Leaving an Imprint

But despite Reik’s enthusiasm, Jaenisch turned him down. “He told me he didn’t want any medics [in his lab]. He knew full well what he was talking about, since he was a medic himself. I think he thought medical students thought PhD research was a sideline that they didn’t take too seriously.” In the end, Reik’s persistence managed to persuade Jaenisch to take him on. “Maybe it’s because I just wouldn’t leave,” he says.

“In the mammalian field, the imprinting field, together with the X-inactivation field, was the birthplace of epigenetics.”

Reik found he enjoyed doing hands-on experiments. Jaenisch’s lab (which has since moved to the Whitehead Institute) had already demonstrated a link between de novo methylation in the mouse embryo genome and inhibition of gene expression. With his postdoctoral work, Reik became an early contributor to the burgeoning field of epigenetics. Thirty years later, he continues to work on the dynamics of epigenetic changes, the role of reprogramming in stem cells, mouse development, and transgenerational inheritance of acquired epigenetic marks.
Here, Reik describes one of his eureka moments, how he converted a farm shed into a molecular biology lab, and how his lab-management philosophy combines lessons learned from two of his scientific mentors.

Reik Rises

The scientific method? Reik’s father is a theoretical physicist who, Reik recalls, worked sitting at his desk with a pencil in hand. “When I was a boy, this was how I thought science worked. I was never exposed to experimentation as science until I started my PhD, which was not even a proper PhD,” says Reik. “I think this is partly where this idea came from, for me, that you can solve many problems by thinking.”

High hopes. Reik, a native of Freiburg, Germany, grew up with many interests other than science, but he chose to focus on medicine, first for two years at the University of Freiburg and then at the University of Hamburg. “I enrolled in the medical program not because I was so much interested in the patient angle, but because I thought of medicine as a broadly scientific and humanities discipline where I could combine my different interests,” says Reik. But in reality, medicine turned out to be less intellectually exciting than he expected.

In on the ground floor. Captivated by the new tools of molecular biology, Reik spent two years doing the equivalent of a PhD thesis. “This was in the early 1980s when the molecular biology revolution was just beginning. You could cut DNA and ligate it back together to make new molecules and manipulate the genome. I caught that excitement by going to lectures and then I thought I could do an MD that was like a PhD, because this sounded really cool.”

A better protocol.  Work in Jaenisch’s lab had previously shown that the expression of retroviruses integrated into the mouse genome depended on where the viral integration occurred—a phenomenon called position effect. Reik’s project was to clone the viral DNA back out of the mouse genome to identify the murine genes adjacent to the insertion point. “I was using the cloning method established in the lab, and again, got slightly bored with the project—I have a great capacity to get bored easily!” To keep himself interested, Reik invented a novel way of altering a retrovirus to make the cloning process easier, by adding an easy-to-select-for bacterial DNA sequence.

Eureka moment. Although Reik was now fully committed to research, he completed the required medical school exams and one year of hospital rotations. At the same time, he shopped around for a postdoc position. Influenced by those researchers in Jaenish’s lab working to decipher how DNA methylation is used to establish heritable gene expression, Reik knew he wanted to study mammalian embryo development. “It was clear to me that it needed to be in the U.K. because that was where the key people were. I went on a lab tour and still couldn’t make up my mind about which lab to join. Then a friend from Hamburg went to do a postdoc with Martin John Evans and told me I must come and speak with Azim Surani at the University of Cambridge who was working on something completely crazy.” Surani and colleagues had discovered the phenomenon of genomic imprinting: epigenetic marks silence certain maternally or paternally inherited genes so that only the gene copy from one parent is expressed. At the time, only about three laboratories were studying this new concept. “As soon as I talked to Azim, I was completely sold. This is the kind of eureka moment I was waiting for. I find it hard to make decisions, so I wait for these moments of inspiration to happen to me. Azim introduced me to this world of how paternal and maternal genomes are different—that was inspiring,” Reik says.

Reik Runs with it

The lab next to the barn. Surani’s laboratory at the AFRC Animal Research Station was located on a farm just outside of Cambridge, U.K. The differences between Jaenisch’s cutting-edge molecular biology lab and the Surani lab were stark, says Reik, who arrived in Cambridge in 1985. “What you saw immediately when you arrived were horses, sheep, and goats. This was work on large-animal physiology and reproduction. Azim took me to an empty room on this converted farm and said, ‘This is our molecular biology lab.’ It was a bit of a shock.” Reik’s first task, along with graduate student Nicholas Allen, was to get a molecular biology lab up and running. Experiments by Surani’s group using reconstituted mouse eggs had suggested that the maternal and paternal genomes in the egg and sperm were modified differently, and he tasked Reik with figuring out the molecular mechanism. “Maybe I should have run away at that point,” says Reik, laughing. “It was scary and exciting at the same time.”

Marked by methylation. Reik set out to identify what distinguished the maternally and paternally contributed genomes in the developing mouse embryo. Because of his exposure to DNA methylation of genes in the mouse embryo in Jaenisch’s lab, he quickly added methylation as a key candidate mechanism for imprinting. “The reason is that the imprinting mark needed to be deposited at a specific point in development and it needed to be mitotically heritable and reversible. DNA methylation fit all the criteria. We thought if we inserted transgenes into the mouse genome at random locations, that one would fall into one of the imprinted regions and would be influenced by the imprinting.” Reik and colleagues compared the DNA methylation patterns of transgenes inherited from mothers or fathers and found that methylation patterns of a particular transgene were dependent on parental inheritance. This methylation pattern was reversed during subsequent germline transmission to the opposite sex, suggesting that DNA methylation was a way to mark heritable differences in maternally and paternally inherited genes.

Epigenetics, validated. “These experiments put the first molecular flesh on to the idea of imprinting. This gave confidence to the field, and some years later, the first imprinted genes were discovered and, later, that methylation was indeed marking these imprinted genes. That was basically the beginning of epigenetics, so to speak, which also has a root in plant biology. But in the mammalian field, the imprinting field, together with the X-inactivation field, was the birthplace of epigenetics.”

Reversibility. In 1987, Reik received a five-year fellowship from the Lister Institute of Preventive Medicine to start his own lab in the U.K. at the Institute of Animal Physiology in Cambridge, soon renamed the Babraham Institute. Still there, he continues to work on how imprinted genes are regulated and what roles they play in normal development and in human diseases such as Beckwith-Wiedemann syndrome, a developmental growth disorder. In 2000, Reik’s lab collaborated with his former postdoc, Jörn Walter, then a lab head at the Max Planck Institute for Molecular Genetics in Berlin, to demonstrate that reprogramming of DNA methylation occurs in the zygote. “We had a view that epigenetic markers were very stable once introduced. But now we discovered that some of the epigenetic marks could be reprogrammed immediately after fertilization in the zygote. This was a very unexpected discovery.” This area of epigenetic reprogramming was expanded in Reik’s lab particularly by two of his long-term colleagues, Wendy Dean and Fatima Santos.

Years later, using whole-genome sequencing, graduate students Stefanie Seisenberger, Christian Popp, and Julian Peat mapped the dynamics of reprogramming DNA methylation in mouse germ cells. “We discovered that the vast majority of the epigenetic marks are erased after fertilization and also in the primordial germ cells. This is incredibly important, to erase the memory of the previous generation and to regain pluripotency of embryonic stem cells.” The marks that are not erased may provide the potential for transgenerational epigenetic inheritance, “an elusive phenomenon that people are incredibly excited about now,” says Reik.

What grandma ate. Focusing on the physiology of imprinted genes, Reik’s lab demonstrated in 2002 that imprinted genes are necessary for placental growth and modulation of nutrition to the fetus. Tied to this, there is also evidence that manipulating the nutritional status of the fetus can have generational repercussions, including obesity, diabetes-like syndromes, and other nutritionally tied phenotypes in offspring over multiple generations. “It’s still a question whether this transmission is caused by epigenetic marks, which can sometimes resist reprogramming. And for the first time we can address this question properly because now we have the technologies to look at the epigenetic marks in the germ cells all at once by sequencing.” In 2014, Reik contributed to a study from Anne Ferguson-Smith’s lab at the University of Cambridge and Mary-Elizabeth Patti’s lab at the Joslin Diabetes Center in Boston that showed that an adverse nutritional environment during gestation may have metabolic consequences in the next generation in part through altered epigenetic marks in sperm.

New frontier. As part of the Sanger Institute–EBI Single Cell Genomics Centre, Reik, with Gavin Kelsey and other colleagues, is developing single-cell whole-genome methylation sequencing methods and a new, not-yet-published technique to map both DNA methylation and the transcriptome from the same single cell. “RNA sequencing is already quite routine in single cells, and also genome sequencing to some extent, but genome-wide epigenetics is very much cutting-edge stuff. We can now identify epigenetic heterogeneity between individual cells and new cell populations that we couldn’t see before. We are discovering how in early embryos, heterogeneity is being created by epigenetic systems, perhaps on purpose to create cell diversity.”

Reik Ruminates

Cultural differences. “One of the key reasons why I am still in the U.K. is the collegial atmosphere and flat hierarchical structure that I enjoy very much. In Germany, it was very hierarchical. In Britain, you can knock on a Nobel Prize winner’s door and the person will have a chat with you over a cup of coffee.”

Best of both worlds. “I see it as beneficial that I had two very different mentors,” says Reik. “Rudolf is very excitable and his mind works super fast. In the middle of a conversation he is ready with the next 10 experiments that need to be done. Azim is very different, reflective. He would think about a problem many times and come back almost to the beginning but not quite and do another loop. I think I took and learned things from each, and I am trying to combine the best things I’ve learned to my own way of teaching, motivating, and mentoring people.”  

Continuous education. “What you assume when you start your own lab is that everyone is the same. But people are not the same in how they learn, communicate, or need to be mentored. One of the most important things is creating a community sense for your group. There are some people that are naturally good at this, but this takes quite a time for most of us to learn. I’m still learning how to give people a sense of freedom, responsibility, and ownership so they find the research fun and productive.”

Sharing a moment. “One of my proudest moments was when I was elected to the Royal Society in 2010 and my father was able to come to the celebration. As a scientist himself, I think he was very proud of that.” 

Greatest Hits

• As a postdoctoral fellow, contributed to the discovery of the molecular mechanism of genomic imprinting by DNA methylation
• Identified an imprinted gene that controls placental nutrition supply to the developing fetus
• Provided evidence that noncoding RNA and the looping of chromatin control epigenetic switches of imprinted genes
• Discovered global epigenetic reprogramming in germ cells and early embryos and its link with pluripotency
• Using genomic sequencing, quantified the extent of methylation reprogramming in germ cells, suggesting the potential for limited transgenerational epigenetic inheritance