Video: Methylation Profiling in Uniparental Tissues Identifies Novel Imprinted Genes




Roche NimbleGen Webinar Series show

Summary: One of the major features associated with imprinting is the presence of parent-of-origin specific Differentially Methylated Regions (DMRs). Thus, the maternal and paternal genomes possess distinct epigenetic marks which distinguish them at imprinted loci. In order to construct an imprinting map of the human genome, we have profiled DNA methylation patterns genome-wide in rare uniparental tissues. For genome-wide studies, we have compared methylation patterns in a panel of complete hydatidiform moles, which have an exclusively paternal genetic contribution, and ovarian teratomas, which have an exclusively maternal genetic contribution. Methylated DNA was immunoprecipitated using anti 5-methyl cytidine and hybridized to Nimblegen high-density oligonucleotide tiling arrays composed of 21 million probes distributed throughout the genome, generating complete profiles of the maternal and paternal methylomes. Comparison of these profiles identifies numerous sites of methylation difference, including sites of methylation polymorphism, novel imprinted loci, and also tissue specific differences. Examination of known imprinted genes showed that many are associated with DMRs, validating this as a system for the detection of imprinting. Many novel putative imprinted loci on nearly every human chromosome were also identified. These include novel DMRs within known imprinted gene clusters, as well as chromosomal regions not previously thought to be imprinted. In order to identify novel imprinted genes specifically on chromosome 15, we have also profiled DNA methylation in cases with uniparental disomy of chromosome 15 (UPD15). Comparison of six individuals with maternal versus paternal UPD15 reveals fourteen DMRs on chromosome 15. Some novel DMRs are located outside of 15q11-q13, and are associated with genes not previously thought to be imprinted, including IGF1R at 15q26.3, which plays a fundamental role in growth regulation. To validate our array data we performed bisulfite sequencing of putative DMRs, giving base-pair resolution of these imprints and confirming the presence of parent-of-origin specific methylation marks in multiple independent samples. Our data provides the first imprinting map of the human genome, demonstrates that the number of imprinted loci in the human genome is much higher than previously thought, and suggests that imprinting may influence the phenotypes of many human diseases.