ABOVE: Agouti Viable Yellow mice share the same DNA sequence, but have different methylation patterns.

WIKIMEDIA COMMONS, RANDY JIRTLE AND DANA DOLINOY

Brown and yellow mice nestle side by side in their cages in Anne Ferguson-Smith’s molecular genetics lab at the University of Cambridge. The mice are Agouti Viable Yellow, naturally occurring mutants, which, though genetically identical, have coats that vary in color—a phenomenon that researchers have long studied as an example of epigenetic inheritance.

All of the mutant mice have a gene, Agouti, that influences coat color, and an adjacent transposable element—a DNA sequence that can move about the genome, creating or reversing mutations—that promotes the gene’s expression. In the brown mice, this element is methylated and, therefore, silenced. But in the yellow mice, it isn’t methylated, meaning that these animals overexpress Agouti signaling protein in many tissues, leading to their yellow hue.

Importantly, Ferguson-Smith says, yellow mother mice tend to have yellow baby mice and brown mother mice tend to have brown baby mice, suggesting that the methylation mark—or lack of it—is passed down from generation to generation. This phenomenon has sparked scientists to hypothesize that other methylation marks on transposable elements can also be passed directly from parent to child, raising the possibility that parents’ diet, behavior, and experiences might affect future generations via this route.

The conceptual framework has already made its way into genetics textbooks, Ferguson-Smith says. “But in fact, the evidence for that is virtually nil.” In mammals, she explains, epigenetic marks are erased completely, and reprogrammed twice during the lifetime of an individual. The first wave of epigenetic erasure happens in primordial germ cells. Then the methylation comes back again in egg-specific marks and sperm-specific marks. And then, upon fertilization, that egg and that sperm meet and the marks are erased again. “So there’s two rounds of epigenetic reprogramming that occur in the germline that basically prevent any epigenetic marks from being transmitted from one generation to the next,” Ferguson-Smith explains. “People don’t seem to appreciate this.”

Epigenetic marks are erased completely, and reprogrammed twice during the lifetime of an individual.

To dig into the problem experimentally, Ferguson-Smith and her colleagues decided to rigorously test the idea that transposable elements act generally as gene promoters and that the methylation marks on these elements could be passed from one generation to the next. Researchers have postulated that transposable elements may have methylation marks resistant to reprogramming—so, in theory, these marks should be most likely to be inherited.

In a series of experiments examining the T cells and B cells of multiple generations of Agouti Viable Yellow mice, the researchers screened the animals’ genomes searching for transposable elements that were methylated similarly to the one that sits next to the Agouti gene. The screen identified dozens of these transposable elements but revealed that only rarely do they work as promoters to control the expression of adjacent genes. The methylation marks on these transposable elements are also wiped clean and reprogrammed after fertilization, the team found, meaning they can’t be directly passed from generation to generation (Cell, 175:1259–71.e13, 2018). “It’s hard to imagine how a memory of methylation can be transmitted from one generation to the next if it’s being erased and reestablished in each generation,” Ferguson-Smith says.

“This study is an enormous technical tour de force,” Dirk Schübeler, a molecular geneticist at the Friedrich Miescher Institute for Biomedical Research in Basel, Switzerland who was not involved in the study, tells The Scientist. In the past, researchers suggested that the epigenetically regulated Agouti trait was the tip of the iceberg for DNA methylation–based epigenetic inheritance, he says. “This study shows there is no iceberg.”

The screen did identify one transposable element that, like the element abutting the Agouti gene, displayed a bit of memory, Ferguson-Smith says, “but our data suggested that memory is not being conferred by DNA methylation.”

The researchers could see that methylation marks on this transposable element were erased between generations, and reestablished again in a form reminiscent of what was found in the parental generation. “So we asked, what might it be that causes that methylation to be reconstructed after erasure in the same way [in the next generation]?” Ferguson-Smith explains. “We think that it’s conferred by genetics.” The study results, she says, suggest that a particular sequence in the genome causes a specific methylation mark on a transposable element to reconstruct itself in the offspring in the exact same way it existed in the parent, and that such genetic sequences are adjacent to the transposable elements in the genome. So “non-genetic inheritance could, in fact, be genetic in origin,” she says.

Schübeler says the idea is perfectly possible, but more work needs to be done to understand exactly how the genetic mechanism underlying these epigenetic marks might work.

University of California, Santa Cruz geneticist Susan Strome, who was also not involved in the study, notes that even if the DNA methylation mode of non-genetic inheritance is rare, as Ferguson-Smith’s team suggests, it doesn’t mean all other modes of non-genetic inheritance are also rare. Modifications to histone tails, which Strome’s lab studies in worms, and small RNAs are passed down between generations and have epigenetic effects in at least some organisms, she says. “I would not extrapolate from the Ferguson-Smith paper to say that epigenetic inheritance is nearly non-existent.”