Islands and shores are always on the mind at this time of the year, but just because winter is coming doesn’t mean we need to put the rest of the CpGenome on the shelf. CpG Shores might be the regulatory master of CpG Islands but new features keep emerging, like CpG Canyons, and now a new sub-type of CpG Islands is coming at you from the lab of Paul Pavlidis at the University of British Columbia: CpG Ravines.
Inspired by the the fact only a fraction of the variance in gene expression correlates with the methylation status of CpG islands, the team mined 30 publicly available projects for gold that wasn’t solely on an Island (using 1,737 samples).
Here’s what this master of a meta-analysis dug up:
- 15,224 (out of >450K) CpGs are ‘ultrastable’ across tissues and developmental stage (974 always methylated and 14,250 always unmethylated).
- By looking into these ultrastable CpGs they identified a brand spankin’ new subset of CpG Islands, which they coined as CpG Ravines.
- CpG Ravines show a consistent pattern of low methylation in their Islands, with highly methylated flanking shores and shelves.
- CpG Ravines can be distinguished from other CpG Islands by a broadly flanking region of low methylation.
- CpG Ravines are associated with a higher level of gene expression and usually regulate housekeeping genes.
Ultimately, this report provides some additional strong support for the regulatory role of CpG sites flanking CpG Islands.
First author Rachel Edgar concludes that “CpG island ravines are a feature of the human methylome that fit well with what is already know about methylome topography. The characteristics of ravines are further evidence of how essential it is to look at regions beyond the CpG island and take the methylation of individual CpGs in the context of the surrounding methylome features.”
Take a closer look at the latest CpG Ravines in Epigenetics & Chromatin, November 2014