C. David Allis (1951-2023).

The Rosetta Histone. One of many chromatin-based cartoons drawn by a former Allis lab member Sean Taverna (now at Johns Hopkins School of Medicine). This one (from 2005) depicts Dave as an intrepid explorer, solving the puzzle of “the rosetta histone.” In Sean’s own words: “It was inspired by Dave’s enthusiasm to keep digging deeper into chromatin biology.”View Large Image Figure ViewerDownload Hi-res image Download (PPT) Every amino acid matters, but the people matter more. —C. David Allis C. David Allis, or “Dave” to his colleagues and friends, was an internationally renowned scientist who was as equally known for his trailblazing discoveries as he was for his kind persona and unbounded, contagious enthusiasm for science. In addition to being a beacon and catalyst in the chromatin and gene regulation fields, Dave is considered by many to be one of the most impactful scientists in the modern era of molecular biology. He passed away to the great shock of his colleagues after battling cancer, as he had kept his illness very private. He will be deeply missed by his friends, family, and the entire scientific community. As a group of scientists who worked with him in the laboratory and whose careers were, and forever will be, inspired by his vision and mentorship, we are truly honored to pay tribute to Dave. Born and raised in Cincinnati, Ohio, Dave attended college in his hometown at the University of Cincinnati. It was there that he “got hooked” on science, as Dave would say, and decided to pursue a PhD in biology. After completing his graduate work with Tony Mahowald at Indiana University, where he studied Drosophila polar granules (large ribonucleotide assemblies that regulate germ cell-specific functions), Dave switched model systems for his postdoctoral training and began working with the unicellular protist Tetrahymena. Although many people doubted the promise of this choice, Dave and his mentor Martin (Marty) Gorovsky at the University of Rochester were convinced that the unique biology of Tetrahymena could be leveraged to uncover novel mechanisms linking histone modifications to gene activity. As we now know, they were proven right. Taking advantage of the unique dichotomy of micro- and macronuclei (a.k.a. “mic” and “mac”), Dave not only characterized distinct patterns of histone modifications in the transcriptionally silent mic versus the transcriptionally active mac but also uncovered novel histone variants unique to the latter. Marty once said of Dave, “I was lucky to get him. We taught him how to grow Tetrahymena, and he taught us a lot about how to do science.” Dave’s work in Tetrahymena ignited his lifelong love for histones and set the stage for many future discoveries in his own laboratory and many others. Walking into Dave’s first lab at Baylor College of Medicine in the mid-to-late 1980s, one would almost certainly see large glass flasks holding liters of Tetrahymena cultures. In those early years of his career, Dave demonstrated that lysine acetylation was not randomly catalyzed on histones and that some sites of acetylation were, in fact, uniquely associated with histone deposition during S phase. These initial discoveries propelled him to pursue the isolation of histone acetyltransferases (HATs), a challenging task that Dave’s laboratory pursued over the next decade. After spending years developing assays and purification schemes to purify a HAT from his favorite “critter” (as Dave fondly referred to Tetrahymena), their big breakthrough was the result of a less conventional method. The idea for using an “in gel” assay came to him when he learned about the use of such approaches for identifying kinases. After Dave and his graduate student, James Brownell, found that the HAT activity in their Tetrahymena extracts could survive SDS treatment and removal, they gave it a try. After years of dogged work to identify the enzyme responsible for histone acetylation, the results were almost too good to be true. Not only had they isolated the first HAT, but it turned out to be a homolog of Gcn5—a transcriptional co-activator previously identified through yeast genetics—clearly linking histone modifications to the regulation of gene expression. Without question, this seminal discovery ushered in an explosive era of chromatin research, leading to the discovery of numerous HATs across model organisms and proving Dave’s long belief that “histones matter.” True to his character, Dave loved sharing this tremendous news. He called past lab members and exclaimed “We found it!” before even saying hello. It was immediately clear what he meant. Dave’s ultimate success illustrates several aspects of his personality and approach to science. First, he was not afraid to tackle big problems or pursue risky and unpopular ideas, many of which turned out to be visionary. Second, he exhibited tenacity in the face of technical, and funding, hurdles. Dave often mentioned that funding for chromatin research in the 1980s was very difficult—not only due to a lack of tools but also because of the perception by some that histones were simply structural proteins that “got out of the way” for important processes like transcription. He would even joke that one should avoid using the “C word” (i.e., chromatin), as it made it even more challenging to obtain funding. In the years following the discovery of HATs, Dave turned his attention to other histone modifications. For example, his group demonstrated that histone H3 serine 10 (H3S10) is highly phosphorylated during mitosis and created an H3S10ph antibody, which he generously shared with many laboratories. To this day, the H3S10ph modification is leveraged as a key marker of mitotic chromatin across diverse species. Histone methylation was somewhat more enigmatic, but Dave was not afraid to jump into those waters. We remember his encouragement to repeat the in vitro HAT assays, swapping the co-factor acetyl-CoA for S-adenosyl methionine (SAM), to see whether histone methylation was an active process in the Tetrahymena mac. This simple experiment arguably put histone methylation “on the map,” as Dave might say. As Dave’s lab continued to make new discoveries, he strongly believed that breakthroughs are made through openly sharing data, reagents, and ideas. One particularly fateful example is Dave’s collaboration with Thomas Jenuwein, initiated at the 1999 FASEB meeting in Colorado. This interaction ultimately led to the discovery of the first site-specific histone methyltransferase activity, mediated by the SET domain of the enzyme SUV39H1. A classic story that Dave repeatedly shared was how his lab members exploded in excitement after their peptide sequencing results revealed that SUV39H1 did, in fact, methylate H3 lysine 9. He laughed and said the enzyme’s name already gave it away: SUV“3" for H3 and “9” for lysine 9. The collaborative discovery that SUV39H1 is a site-specific histone methyltransferase had a major impact on the field, as Drosophila genetics had previously linked its homolog Su(var)3–9 to position-effect variegation and heterochromatin formation. In addition, other genes encoding SET domain-containing proteins had been genetically linked to Hox gene expression during fly development, both to their “on” (Trithorax) and “off” states (Polycomb). Recognition that the key biochemical function of these proteins is histone methylation, and that many more such proteins existed, cracked histone methylation research wide open. Work by many laboratories began uncovering associations between site-specific histone lysine methylation and diverse chromatin functions, including transcription initiation and elongation, heterochromatin formation, and many others. The subsequent discovery of a histone demethylase in 2004 by Yang Shi’s group demonstrated that histone methylation was indeed also reversible and dynamic, like many other post-translational modifications. How can the same chemical modification (e.g., methylation) be associated with so many distinct, and sometimes opposing, biological processes? Work from Dave’s laboratory and others revealed that histone methylation is recognized by distinct binding proteins with specific structural folds, including those of chromodomains and PHD fingers, providing a molecular basis through which histone methylation can exert diverse downstream effects. Similarly, lysine acetylation was shown to be recognized by another class of effector domains called bromodomains. As the field untangled this complex chromatin language, Dave was determined to communicate it clearly to a broad audience across the scientific community. He thus introduced simple terminology, which was ultimately adopted by many inside and outside the field: writers and erasers, with “writers” and “erasers” as a general term for the enzymatic machinery that, respectively, adds and removes these modifications and “readers” for the effector proteins that recognize them. By creating this language, he deconstructed barriers to entering the chromatin field and attracted many new people. Perhaps the most recognized concept that Dave put forward is the “histone code” hypothesis, a forward-thinking and visionary framework that proposed how histone modifications, their combinations, and their readers could contribute to regulatory processes on the chromatin template. Originally formulated in 2000 while at the University of Virginia, this hypothesis remains one of the most cited concepts in chromatin biology. Many of its tenets, such as histone crosstalk (whereby certain modifications act synergistically or antagonistically) and combinatorial readout of histone modifications by proteins or protein complexes containing multiple effector modules, have now borne out. With the advent of new technologies, such as genome and epigenome editing, some of the predictions are only now becoming directly testable in mammalian cells and other complex in vivo models. These studies have revealed nuanced and context-dependent contributions of histone modifications and their associated enzymatic machinery to various DNA-templated processes, with many more lessons undoubtedly to be learned. While it is important to mention that aspects of the histone code have been debated over the years, Dave always emphasized that the concept was not meant to minimize or supersede the importance of other gene regulatory mechanisms. Rather, it provided a framework for thinking about how post-translational modifications on histones may expand such regulatory functions and did so using terminology that is easy to grasp across fields. Beyond deciphering the complexity of histone modifications, Dave made enormous contributions to the area of histone variants, which are genetically encoded variations in histone proteins that provide another mechanism for a functional diversification of the nucleosome. From his early work in Tetrahymena to the mechanistic understanding of histone variants in human disease in recent years, Dave and his team helped characterize several functionally distinct histone variants and their unique post-translational modifications. They also investigated variant-specific chaperones dedicated to the faithful deposition of these specialized histones into chromatin. For example, his lab uncovered a new histone deposition pathway for H3.3 that unexpectedly placed this variant into heterochromatin. While one might not have predicted at the time that this histone variant and its deposition machinery would be altered in disease, Dave’s lab was primed for discovery when genome sequencing studies of rare adult and pediatric tumors revealed mutations in H3.3, ATRX, and DAXX. By collaborating with physician scientists and cancer biologists, Dave’s team led the way into the mechanistic understanding of these histone mutations or, as he so aptly coined, “oncohistones.” The cancer biology field is now fervently studying these mutations, as well as mutations (and other alterations) in chromatin readers, writers, and erasers that are emerging as critical players in the very disease to which Dave ultimately succumbed. Given Dave’s incredible accomplishments, including many we have not described, it is evident why he received so many notable awards and recognition. To name a few, he was elected into the National Academy of Sciences (2005) and he received the Japan Prize for Life Sciences (2014), the Breakthrough Prize in Life Sciences (2015), and most recently the Albert Lasker Basic Medical Research Award (2018), which he shared with another pioneer in the field, Michael Grunstein. Dave was always humble about these awards and deflected the attention away from himself. At every talk and award ceremony he insisted that we, his trainees, “are a big reason for any of my successes; they are the unsung heroes.” However, we are well aware that Dave’s incredible vision and unwavering support and encouragement was the foundation for our success. He was most deserving of all the above awards and of the one he missed but, in our view, truly deserved. As remarkable as his discoveries and awards are, arguably Dave’s biggest contribution to science is through his mentorship of trainees, not only those in his lab but also countless others whom he did not train directly but nonetheless found time to advise and support. “Every amino acid matters,” Dave frequently said, focusing our attention on the specific biochemical properties of different histone residues and their potential to be modified or contribute to functional variation in other ways. Yet, he often quickly added, “but the people matter more.” Dave not only said it but lived by it. His impact on his trainees cannot be overstated—his enthusiasm for science was infectious; he gave us freedom to pursue risky and bold projects, encouraged us through successes and failures, and always championed our wins. In his own words, Dave was a "cheerleader" for his people and we all lived for those moments when he said “Good show!” Anyone who has witnessed Dave giving a talk knows how he radiated excitement about science. Many of us recall how he would burst out of his office into the laboratory with a new idea. Anyone in his vicinity would be drawn into his office where he would share (at length) his enthusiasm for a new paper or lay out new hypotheses and critical experiments for the next big breakthrough. If Dave asked "Got a minute?" it usually meant that you would exit his office hours later, buoyant and ready to hit the bench. The level of passion Dave displayed was truly beyond what any of us had ever experienced. At the same time, he took his responsibility as a mentor very seriously, especially with his graduate students who were just starting their careers. His number one rule was to show respect: to lab colleagues, members of thesis committees, and collaborators and to the discoveries that came before ours. Dave had high standards and expectations, which drove us to try to rise to the occasion. He taught us what is important in science—a well-controlled experiment and the courage to do it. What’s more, Dave’s commitment to his trainees did not stop when we left his lab. He continued to encourage and support us, even years after we moved on. Despite being incredibly busy, Dave miraculously found time for all of us, whether making insightful comments on manuscripts and grant proposals or sharing reagents his laboratory had generated. As a result, many of Dave’s former trainees have stayed on in academia and lead their own successful laboratories. We strive to pay forward the privilege we gained from his mentorship and support. Dave’s generosity of spirit also extended well beyond his own trainees. Although academic research can be a highly competitive environment, Dave believed that rising tides would lift all boats and refused to view scientific discovery as a zero-sum game. He gave his time, reagents, and ideas generously because he wanted to expand and deepen the field, rather than create a narrow path for himself. Many careers were kick-started by his open-handed sharing of histone modification antibodies and creative ideas. Moreover, Dave had a deep and genuine respect for his colleagues and biology itself. He believed that there were so many interesting organisms and mechanisms to understand, technical problems to tackle, and discoveries to be made that it was foolish not to collaborate. In fact, he would frequently pick up the phone and call a colleague to initiate a new collaboration on our behalf. These collaborations were often magical, as they usually cross-fertilized different areas of research (e.g., structural biology, development, or disease), increasing our opportunities for discovery and helping us develop valuable relationships with other scientists and experts. Dave’s love of histones and dedication to colleagues was only surpassed by his devotion to his family. He often spoke proudly about his children and, more recently, his grandchildren. Above all, he was incredibly grateful to call Barbara (Barb) his wife. He also frequently inquired about our families and kept a huge board of pictures outside his office at The Rockefeller University with all the lab members and their momentous occasions such as weddings, birth of a baby, etc. The absence of David Allis will be far reaching, in the chromatin and transcription fields and beyond. However, for many of us in his “Allis lab family,” our greatest sadness is the loss of the person we would be most excited to call and say, “Dave, we found it!”