It is one of the great mysteries of life: A tiny ball of identical cells implants itself in the uterus, and somehow, these cells begin to differentiate – each heading for a different fate. Ultimately, using the same “list of ingredients,” these cells will differentiate into the hundreds of diverse cell types it takes to make up a living being. Scientists recently opened a window onto that mystery by observing, in unprecedented detail, one of the chief ways in which these early cells begin to shape their identities, finding changes taking place even earlier than had been thought. The results of this research were recently published in Molecular Cell.

Dr. Yonatan Stelzer, a member of the Weizmann Institute of Science’s Molecular Cell Biology Department, explains that every cell in our body contains the same genome, but the epigenetics – changes on top of the genome that regulate the cell’s activities – differ from cell to cell. Epigenetic changes are especially crucial during prenatal development, since at any given time, numerous genes must temporarily be turned on while others are kept silent. During his postdoctoral research in the lab of Prof. Rudolf Jaenisch of the Massachusetts Institute of Technology (MIT), Stelzer had combined several advanced techniques to develop a method for tracking epigenetic activity in real time, with single-cell resolution. “For years we have had ‘reporters’ – DNA encoding glow-in-the-dark proteins -- that can track gene expression,” he says, “but until now, we have not had the same tools for epigenetics. The new technique is, essentially, a reporter we can insert into the genome to reveal its epigenetics, so we can now observe these changes – even minute ones – within single living cells.”  

Stelzer, Jaenisch and Yuelin Song, a PhD student in Jaenisch’s lab, in research conducted both at MIT and at Weizmann, investigated what is probably the most widespread epigenetic change to the DNA: the addition of a chemical tag called a methyl group, an alteration known as methylation. Methylation is mainly a means of silencing genes, and it starts quite soon after the early embryo reaches the uterus. Around the time the tiny ball of just 100 cells called a blastocyst is implanted, the cells’ genomes undergo drastic methylation. But in some regions, methylation appears to be less of an off switch and more of a “thermostat” – one that regulates the expression of certain genes. Recent research had suggested that many of these regions are enhancers – segments of DNA that act on other genes from a distance – and that these enhancers appear to be specific to genes for certain cell or tissue types. 

How do these enhancers produce their effect – specifically at the blastocyst stage? Stelzer and the MIT group inserted their new reporters into two enhancer sites in a mouse blastocyst and observed the process of methylation there.

Enhancer-gene interactions are mediated by a 3D loop; reporters (green and red lollipops) reveal these interactions

The mechanics of methylation at these sites turned out to be somewhat unexpected: Methyl tags were attached and after a short period removed by proteins, which then moved away, allowing the methyl tags to reattach. Remarkably, the reporter system allowed the researchers to capture, in precise detail, the effects of these changes on genes located far away. It appears that removal of the methyl tags promotes long, 3-D interactions between the enhancer regions and the genes under their control.  Methyl tag interactions with the two copies of the genes – one from each parent – were found to be unsynchronized; and the end result of this seemingly random activity was that the level of gene expression – the gene dosage – was different for each cell as sometimes one was silenced, sometimes both, sometimes neither. The researchers speculated that the expression of these enhancers – which then led to the further uneven expression of genes – was already priming a cell for a particular fate, even at this very early stage, when all the cells still appeared to be identical.

“The entire process of methylation and demethylation at the enhancer site, and the ensuing differentiation, turned out to be quite complex. We can now begin to put together the rather elaborate mechanics of the cell’s decisions in the very first days and weeks of embryonic development, including the activation of the various genes downstream from the enhancers, to understand how the potential of an embryonic stem cell – which can become any type of cell – is eventually narrowed down to a particular cell fate,” says Stelzer. “We were surprised to find that even as the blastocyst is just settling in – at a stage at which we had assumed the embryonic stem cells would still have their full potential – its cells are already beginning to close off some of their options.”

Dr. Yonatan Stelzer grew up on a collective moshav in the north of Israel and received his BSc, MSc and PhD from the Genetics Department of the Hebrew University of Jerusalem. In his postdoctoral research at MIT, he developed a new method of investigating the epigenetic changes to the genome – changes that are crucial for embryonic development, and which can, if they go wrong, lead to disorders or diseases or, later in life, to cancer.

Stelzer has been at the Weizmann Institute of Science since the end of 2017, and he and his team are currently researching epigenetics from several angles. “How a single cell in a blastocyst decides its fate – that is really one of the wonders of life, and we now have the tools to start understanding that mystery,” he says. “We are starting to fill in the cell lineage – from the first embryonic stem cells through the various stages of embryonic development.” Among the directions his research is taking is an investigation into the decision to become a germ cell – one that will ultimately become an egg or a sperm. These cells follow a unique developmental course that preserves the genome for the next generation, but with half the chromosomes of a normal cell.

Dr. Yonatan Stelzer's research is supported by the Benoziyo Fund for the Advancement of Science; the Helen and Martin Kimmel Institute for Stem Cell Research; the Jean - Jacques Brunschwig Fund for the Molecular Genetics of Cancer; the Hadar Impact Fund; Janet and Steven Anixter, JoAnne Silva, and  the Lester and Edward Anixter Family Foundation; and the European Research Council. Dr. Stelzer is the incumbent of the Louis and Ida Rich Career Development Chair.