The genetic code in mammals may have gained another letter—or at least a significant footnote. Textbooks speak of four DNA building blocks, whose order specifies genes. But researchers in the field of epigenetics have also identified four chemically modified versions of these nucleoside bases, which affect how genes are expressed. Three of them are altered versions of cytosine, one of the original four bases. The last, methylated adenine, is mired in controversy about whether it exists in mammals.
Now, researchers at Yale University have not only identified plenty of this modified base in mouse embryonic cells, but also found it plays a key role in the development of the placenta. The methylated base—methyladenine for short—gives cells another epigenetic tool for turning genes on or off during normal development or in disease. “This is a very important study for our understanding of the role of [methylated adenine] in gene regulation,” says Peng Jin, a geneticist at Emory University who was not part of the work.
Animal cells often add methyl or other chemical groups to a cytosine to help switch a gene on or off, whereas bacteria rely heavily on methylation of adenines. But in the past 5 years, researchers have also detected methyladenines in fruit flies, nematode worms, and frogs. Hints of the modified base also turned up in mammals. “If [they] exist, it’s an exciting new layer of biology,” says Eric Greer, an epigeneticist at Harvard University.
But the reported levels were minuscule, and Greer and others found that many “detections” were the result of bacterial DNA contaminating samples, equipment, and even commercially available enzymes used in experiments. “It’s difficult to rule out contamination by bacterial DNAs,” agrees molecular biologist Ying Liu of Peking University, who has studied methyladenine in nematodes.
In addition, an antibody sequencing technique that the new study and others have used is often not specific enough to isolate these bases, picking up methylated adenines in RNA as well as in DNA. “The reality is, the techniques we have are not robust enough,” says Colm Nestor, a molecular geneticist at Linköping University.
But Yale epigeneticist Andrew Xiao persisted. In 2018, his team found methyladenine in high amounts in human glioblastoma cells, where it seemed to affect the growth of this brain cancer. The researchers showed that when they inhibited a protein that removes adenine’s methyl groups, causing methyladenine to accumulate, tumor growth slowed.
Earlier this month in Nature, Xiao, epigeneticist Haitao Li at Tsinghua University, and their colleagues reported that they have found the modified base in normal mouse cells: the trophoblast stem cells, which eventually give rise to the placenta. The methyladenines are prevalent at places in DNA called M/SAR regions, which help create temporary “compartments” dividing active and inactive regions of the genome. As these compartments form, DNA’s double helix unwinds briefly.
Using the antibody sequencing methods and taking precautions to avoid the known specificity issues with methyladenine, Xiao and his colleagues discovered that methyladenines in unwound DNA prevent the binding of the SATB1 protein needed to rewind the DNA. The unwinding in turn blocks the expression of genes that would make trophoblast stem cells differentiate and stop growing. Instead, the cells multiply, ensuring there are enough of them to make the full placenta. Later, the methyls are removed—the researchers don’t know how—and the cells start specializing to make the placenta.
The same process may govern placental development in humans—and disrupt embryonic growth and development when it goes awry—says Indira Mysorekar, a reproductive biologist at Washington University School of Medicine in St. Louis. “The paper is exciting.”
Researchers pursuing methyladenine also see it as vindication. “It provides one of the best supports so far of [the importance of methyladenine] in a mammalian system,” says Chuan He, a biochemist at the University of Chicago. In the May issue of Molecular Cell, his group reported that methyladenine increases more than 1000-fold in mammalian mitochondrial DNA when cells are starved of oxygen—an earlier hint that it plays a biological role.
Nestor admires Xiao’s careful experiments, but stresses that “the devil is in the details.” Methyladenine, he says, “could be one of the epigenetic discoveries of the last few decades, or it could be just a cautionary tale,” about researchers being too hopeful when contamination and imprecise methods prevail.
But even if the discovery is confirmed, Peng says he is leery of calling the modified adenine an addition to the genetic code. “Maybe [part] of the ‘epigenetic code’ instead?”