Looking for Timebombs in the Genome — Retrotransposons & Epialleles

Buried in the mammal genome are more than a million virus-like stretches of DNA that epigenetic mechanisms work constantly to suppress — but once in a while, they slip up. If that happens nearby an important gene, it could mean physical changes, or even disease. And with bioinformatics and lab work, Muhammad Ekram and colleagues at Louisiana State University are trying to find out where these timebombs might be. They’ve found 143 candidates so far.

They’re working with mice in Joomyeong Kim’s LSU lab, but the virus-like DNA sequences — retrotransposons — make up a large chunk of the genomes of most mammals. In mice, they’re about 40 percent of the genome, and in humans they account for more than 50 percent. A handful of these unwelcome guests moves around from time to time — during early embryo development, for example — sometimes plopping down within one of the host’s genes or other sensitive locations, and creating genetic variation or even causing diseases.

Most of the stowaways are dead or inactive. And most of the time, cell mechanisms keep retrotransposon territory subdued by methylating particular histone proteins in the area, as well as CpG sites within transposons. But some retrotransposons aren’t always completely inactive, and they can play havoc with the host’s phenotype.

The mouse genes agouti and axin are well-known examples — they have mutant alleles in which the long-terminal repeat of a nearby retrotransposon triggers transcription that runs through to the host gene. The resulting protein is a fusion — such as a transposon-agouti protein — with a striking effect on some of the mice that carry it. “With the case of the agouti gene,” says Ekram, “depending on how much DNA methylation an IAP element [retrotransposon] has, the mouse gets a different phenotype — they have a change of coat color and develop obesity.” In the case of axin, they develop kinky tails.

But mice with these mutations don’t always have these traits — even when they’re genetically identical to mice who do. And best of all, it’s possible to affect the expression of these traits by altering environmental factors — specifically, the diets — of growing mice. These are the strange effects of metastable epialleles — genome locations where epigenetic marks aren’t consistent from individual to individual.

Ekram and colleagues suggest that these partly-subdued retrotransposons might be responsible for more than fat and kinky-tailed mice — they might control other traits or diseases in mice and humans, and they might even help explain why identical twins begin to look different over time.

There aren’t many known metastable epialleles like agouti and axin, though.  “Only those two alleles and another one,” says Ekram. “People really haven’t found a lot more of those, yet there are millions of retrotransposons in the genome. ” So, he and his colleagues decided to narrow down the list of metastable epiallele candidates.

With a list of the mouse genome’s long interspersed elements and long-terminal repeats — LINEs and LTRs, respectively — the team identified mRNAs from the UCSC Genome Browser that featured nearby transcription start sites. They trimmed the set down further by restricting it to LINEs and LTRs of a certain size, and containing at least three CpG sites. And then kept in the set only those retrotransposons known to be associated in embryonic stem cells and other cells with the “active” histone mark H3K4me3, as well as a lack of repressive histone marks at H3K9me3 and H3K20me3.

In the end, the researchers produced a list of 143 potential metastable epialleles. “We tested 13 of these and sequenced five of them in individual littermates, and even within that group, especially epialleles associated with [genes] Eps and Bcat — they tend to show quite a lot of variation between individuals.” The candidates offer good places to start looking for nearby disease genes, and if environmental exposures affect their activity, they might offer clues about why some mammals get certain traits or maladies as they age.

In upcoming research, “we’ll definitely try next-generation sequencing on more of those, says Ekram. “And if we get a handful more of these epialleles, we have a plan to test some diet-specific methylation variation, which people have already done with agouti and axin.”

Also, they’re already hunting for human equivalents. “We already got some isogenic DNA — from identical twins — and we’re trying to look at that too,” he says.

[The cartoon-y Boom! illustration by Flickr user thomashaugen is used here under a Creative Commons license.]

Ekram MB, Kang K, Kim H, & Kim J (2012). Retrotransposons as a major source of epigenetic variations in the mammalian genome. Epigenetics : official journal of the DNA Methylation Society, 7 (4) PMID: 22415164

This entry was posted in Applications, DNA Methylation, Histone Modifications, Transcriptome and tagged , , , , , . Bookmark the permalink.

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