It’s difficult these days not to notice the buzz about epigenetics, a word many researchers employ to describe inherited patterns of gene expression not directly reflected in the DNA sequence. This year, Cold Spring Harbor Laboratory Press issued the first epigenetics textbook, with chapters by several HMS authors. In May, the National Institutes of Health enshrined epigenetics as a major initiative in its Roadmap for Medical Research.
But beware: A backlash is brewing among scientists who take umbrage at loose use of the term, especially when invoked about the state of the packaging of silent and active genes.
The semantic tension felt by some reflects sincere attempts to make sense of massive amounts of new information. The already staggering list of molecular players and unexpected mechanisms keeps growing in subcategories of placing, removing, and reading various histone marks—or the lack thereof—at innumerable locations in the chromatin. The heightened attention also reflects a sense of excitement about potential clinical applications based on gaining greater control over the genes threading through the chromatin.
The DNA code is insufficient, even if necessary, to explain how genes give rise to the dynamics of life and its vagaries. The most oft-cited example of a persistent mystery is how the many cells in our body can share identical DNA, yet look and act as differently as skin and bones—and pass those traits on when dividing. Now many scientists have pinned their hopes on chromatin studies to provide some of these answers.
“Epigenetics is central to the fact that we have fingers and toes in the right place and that our skin and liver are functioning, and it is fundamental to what goes wrong in development and cancer,” said Robert Kingston. Starting with proteins previously implicated in epigenetic events in fruit flies, Kingston’s lab has discovered how two major protein complexes remodel the chromatin packaging around genes—an ATP-dependent complex of the trithorax group, which mostly maintains genes in an active state, and a polycomb group complex, which primarily represses gene activity along stretches of chromosome.
Kingston admits to being (quietly) frustrated when he hears colleagues refer to chromatin marks as epigenetics. “We know a lot about the players involved in epigenetics,” said Kingston, HMS professor of genetics at Massachusetts General Hospital. “We know a lot about what the players are capable of doing. But we don’t know which of those things are epigenetic events, or if they are causal or markers of some other epigenetic event. It’s still largely uncharted territory, which is what makes it fun.” Kingston is not asking how the histone marks are inherited, but others are.
Kilroy Was HereOn the Quad, Kevin Struhl is more vocal about his objections to equating epigenetics with the presence or absence of acetyl, methyl, and other small molecular marks at specific points along the tails of the repeated histone spools within chromatin. He predicts the mystical aura surrounding epigenetics will eventually fade to reveal basic principles and molecular mechanisms analogous to those of gene transcription. “People treat this stuff as if it was brand new,” said Struhl, HMS professor of biological chemistry and molecular pharmacology. “There is quite a bit of understanding of epigenetic mechanisms in earlier work.”
Using baker’s yeast, Struhl’s lab has found that normal transcription activity deposits methyl at a certain histone location as a kind of transcriptional memory or molecular graffiti akin to “Kilroy was here.”
The idea that histone marks predispose genes to transcription is completely backwards, he said. “You need mechanisms that make the gene inactive here or active there, and histone marks lack the specificity to do this. Specificity comes primarily from transcription factors that recognize specific sequences and bind DNA. Such transcription factors recruit enzyme complexes that modify chromatin, and the resulting histone modifications are important for transcriptional regulation, but the marks themselves are not the primary determinant of gene regulatory patterns or epigenetic inheritance.”
Even the most skeptical scientists have a strong hunch that certain chromatin modifications must play some part in sustaining their signatures during mitosis from mother cell to daughter cells. Yet there is no direct evidence that any single histone modification is epigenetically inherited, said Danesh Moazed, HMS professor of cell biology.
Researchers in Moazed’s lab discovered a new specific mechanism in fission yeast that may build and maintain long gene-suppressing stretches of heterochromatin with transcription. The nascent RNA, synthesized by RNA polymerase, attracts a local small interfering RNA complex, which in turn recruits a specific histone methylation that shuts the process down. The RNA-interfering machinery sets up a positive feedback loop with epigenetic potential.
“Transcription could be required for assembling heterochromatin, and it could be that you need transcription to establish the positive feedback loop that maintains epigenetic states,” Moazed proposes.
Independent of their epigenetic status, histone modifications are important, points out Stephen Buratowski, HMS professor of biological chemistry and molecular pharmacology. Twelve years after the first histone deacetylase (HDAC) was co-discovered in the Harvard lab of chemical biologist Stuart Schreiber, more than 14 HDAC inhibitors are in clinical trials as targeted anticancer agents by themselves or in combination therapy.
“When you see basic science moving into clinical applications only a few years later, it’s really amazing,” said Buratowski, whose group has also shown in baker’s yeast that a methyltransferase comes along for the ride on the polymerase during gene transcription, leaving a certain methylation in its wake.
New Game in TownOne of the big shakeups in histone biology came when researchers in the lab of Yang Shi, HMS professor of pathology, discovered an enzyme that removes methyl from a certain spot on histone tails. Previously, scientists believed methylation was a permanent and irreversible event. Another demethylase discovered in his lab will be reported within weeks.
“We’re not asking the question about whether or not the modification is epigenetic,” Shi said. “We’re studying modification states, how they are regulated, how they affect chromatin and gene transcription, and their reversibility. We are at the stage of accumulating information and collecting players. Eventually, we’ll get to the stage of better understanding.” (See “Zero Discovered…”)
In contrast to the race to identify new chromatin players, Bradley Bernstein, HMS assistant professor of pathology at MGH, has been analyzing genome-scale patterns of chromatin modifications, looking for characteristic patterns at different stages of development. In a recent comparison of mouse embryonic cells fated to become bone and fatty tissue compared with those destined to make neurons and glial cells, he found chromatin marks that correspond with or predict the developmental fate of the cell.
“From looking at the global patterns, there are characteristic chromatin structures that sit over master regulator genes and appear to either keep them poised or shut off or turned on,” he said. The new high-throughput tools will provide powerful datasets that will ultimately bridge to or enable mechanistic studies about how the chromatin states are established and how they define cellular phenotypes and the developmental potential of stem cells, he said.
Some chromatin modifications will probably come to include some epigenetic phenomena, but epigenetics clearly extends beyond chromatin. Jeannie Lee, who has worked out many details of the classic epigenetic phenomenon X inactivation, dismisses the fuss about epigenetic terminology. “Everyone is calling epigenetics something slightly different based on their research experience,” said Lee, HMS professor of genetics at MGH. “There are all kinds of interesting definitions, and they’re all correct to some extent. There’re going to be a lot of mechanisms. We don’t agree because we don’t understand the mechanisms yet.”
The epigenetics buzz delights Ting Wu, HMS professor of genetics, who believes that scientists became too focused on DNA after they rediscovered Mendel’s laws in 1900, to the exclusion of other heritable genetic material and mechanisms. Wu’s lab studies how the behavior of whole chromosomes, not just chromatin, affects gene expression, including how chromosome pairing allows enhancers on one chromosome to act on promoters lying on the next.
“Epigenetics was originally defined as the study of how a genotype becomes a phenotype and will therefore necessarily involve a plethora of mechanisms, but I don’t mind the many other definitions,” Wu said. “I’m most excited that people are realizing that there are forms of inheritance that are not easily explicable by simple paradigms. The paradigms we recognize now are very good, but people are realizing that they don’t apply as broadly as we once thought. That’s what’s so great about nature, the vista is so much more interesting.”
