Description

Genomic imprinting is the small set of exceptions to the rule that both copies of a gene are expressed. At an imprinted locus only the maternal or only the paternal copy is active, and which one it is was decided in the germline of the parent that passed it on. The instruction is carried by DNA methylation: one allele has methylated CpG sites and the other does not, so the two copies look different to the transcription machinery even though their sequence is the same. The regions that hold this asymmetry are called imprinting control regions, and a single one can govern the expression of a whole cluster of neighboring genes. Losing or gaining methylation at these regions is the cause of several developmental syndromes.

This collection brings together annotations that mark imprinted loci and the allele-specific methylation that defines them.

Subtracks

• Monk iDMRs — 50 imprinted differentially methylated regions recommended by Monk et al. for reporting methylation changes in clinical diagnostics, with their nomenclature, aliases and germline origin.
• Mackay iDMRs — 48 imprinted differentially methylated regions from the joint statement on multi-locus imprinting disturbance, classified as clinically associated or non-clinical and linked to the imprinting disorders they are involved in. A more recent counterpart of the Monk list.
• OMIM Genes — the genes that the OMIM staff curate as imprinted or candidate imprinted, published through OMIM's GeneScout tool. The two are not distinguished in what OMIM publishes.
• Geneimprint Genes — the genes that Geneimprint curates as imprinted or candidate imprinted, colored by which parental copy is expressed.
• MethBase2 ASM — for every CpG site, the fraction of MethBase2 human methylomes in which the site was part of an allelically methylated region. Peaks mark candidate imprinting control regions.
• Akbari iDMRs — 192 imprinted differentially methylated regions that Akbari et al. compiled from five genome-wide studies, colored by which parental copy is methylated.
• Rosenski ASM — three annotation sets from a survey of allele-specific methylation in about 40 purified cell types: regions whose methylation follows the parent of origin, known control regions with their boundaries redrawn, and the much larger pool of regions carrying two methylation states that these were drawn from.
• Kim DMRs — regions where methylation differs between the maternal and the paternal haplotype in 123 trio-phased genomes of the Human Pangenome Reference Consortium, colored by the parent whose copy is more methylated.
• Kim DMCs — the maternal minus paternal methylation difference at the individual CpG sites behind those regions.

The first five sets above are gene or region catalogs assembled from the literature, so they overlap by design: a gene called imprinted by OMIM is usually also in Geneimprint, and its control region is usually among the Akbari iDMRs. The Rosenski ASM annotations are different in kind, since their regions were called from sequencing data rather than collected from papers, and most of them have never been linked to imprinting.

DNA methylation itself is annotated elsewhere in the browser rather than here. The Kaplan lab human methylation atlas, which gives methylation and unmethylated regions for a large panel of purified cell types, is a separate track: Human Methylation Atlas Summary, under DNA Methylation.

Color Conventions

The tracks that name a parental copy use the same two colors:

What is being marked differs by track, because the sources annotate different things: Geneimprint names the copy that is expressed, while the Akbari and Monk iDMR tracks name the copy that is methylated, and the Kim DMRs name the copy with the higher methylation. So H19 is red in Geneimprint and blue in the iDMR tracks, and both are correct. Each track page states which copy its colors refer to, and adds any categories that only it uses. In Geneimprint, genes with the status Predicted are gray and genes with no parent of origin are black. The OMIM track does not state a parental copy and is drawn in black. The Rosenski ASM tracks use the same red and blue for the oocyte and the sperm gamete, in which the methylation is established.

Data Access

Each subtrack has its own description page with the details on how the data was made and how to download and intersect the annotations. Use the links above.