Aberrant imprinting in humans: Application of genomewide approaches to better understand imprinting regulation and its disturbances

• Applicants: Professor Thomas Eggermann, Ph.D.; Dr. Florian Kraft
• Subject Area: Human Genetics
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 497659591

Imprinting disorders (ImpDis) comprise congenital diseases which are characterised by disturbances of parentally imprinted genes. These genes are expressed either from the paternal or the maternal allele, and the disturbances consists of both genomic and epigenetic alterations. The clinical diagnosis of ImpDis is often hampered by the lack of clinical specifity, as the symptoms can overlap. ImpDis are caused by four different molecular changes: Three of them represent classical molecular changes, but epimutations comprise DNA modifications (e.g. 5-methylcytosine). The causes of epimutations are unknown in the majority of cases, but molecular alterations in imprinted regions themselves (cis factors) as well as in other genomic regions (trans factors) probably play a role. However, systematic approaches are currently missing, due to technical limitations as well as the rareness of ImpDis. With the implementation of NextGenerationSequencing and Longread-Sequencing techniques suitable assays are now available fort he comprehensive analyses of genomic, structural, epigenetic and transcriptional factors of epigenetic regulation and ist disturbances. This proposal combines second and third generation sequencing approaches with a unique cohort of patients with 11p15.5 and 14q32 epimutations to address genomic and epigenetic variations at allelic resolution in protein and nonprotein coding regions. The strategy to identify the molecular basis of ImpDis includes (a) Genome-wide analysis of methylation in carriers of 11p15.5 and 14q32 epimutations to identify multilocus imprinting disturbances (MLID) and to discriminate ImpDis subgroups. (b) Identification of genomic variants in cis and trans factors causing both MLID and isolated epimutations. (c) Determination of allele-specific methylation patterns on single molecule level over long distance covering whole differentially methylated regions at once. (d) Characterization of large structural variants to identify new regulating elements. Altogether, we aim to identify factors and functional genomic regions which regulate genomic imprinting and the expression of imprinted genes. We will both determine epigenomewide patterns of aberrant methylation as well as chromosomal regions and factors involved in the regulation of imprinting in the same assays. The analysis will not be restricted to specific genomic regions but the proposal will cover whole genomes of both the patients and their parents. In combination with transcriptome data functional consequences of disturbed imprinting can be delineated. This approach will help to understand the pathoetiology of ImpDis, but it will also be translationally used for clinical management of the patients.

• DFG Programme: Research Grants