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Decode Researchers Generate Map of Imprinting Patterns in Human Genome

NEW YORK (GenomeWeb) – A team led by researchers at Decode Genetics has mapped imprinting patterns within the human genome.

Some 160 human genes have been reported to be under the influence of imprinting, in which one parental allele is preferentially expressed over the other. During development, there are waves of demethylation and remethylation, but some regions escape this process and retain their parental methylation status.

Researchers led by Kari Stefansson of Decode, which is part of Amgen, and the University of Iceland combined whole-genome sequencing, oxidative bisulfite sequencing, and SNP genotyping to determine both the parent-of-origin phased haplotypes and the genome-wide CpG methylation status within an Icelandic population. From this, as they reported yesterday in Nature Genetics, the researchers generated a map of imprinted methylation and gene expression patterns, including ones at disease-linked loci.

"[O]ur observations support the view that imprinting is a more quantitative than categorical phenomenon, having nuances that are yet to be fully explored," Stefansson and his colleagues wrote in their paper.

The researchers turned to their cohort of Icelandic individuals — 150,000 Icelanders out of a total population of 320,000 have undergone genotyping — to tease out haplotype phases. They also sequenced the genomes of 15,200 individuals and used the genotyping information they had plus the Icelandic genealogical record to determine parent-of-origin phased haplotypes.

At the same time, they conducted oxidative bisulfite whole-genome sequencing of peripheral blood samples collected from 200 individuals to determine genome-wide methylation status. When combined, the researchers could determine the phase and parent of origin for each read and any methylation sites it contained.

In all, they uncovered 229 parent-of-origin differentially methylated regions, 64 of which overlapped with previously reported regions and 165 of which were novel.

Some of these regions map to regions previously linked to Prader-Willi syndrome and Angelman syndrome, both rare conditions caused by the loss of parts of paternal chromosome 15. A previous report had noted parent-of-origin methylation preferences in this region on chromosome 15, and the Decode researchers found that maternally methylated regions tended to be near regulatory regions like promoters or transcription start sites, while paternally methylated regions were spread more broadly.

When the researchers compared these methylation patterns to the methylomes of sperm cells, oocytes, and blastocysts, they found the majority of the PWS/AS parent-of-origin differentially methylated regions were highly methylated in sperm. However, much of that methylation was lost by the blastocyst stage, though later re-instated.

Based on this, the researchers determined that the paternally methylated regions were actually established somatically, and they further noted that these regions exhibited a pattern consistent with stochastic methylation.

Other novel parent-of-origin differentially methylated regions fell outside the PWS/AS region. Some mapped near other reported parent-of-origin differentially methylated regions or near genes with a known imprinted expression pattern or near promoters, transcription start sites, heterochromatin, and CpG islands. These parent-of-origin differentially methylated regions showed a methylation pattern during development that was distinct from that of the PWS/AS region: most were maternally methylated, the researchers noted.

Meanwhile, the researchers performed RNA-seq on blood samples from 6,800 individuals to search for parent-of-origin allele-specific expression and related that to methylation changes. They uncovered 137 genes with parent-of-origin allele-specific expression, 128 of which they then replicated in a separate cohort. Ninety-nine of these were close to a parent-of-origin differentially methylated region, they reported.

They also examined an in-house database to search for SNPs whose effects differed by parent of origin to find links at DLK1/MEG3 and GNAS, genes linked to imprinting disorders. For instance, the GNAS rs425881[A] allele increases thyroid-stimulating hormone levels when it is inherited maternally, the researchers found, but decreases levels when it is paternally inherited.

The researchers noted that the novel parent-of-origin differentially methylated regions and parent-of-origin allele-specific expression they found have smaller effects than those uncovered previously. "These smaller differences may indicate that imprinting is confined to subsets of cells or particular cell types," they wrote.