Profile of Patrick Cramer

Patrick Cramer’s interest in the scientific method may have been sparked by a childhood gift. While growing up, his parents gave him a kit to try little experiments at home that inspired him to become a scientist.

Patrick Cramer. Image credit: Patrick Cramer.

Cramer studied chemistry, first at the University of Stuttgart and later at Heidelberg University in Germany. “I was in love with the beauty of biological molecules, so I moved into biochemistry and then into structural biology,” says Cramer. This move was facilitated by stints at the University of Bristol and Cambridge University. “At Cambridge I really fell in love with structural biology, and so I chose that as a subject for my PhD studies at the European Molecular Biology Laboratory,” he says.

At the European Molecular Biology Laboratory in Grenoble, France, Cramer began to study gene transcription, launching a career unraveling the mysteries of this fundamental biological process. Cramer has determined the three-dimensional (3D) structure of transcription complexes, providing numerous insights into the mechanisms of transcription initiation, elongation, and regulation. He has also contributed to the development of functional genomics and computational biology to study how the genome is transcribed and regulated in living cells and understand how gene activity is controlled.

Now director at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, Cramer was elected to the National Academy of Sciences in 2020. In his Inaugural Article (1), his team describes the first structures of the highly conserved transcription factor TATA-box binding protein (TBP) in complex with a nucleosome.

Structure of RNA Polymerase

When Cramer received his doctorate in 1998, a major question about transcription was the structure of RNA polymerase II, the central enzyme that makes messenger RNA. To work on this problem, he joined Roger Kornberg’s laboratory at Stanford University as a postdoctoral researcher, funded by a fellowship of the German Research Council. “That time was wonderful because we could indeed solve the structure of the polymerase, which was important for Roger receiving the 2006 Nobel Prize in Chemistry for the structural basis of transcription,” says Cramer. He still recalls the wonderful moment when, one early morning, working at the synchrotron, he realized that the problem could be solved. He treasures the articles in Science in which he and his colleagues first described these findings (2–4).

Cramer received a tenure-track professorship in biochemistry at the Ludwig Maximilian University of Munich in 2001, where he continued to study transcription. “When I started, some colleagues asked, ‘Now that transcription is solved, what are you going to do?’” he remembers. “But it was actually just the beginning of a new era of transcription research, as we could now decipher the mechanisms underlying the process, by solving structures of the polymerase in complex with nucleic acids and with different factors,” says Cramer.

Cramer became a tenured professor at Munich University in 2004 and also served as Director of the Gene Center and later as Dean of the School of Chemistry and as Chair of the Department of Biochemistry. His laboratory had many successes over the following 10 years, but he eventually ran into a technological barrier. “We were trying to determine structures of polymerase complexes, but at the time X-ray crystallography was the only method to do so, and the complexes were very transient and would fall apart during crystallization,” says Cramer. Indeed, the laboratory could solve crystal structures of other polymerases and of RNA polymerase II in complex with individual factors, but polymerase complexes with multiple factors remained beyond reach (5–9).

“What enabled us to take the next big step was the development of cryoelectron microscopy methods,” says Cramer. “This provided a totally new perspective because we didn’t have to crystallize the samples anymore and thus transient complexes also could be investigated,” he says. This advance enabled Cramer to solve structures of very large complexes, some of them containing up to 50 proteins. “I would always tell my students that I wanted to solve these structures before I retire, but thanks to the incredible acceleration provided by cryoelectron microscopy, we have solved many of them already, and I still have plenty of time,” says Cramer.

Large Complexes and Transcription Regulation

In 2014, Cramer was recruited as director to the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany. Around this time, he became increasingly interested in the interface between transcription and other events occurring in the cell. “It’s not only transcription that takes place in the nucleus, but also transitions in chromatin and processing of RNA,” he says. “Now we can look at how the transcription machinery interacts with various machineries that are conducting other processes, and begin to understand how these processes are coordinated, which is fascinating,” says Cramer. Such work often required collaborations with other laboratories (10–14).

To pursue this avenue of research, the Cramer laboratory had to overcome multiple technical challenges. “We participated in an effort of the community to develop methods to structurally resolve difficult complexes,” he says. “We derived new protocols to prepare large and transient complexes, we came up with new tricks for difficult crystallographic structure solutions, and we provided software tools for processing data from the electron microscope,” says Cramer. “We always share software and reagents with the community because I believe that open science increases the speed of generating new knowledge, to the benefit of people,” he says.

These advances enabled Cramer’s laboratory to solve structures of the mammalian RNA polymerase II and of large complexes regulating transcription in the context of chromatin (15–19). The group determined the structure of the RNA polymerase II preinitiation complex with a bound coactivator—known as Mediator—in both yeast and humans (20–25). “Now we could benefit from our prior crystallographic studies of the multisubunit Mediator complex,” he says. The Mediator crystal structures were fitted into electron microscopic reconstructions of larger assemblies like pieces to a 3D puzzle (26, 27). The group also showed how the mechanisms of initiation differ in other transcription systems, including the RNA polymerase I machinery (28, 29). “Together with recent work of colleagues, these papers firmly establish the structural basis of transcription initiation,” says Cramer.

Cramer also increasingly worked on the regulation of transcription, including transcriptional pausing. “Transcription is regulated at two major steps: one is initiation, when the polymerase first starts to make an RNA, and the other one is pausing, which happens at the beginning of genes where the polymerase pauses and waits for a signal before it exchanges factors to transcribe the gene,” he says. Recent work by his laboratory has helped to structurally define polymerase pausing and factor exchange as the second step of transcriptional regulation (30–32). These results highlighted the importance of allosteric transcription regulation by factors that interact with the polymerase, a concept the Cramer laboratory had reported earlier (33).

Cramer’s work has also revealed how such pausing can control the transcription initiation step, showing how these two transcriptional control points are coupled in vivo to regulate genes (34, 35). “We were able to extract kinetic information by combining different functional genomics methods, and this way we could define a fundamental process in living cells,” he says. “Our work was based on published results by colleagues and benefited from a lively international community, which we try to serve,” says Cramer. “Structural biology alone is not enough to decipher the mechanism; in order to find out how a process really works in cells you also need kinetics, which we showed can be carried out with the use of functional genomics and computational biology,” he says.

Before such a kinetic analysis could be done in human cells, the required methods had to be developed in simple yeast cells. In this earlier work, Cramer uncovered fundamental aspects of the RNA metabolism in cells (36–39). “We learned to measure unbiased rates of RNA synthesis in vivo, but also to estimate RNA degradation kinetics, and how to relate such kinetic rates to the occupancy of particular regions of the genome with various factors,” Cramer says.

Serendipitous Findings

Recently, Cramer’s team made an interesting observation about TBP, the most conserved of all of the transcription factors. “We were trying to make larger transcription complexes, but they fell apart and what remained was this TBP–nucleosome complex,” he says. “It was really unexpected because TBP has been thought to bind to naked DNA, not nucleosomes,” says Cramer. “When I see something unexpected, I am happy because it means I can learn something new by following up on it,” he says. This led to the findings described in Cramer’s Inaugural Article (1).

“We could solve structures of TBP bound to a nucleosome, which revealed new ways of how this factor interacts with DNA,” he says. Such TBP–nucleosome complexes may exist in cells, and Cramer’s findings raised the question of what they might be doing there. “One idea is that TBP can bind to the TATA box when it’s still located within a nucleosome, to first mark the site for transcription,” says Cramer. Some transcription factors that bind nucleosomes are also known to help open chromatin for cell regulation, and Cramer’s group has recently investigated an example (40).

Given Cramer’s passion for polymerases, it is not surprising that his group also became interested in solving the structure of the polymerase from the novel coronavirus SARS-CoV-2. His group successfully solved this structure, which provides a basis for understanding how antivirals, such as remdesivir or molnupiravir, work against this novel coronavirus to interfere with its RNA synthesis (41–43). “We have now teamed up with chemists to search for new antiviral compounds,” Cramer says.

Cramer still sees many questions left to answer about transcription. One of his long-term goals is inspired by physicist Richard Feynman’s adage about being able to truly understand a system only if one can reconstitute it. “Will it be possible to transcribe a genome in a test tube by fragmenting the genome and then adding polymerase and transcription factors?” he wonders.

Transcribing a eukaryotic genome in the test tube will constitute a major conceptual and technical challenge, but the payoff may be worth it. “In a controlled system like that, we should be able to answer some of the remaining big open questions about transcription and its regulation,” says Cramer. “I have always had the great pleasure to work with outstanding young scientists who contribute their own ideas and want to achieve, so hopefully we can get there in the next couple of years.”