From lipid- and diabetes-associated DNA methylation at the SREBF1 locus to gene regulatory mechanisms

• Applicants: Dr. Melanie Waldenberger; Professor Dr. Heiko Witt, since 1/2021
• Subject Area: Endocrinology, Diabetology, Metabolism
• Term: from 2018 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 391322950

High levels of blood lipids, such as triglycerides and cholesterol, contribute to the pathophysiology of several common diseases. Genome-wide association studies have found numerous genetic risk loci associated with lipid levels or with related diseases such as diabetes and coronary artery disease. However, in most cases genetics only partially explains heredity. For example, the 157 lipid-related loci found through genetic association studies explain approximately 12% of lipid level variance estimated as attributable to heredity. Epigenetic mechanisms, such as DNA methylation, may account for the missing heritability of inter-individual lipid level variability and contribute to the lipid-related risk profile. In fact, recent epigenome-wide association studies have found several CpG sites at different gene loci associated with altered lipid levels. However, the precise molecular mechanisms which are modulated by the identified differential DNA-methylation remain elusive in most cases. DNA methylation contributes to the regulation of gene expression, classically by methyl-CpG-binding domain proteins, but recent analyses have also found the activity of diverse sequence specific transcription factors to be modulated. Here, we will focus on in depth-analyses of DNA methylation at the SREBF1 locus, a locus for which we recently reported an association with increased triglyceride levels, but also adiposity and type 2 diabetes. We will find methylated CpGs related to lipid metabolism and gene regulation at the SREBF1 locus by combining methylation fine-mapping with bioinformatics strategies and analysis of public domain data for epigenomic marks of regulatory regions. Next, we will identify methylation-specific binding transcription factors and cofactors, using a highly efficient proteomics methodology. Through diverse approaches, such as reporter- and DNA-binding assays, genome-wide expression profiling and CRISPR genome editing, we will confirm methylation-dependent modulation of transcriptional activity of nearby and distant SREBF1 gene regulation through the identified transcription factors and cofactors. Finally, we will assess modulation of lipid-metabolism and disease specific phenotypes. We will uncover the mechanisms at the SREBF1 locus which are modulated by DNA methylation and ultimately contribute to increased blood lipid levels. Our in-depth analysis at the SREBF1 locus, the identification of relevant methylated CpGs, binding protein complexes, regulated genes and modulated phenotypes, may guide identification of previously unknown entry points for personalized intervention.

• DFG Programme: Research Grants
• Ehemaliger Antragsteller: Dr. Helmut Laumen, until 12/2020