An ancient battle is being played out in the DNA of every embryo

The new paper is the result of Herculean computer analyses, involving researchers in Germany, Spain and the UK, to better understand the role ancient retroviruses play in early embryonic development – how they harm and how they help. It grew out of work Singh had done as a doctoral student at the Max Delbrück Center in Berlin, when he brought together datasets from 11 studies to painstakingly trace individual embryonic stem cells from fertilization to implantation.

He performed an analysis that grouped the cells based on the similarity in their gene expression. Most have been grouped according to genetic markers that determine their fate within the growing embryo – for example, whether they will become part of the ectoderm, the precursor to skin and brain cells, or the endoderm, which develops into the respiratory and digestive tissues.

But one cluster seemed marked for no future. Instead, they had the signatures of DNA damage and precursors to apoptosis, a controlled mechanism the body uses to eliminate stressed or damaged cells. This damage, Singh suspected, was LINE-1’s calling card. Singh’s team dubbed these damaged cells “REjects,” a nod to their cause of death: RE for “retroelements” like LINE-1, “rejected” from the growing embryo.

On the embryo’s fifth day after fertilization, Singh’s team discovered that the self-destructing suckers still exist alongside the healthy cells they will sacrifice themselves to protect. But the surviving cells express something that the REjects do not: HERVH. Despite being another former invader, HERVH actually delete LINE-1, protecting pluripotent cells from damage and ensuring they can continue to divide. “It’s kind of a romantic relationship,” Singh says. “These retroviruses had invaded to kill the system, and now they are working to protect the system from other retroviruses.”

The five-day-old embryo is surrounded by an outer layer of cells that will soon become the placenta. LINE-1 is also active in these cells, but unlike suckers, they do not die. Singh suspects that because the placenta lasts only nine months, rather than a lifetime, its cells don’t last long enough for significant DNA damage.

These findings are “remarkable,” says Ware. But drawing firm conclusions about embryonic development in the womb based on a laboratory study is tricky. While the expression of LINE-1 and HERVH seemed to be mutually exclusive—rejectors expressed LINE-1 and not HERVH, and vice versa for surviving cells—these researchers had no way of finding direct evidence that HERVH LINE-1 control, explains Cédric Feschotte, specialist in molecular biology and professor of genetics at Cornell University who did not participate in this study. Ware adds that it’s also unclear if the suckers are just garbage or if they play a functional, albeit brief, role in the developing embryo.

Embryonic stem cell research is also difficult to do because it is ethically burdensome. Many regions don’t allow it, and in those that do, researchers rely on leftover embryos, frozen at around five days old, donated by parents after having had a successful IVF cycle. Since these embryos are observed outside the parent’s body, the researchers “can’t quite rule out that some of the results are an artifact of in vitro culture,” says Feschotte.

With the introduction of synthetic embryos three-dimensional balls of cells derived from stem cells rather than sperm and eggs, Feschotte thinks scientists might be able to answer some of these lingering questions.

Singh says the ability to select pluripotent cells from REject cells within the early embryo will be critical for researchers studying regenerative medicine, who need to be able to grow different types of body tissues in order to create models of disease laboratory. Identifying potential causes of embryonic cell damage also expands our understanding of early pregnancy. Perhaps one day, Feschotte says, monitoring LINE-1 expression levels in growing embryos at fertility clinics could help explain very early losses at the implantation stage.

But more than anything, these discoveries show that the genome is not just an instruction manual but an entire ecosystem. “There are interactions between prey and predators,” Feschotte explains. “All of these really complicated biological interactions, they all happen in the genome.”

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