It was the best of times, it was the worst of times-one parental allele was transcribing like gangbusters and the other was permanently stalled. Each of us carries a set of genetically distinct chromosomes from mom and dad, and increasing evidence indicates that the two parental genomes also have widespread epigenetic differences. But how can researchers easily identify genes that show allele-specific differences in expression? With a new method that does not rely on SNP analysis, Andrew P. Feinberg and colleagues at Johns Hopkins University School of Medicine, Johns Hopkins Bloomberg School of Public Health, and NimbleGen Systems, Inc., developed a generalized strategy to distinguish parental epigenomes by allele-specific marks.
To identify genomic regions with euchromatin-associated marks, the investigators performed ChIP-on-chip with chromatin from a lymphoblastoid cell line or from freshly obtained T lymphocytes. The immunoprecipitating antibody was specific for histone H3 lysine-4 dimethylation (H3K4Me2), a widely used marker of active chromatin. To find heterochromatin, methylated DNA, a mark of inactive chromatin, from the same cells was analyzed by methylated DNA immunoprecipitation (MeDIP)-on-chip. Genomic regions with “double hits” for H3K4Me2 and DNA methylation were identified.
Overlapping euchromatin/heterochromatin-associated marks were enriched 5.4-fold in regions of known imprinted genes, and the double hits were on different parental chromosomes. Interestingly, the double hits usually occurred at sites of alternative or antisense transcripts. When the locations of known binding sites for CTCF (a insulator protein that has been linked to imprinted genes) were added to the analysis, the researchers observed that “triple hits” were enriched 76-fold in imprinted genes. Therefore, the triple hits were found to be very specific markers of allele-specific expression imbalance in the human genome. Check out the details in Genome Research, September 2008