Epigenetics reveals unexpected, and some identical, results

One study finds tissue-specific methylation signatures in the genome; another a similarity between identical twins in DNA’s chemical tagging

Tattoos on the skin can say a lot about a person. On a deeper level, chemical tattoos on a person’s DNA are just as distinctive and individual — and say far more about a person’s life history.

A pair of reports published online January 18 in Nature Genetics show just how important one type of DNA tattoo, called methylation, can be. Researchers at Johns Hopkins University report the unexpected finding that DNA methylation — a chemical alteration that turns off genes — occurs most often near, but not within, the DNA regions scientists have typically studied. The other report, from researchers at the University of Toronto and collaborators, suggests that identical twins owe their similarities not only to having the same genetic makeup, but also to certain methylation patterns established in the fertilized egg.

Methylation is one of many epigenetic signals — chemical changes to DNA and its associated proteins — that modify gene activity without altering the genetic information itself. Methylation and other epigenetic signals help guide stem cells as they develop into other types of cells. Mistakes in methylation near certain critical genes can lead to cancer.

The Johns Hopkins group has now shown that DNA methylation is more common at what they call “CpG island shores” instead of at the CpG islands that most researchers have focused on. CpG islands are short stretches of DNA rich in the paired bases cytosine and guanine, letters “C” and “G” in the genetic alphabet. Methyl groups attach to cytosine bases in DNA.

CpG islands are located near the start sites of genes and help control a gene’s activity. It’s been thought that planting a methyl group on an island declares the nearby gene off-limits, blocking activity.

Researchers have thought of methylation as a type of long-term memory, preserving environmental effects on genes long after those cues have disappeared, says Rolf Ohlsson, a geneticist at the Karolinska Institute in Stockholm.

Scientists have long suspected that differences in epigenetic marks shaped by environmental cues could account for why identical twins don’t look, behave or get sick exactly alike despite having identical genetic makeups. But no one had mapped out all the places, if any, where epigenetic marks differ between twins.

Now a team led by Arturas Petronis of the University of Toronto has explored all of the CpG islands dotting the genome to see which sport methylation flags. The team compared the methylation patterns of twins from monozygotic pairs — twins created when a single embryo splits. Although the twins had identical DNA, their methylation of CpG islands varied. But the methylation patterns in monozygotic twins were more similar than those in fraternal twins, who develop from separate eggs. And the group found that the amount of variation between monozygotic twins correlates with the time the embryo split: Counterintuitively, twins from an early-splitting embryo have more similar methylation patterns than twins from a later split.

Epigenetic patterns established in the early embryo are carried throughout life, with some differences introduced by the environment and others by random chance and error in replicating the patterns as a person develops. DNA is reproduced with high fidelity — mistakes happen in about one in a million bases — but the process of reproducing epigenetic patterns in dividing cells is more error-prone, with one in a thousand epigenetic marks going awry.
Petronis thinks the similarity between monozygotic twins results not from shared DNA sequences but from having come from the same embryo. “We don’t see any reason to think that the DNA sequence makes up the epigenetic profile,” Petronis says.

But swimming away from CpG islands may offer a different perspective. Andrew Feinberg, director of the Epigenetics Center at Johns Hopkins University in Baltimore, and colleagues embarked on a genome-wide tour to chart DNA methylation in different human tissues. The researchers had expected that each tissue would have a characteristic methylation pattern, indicating which genes are turned off and which are turned on to build a liver, spleen, brain or other tissue. Often researchers examine methylation only at CpG islands, but Feinberg says that most islands are surprisingly free of methylation in most tissues.

“We were always a bit skeptical of this island thing,” he says. So the team used a method that could reveal every place in the genome where a methylation flag was staked.

The team did find characteristic patterns in each tissue type, but not in CpG islands, where researchers expected. Methylation flagged DNA in liver, spleen and brain at thousands of places along the CpG island shores. The shores contained about 76 percent of the methylation flags shown to be characteristic of specific tissue types.

“This is a discovery that is totally unexpected,” says Ohlsson. Feinberg’s team has found “a signature of the genome that we weren’t aware of before.”

DNA in mouse tissues also has “shore” methylation patterns similar to those in corresponding human tissues. About 51 percent of the shores methylated in mouse tissues were also methylated in human tissues, indicating that DNA methylation of CpG island shores is an ancient, and important, method of controlling genes, Feinberg says.

When looking at colon tumors, the team found that methylation patterns in the shores of the cancer cells were more eroded than those in healthy colon cells. Feinberg says a breakdown in the patterns may cause colon stem cells to develop inappropriately, leading to cancer.

Unpublished research by Dag Undlien of the University of Oslo, done on sabbatical in Feinberg’s lab, indicates that monozygotic twins share more shore methylation patterns than fraternal twins do, and are even more similar than Petronis’ research suggests, Feinberg says.

Feinberg thinks evidence from his lab, though preliminary, indicates that DNA sequence does help determine epigenetic patterns. He calls Petronis’ report, “a terribly interesting paper,” but adds, “I think there may be a stronger genetic contribution than is suggested by his data.”

Regardless of who is correct, Ohlsson says that Feinberg’s discovery of CpG island shores will force scientists “to refocus our efforts to figure out what DNA methylation is doing.”
Tina Hesman Saey

Tina Hesman Saey is the senior staff writer and reports on molecular biology. She has a Ph.D. in molecular genetics from Washington University in St. Louis and a master’s degree in science journalism from Boston University.

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