Genetic determinants of inter-individual variations in DNA methylation

DNA methylation and histone modifications are epigenetic mechanisms that affect the chromatin structure and thus the readout of the underlying DNA sequence. Hence, variations in the DNA methylation profiles of individuals may contribute to phenotypic differences and disease susceptibility. However, the extent of such epigenetic variations is unclear. With regard to DNA methylation, little is known on how these differences are established or inherited. This thesis was concerned with elucidating the role that genetic determinants play in maintaining specific DNA methylation patterns. Two common inbred mouse strains (C57BL/6 and BALB/c) were used to address inter-individual variations in DNA methylation. Little is known about trans-acting epigenetic modifiers that control the epiphenotype at distinct target loci. Therefore the presented work focussed primarily on the identification of the trans-acting epigenetic modifier regulating the strain-specific DNA methylation pattern at the Isoc2b promoter. It could be demonstrated that the DMR is established during early embryonic development in BALB/c, but not in C57BL/6. The DMR could further be found in other inbred mouse strains. Using embryonic stem (ES) cell differentiation models, the strain-specific DNA methylation patterns were also detectable in vitro. Linkage analysis in C;B6 backcrosses narrowed down the genomic localization of the modifier to a highly repetitive 9 MB region on chromosome 12. To further characterize the epigenetic modifier gene, complementation assays with BAC clones covering the candidate regions as well as expression analyses (RNA-seq) in the in vitro ES cell differentiation models were performed. The latter identified Nol10 as a candidate gene to propagate the observed strain-specific epiphenotypes. Additionally, novel candidate DMRs based on strain-specific patterns of active histone modifications were selected and validated to identify additional trans-regulated DMRs. In future, the investigation of DMRs will be extended, since to date only novel cis-regulated DMRs have been discovered. Further characterization of the potential epigenetic modifier Nol10 might provide fundamental insights into mechanisms that establish DNA methylation patterns during embryonic development and how inter-individual differences can be introduced.