‘Cellf’-determination through epigenetic regulation

Few prompts start as many tussles between collegial scientists as trying to define “epigenetics.” I once attended a conference where two well-regarded scientists from two famous research institutions shouted at each other about the term and its definition in a hundred-person lecture hall. Frustratingly, both sides had sound points that defended their own personal borders of the subject. Even if these borders are in question, they encompass a vast field with patches dedicated to physics and chemistry and even a type of geography, with paths connecting these supposedly disparate disciplines to solve a Big Problem. The field of epigenetics generates so much — ahem — excitement because many believe it contains ways of understanding disease and can guide us toward exploiting mechanistic knowledge for therapeutic gain. The boundaries matter much less than the rich terrain within.

“One genome, many epigenomes”

My doctoral advisor, Keji Zhao, PhD, National Heart, Lung and Blood Institute, would start all his lectures with the same message: “One genome, many epigenomes.” This simple math problem forms the basis for our field. Multicellular life had to evolve ways for cells to do specialized jobs. Trillion-celled humans have hundreds of cell types, yet these cells all have the same set of genes that encode proteins that do tasks. Cell specialization happens when not all genes and proteins are relevant for a given cell type, since not all types of cells do the same jobs. This is intuitive: Blood cells do different things than brain cells, which do different things than skin cells, so they don’t need the same parts or processes.

At the risk of personifying them, cells pick and choose gene combinations to draw from. Only a certain set of genes is transcribed, that is, read by cellular machinery for eventual translation into proteins. Some people talk about transcriptional status in terms of genes being on or off, but I like to think of them as being chosen for transcription because of their relevance to current conditions in the cell. In each cell type, only about half of our 20,000 genes are transcribed, making permutations of transcribed genes virtually infinite. Gene transcription represents the eventual output of epigenetic regulation, which chooses the genes that get transcribed by a protein complex called RNA polymerase II (Pol II). Epigenetic mechanisms explain how and why Pol II transcribes specific genes.

Through Rube-Goldberg-style machineries, intracellular and extracellular cues influence which genes are fundamentally important in each condition/cell type by controlling which proteins go to which locations within the cell. A popular destination for proteins is DNA itself; DNA is almost always decorated by proteins that carry out physical or enzymatic steps, ultimately guided by specific DNA letter sequences. This is how one camp of scientists draws their boundary of “epigenetic,” meaning literally, upon the genetic material (DNA). Proteins bind DNA “words” and control which genes have their information transcribed to eventually make other proteins. It’s complicated, this machinery-for-identity, and at least a little bit cyclical, but it helps explain the almost Newtonian tendency for a cell to remain that type of cell unless acted upon by a force. (This identity inertia is particularly relevant in pediatric cancers.) Proteins bind DNA to guide proteins to produce proteins that bind DNA, ad infinitum.

Mutual flourishings

Epigenetic regulation involves multifaceted collaboration among biomolecules — mostly proteins and bits of DNA — to control whether a gene is transcribed. Stretches of DNA called enhancers contain specific letter sequences that, on a physical level, are groups of specially arranged chemical molecules that only interact with certain complementary proteins. These interactions can be altered at a short range by adding chemical groups to the DNA letters themselves. In fact, one type of chemically modified DNA, methylated cytosines, is the least controversially “epigenetic” mark. This is the second camp’s definition of epigenetics: It can be passed from parent cell to daughter cell, and even from parent to child. It is heritable, but it is not the DNA sequence itself.  

Proteins called transcription factors bind specific DNA words at enhancers and are the feature players in establishing cell identities. Other proteins called co-factors are drawn toward specific DNA regions by interacting with these sequence-specific transcription factors. Regions bound by transcription factors and co-factors make up less than 2% of the DNA in any one cell type, but it’s usually a different 2% in each cell type since each transcription factor might be present in only a few cell types. The rest of the DNA is not protein-free, however, and is mostly wrapped into spool-like protein complexes called nucleosomes. This wrapping helps fit the genome into a pinpoint-sized nucleus. Some proteins form molecular machines that add, remove or shove these nucleosomes around as needed to expose the DNA to other proteins that might recognize words/structures. Since most of the DNA is wrapped in nucleosomes, managing nucleosome positions and their compositions is important. Beyond physically shifting their locations in DNA, chemical modifications can be added to, read or removed from nucleosomes that can change their properties and consequences for transcription.

Movers, shakers, fence-breakers

While the sequence in the genome is stable, the epigenome is highly dynamic. Proteins bind and dissociate from DNA. Individual protein complexes assemble and fall apart. Dense accumulations of proteins called condensates blink in and out of existence in seconds. Stretches of DNA separated by millions of letters make contact and separate. Individual protein residues can be battlegrounds for competing enzymes that add and remove the same chemical mark. Cues from a cell’s environment — what other cells are nearby, what metabolites are available, what time of day it is(!) — are transmitted into the nucleus by a “Pony Express” of biomolecules for eventual interpretation by DNA and its bound protein apparatus. This dynamism allows a cell to meet the needs of the body quickly, often in a matter of minutes. My own lab studies several levels of these dynamics from DNA folding and condensation to protein-DNA interactions to understand how regulatory differences emerge across tumor cells and tumor types.

Even if you’re not a fellow mechanism wonk, pediatric diseases give several fields abundant reasons to care about epigenetic mechanisms:

1. Pediatric cancer genomes have very few mutations, but the mutations they do have tend to fall in genes that control transcription of other genes.
2. The problems caused by many pediatric cancers depend on continued transcription of certain genes that are not required in the corresponding healthy tissue.
3. Some early studies suggest that epigenetic alterations may be sufficient to cause cancers.
4. Scientists and engineers can control epigenetic processes to, for example, force the transcription of therapeutic genes.
5. Proteins in epigenetic pathways often have enzymatic activities and have to bind other proteins to do their jobs, which are both ideal options for finding drug targets.

These are not all of the reasons to care about epigenetics in pediatric diseases, and, even if they were, this list is likely to grow. This field is big, this field is important, and this field is exciting. Whether you subscribe to the upon-the-DNA definition or the mark-passed-down one, there’s valuable information inside the boundaries of each camp.

Inside this vast, complex and energetic field, researchers at St. Jude are studying epigenetic regulation and the opportunities it grants from several angles. Normal development is tightly controlled through these processes, so understanding their basic components is critical for figuring out how the body maintains homeostasis while also being environmentally responsive. Epigenetic regulators can be mutated in ways that lead to both cancers and developmental diseases, and breaking an epigenetic regulator can have direct and secondary effects that make tracing back the mutation’s role especially tricky. Patterns of mutations in epigenetic controllers can allow physicians to distinguish forms of the same disease, and, on the basis of these differences, tailor therapeutic interventions that take advantage of the broken regulator and its consequences. Epigenetically misconfigured cells might be unsteady and vulnerable to different perturbations compared to normal cells. The combined study of mutations and epigenetics is starting to uncover why mutations might only matter in specific cell types and can only form cancers at specific developmental stages. Less invasive tests are even being developed to diagnose certain tumor types based solely on epigenetic profiles.

From diagnosing to discovering biology to developing treatments, epigenetics research centers deep mechanistic understanding of how cells go about their specialized business in a complex organism. The same biomolecular processes that enable us to develop a complex body plan can be co-opted by disease. St. Jude is working to disentangle these processes, how they go wrong and what we can do with that knowledge to improve human health. This is still open country, but with every mechanism understood, we advance the frontier one step further.