are the key findings or observations of your doctoral research?
This doctoral research highlights genetic variation as a key driver of regulatory differences. We observed that chromatin accessibility, a commonly used proxy for TF binding, is heavily affected by genetic variation and poorly dynamic upon dietary stress in metabolically relevant tissues in a mouse model for polygenic obesity. Through integrative analysis of chromatin accessibility and the active regulatory region marker H3K27ac, the research suggests that chromatin accessibility can serve as an indicator for detecting genetically altered TF binding. The findings reveal that differentially accessible regions contain sites for altered TF binding motifs, which correlate with changes in chromatin accessibility. Moreover, the study identified significant variability in the predictiveness of differential accessibility of genetically determined binding sites across different TFs in bulk-tissue analysis, highlighting an important consideration for future research in this field. We also show that TCF7L2 binding is highly specific to a subset of hepatocytes in the liver and that it might exhibit pioneer activity, suggesting that further research on identifying novel pioneer factors is needed to understand the genetically determined chromatin landscape.
How can the results of your doctoral research be utilised in practice?
The results of this doctoral research provide a comprehensive integrated analysis of multiple genome-wide analysis methods that improves the understanding on how genetic variation is linked to the different layers of gene regulation in a model for polygenic disease. This research also evaluates the utility of using chromatin accessibility and in silico tools to identify genetically affected TF binding sites compared to more direct methods like ChIP-seq, offering valuable information for researchers planning future studies.
What are the key research methods and materials used in your doctoral research?
In this doctoral research an integrated analysis was carried out using multiple genome-wide sequencing techniques, including ATAC-seq, H3K27ac ChIP-seq, and RNA-seq. This approach allowed us to connect genetic variation to differences observed in the regulatory landscape in the liver and white adipose tissue of C57BL6/j and 129S1/SvImJ mice, which are commonly used to study polygenic obesity. We used several approaches to study genetically determined TF binding including strain-specific footprint analysis to estimate TF occupancy. Our analysis identified candidate regulatory variants in the liver, which were then transferred to a human context. We utilised public datasets for transcription factor binding sites in both humans and mice to estimate and validate these candidate regulatory variants. In addition, we performed TCF7L2 and CTCF ChIP-seq to connect genetic variation with altered TF binding. For TCF7L2, we incorporated multiomic single-cell analysis to validate our findings on TCF7L2 binding and function in the liver.
The doctoral dissertation of Juho Mononen, MSc, entitled Genetic variation is a key determinant of chromatin accessibility and transcription factor binding: A case study using a mouse model for polygenic obesity will be examined at the Faculty of Health Sciences. The Opponent in the public examination will be Docent Biswajyoti Sahu of the University of Oslo, and the Custos will be Docent Sami Heikkinen of the 91. The public examination will be held in English.
