Decoding the Cell’s Genetic Filing System (Nature Chemistry)

By Tien Nguyen, Department of Chemistry

A fully extended strand of human DNA measures about five feet in length. Yet it occupies a space just one-tenth of a cell by wrapping itself around histones—spool-like proteins—to form a dense hub of information called chromatin.

Access to these meticulously packed genes is regulated by post-translational modifications, chemical changes to the structure of histones that act as on-off signals for gene transcription. Mistakes or mutations in histones can cause diseases such as glioblastoma, a devastating pediatric brain cancer.

Source: Nature Chemistry

Source: Nature Chemistry

Researchers at Princeton University have developed a facile method to introduce non-native chromatin into cells to interrogate these signaling pathways. Published on April 6 in the journal Nature Chemistry, this work is the latest chemical contribution from the Muir lab towards understanding nature’s remarkable information indexing system.

Tom Muir, the Van Zandt Williams, Jr. Class of ’65 Professor of Chemistry, began investigating transcriptional pathways in the so-called field of epigenetics almost a decade earlier. Deciphering such a complex and dynamic system posed a formidable challenge, but his research lab was undeterred. “It’s better to fail at something important than to succeed at something trivial,” he said.

Muir recognized the value of introducing chemical approaches to epigenetics to complement early contributions that came mainly from molecular biologists and geneticists. If epigenetics was like a play, he said, molecular biology and genetics could identify the characters but chemistry was needed to understand the subplots.

These subplots, or post-translational modifications of histones, of which there are more than 100, can occur cooperatively and simultaneously. Traditional methods to probe post-translational modifications involved synthesizing modified histones one at a time, which was a very slow process that required large amounts of biological material.

Last year, the Muir group introduced a method that would massively accelerate this process. The researchers generated a library of 54 nucleosomes—single units of chromatin, like pearls on a necklace—encoded with DNA-barcodes, unique genetic tags that can be easily identified. Published in the journal Nature Methods, the high throughput method required only microgram amounts of each nucleosome to run approximately 4,500 biochemical assays.

“The speed and sensitivity of the assay was shocking,” Muir said. Each biochemical assay involved treatment of the DNA-barcoded nucleosome with a writer, reader or nuclear extract, to reveal a particular binding preference of the histone. The products were then isolated using a technique called chromatin immunoprecipitation and characterized by DNA sequencing, essentially an ordered readout of the nucleotides.

“There have been incredible advances in genetic sequencing over the last 10 years that have made this work possible,” said Manuel Müller, a postdoctoral researcher in the Muir lab and co-author on the Nature Methods article.

Schematic of approach using split inteins

Schematic of approach using split inteins

With this method, researchers could systematically interrogate the signaling system to propose mechanistic pathways. But these mechanistic insights would remain hypotheses unless they could be validated in vivo, meaning inside the cellular environment.

The only method for modifying histones in vivo was extremely complicated and specific, said Yael David, a postdoctoral researcher in the Muir lab and lead author on the recent Nature Chemistry study that demonstrated a new and easily customizable approach.

The method relied on using ultra-fast split inteins, protein fragments that have a great affinity for one another. First, one intein fragment was attached to a modified histone, by encoding it into a cell. Then, the other intein fragment was synthetically fused to a label, which could be a small protein tag, fluorophore or even an entire protein like ubiquitin.

Within minutes of being introduced into the cell, the labeled intein fragment bound to the histone intein fragment. Then like efficient and courteous matchmakers, the inteins excised themselves and created a new bond between the label and modified histone. “It’s really a beautiful way to engineer proteins in a cell,” David said.

Regions of the histone may be loosely or tightly packed, depending on signals from the cell indicating whether or not to transcribe a gene. By gradually lowering the amount of labeled intein introduced, the researchers could learn about the structure of chromatin and tease out which areas were more accessible than others.

Future plans in the Muir lab will employ these methods to ask specific biological questions, such as whether disease outcomes can be altered by manipulating signaling pathway. “Ultimately, we’re developing methods at the service of biological questions,” Muir said.

This research was supported by the US National Institutes of Health (grants R37-GM086868 and R01 GM107047).

Read the articles:

Nguyen, U.T.T.; Bittova, L.; Müller, M.; Fierz, B.; David, Y.; Houck-Loomis, B.; Feng, V.; Dann, G.P.; Muir, T.W. “Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.” Nature Methods, 2014, 11, 834.

David, Y.; Vila-Perelló, M; Verma, S.; Muir, T.W. “Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins.” Nature Chemistry, Advance online publication, April 6, 2015.

Frustrated magnets – new experiment reveals clues to their discontent (Science)

By Catherine Zandonella, Office of the Dean for Research

A crystal of frustrated magnet (Tb2Ti2O7). Image credit: Jason Krizan.

A crystal of frustrated magnet (Tb2Ti2O7). Image credit: Jason Krizan.

An experiment conducted by Princeton researchers has revealed an unlikely behavior in a class of materials called frustrated magnets, addressing a long-debated question about the nature of these discontented quantum materials.

The work represents a surprising discovery that down the road may suggest new research directions for advanced electronics. Published this week in the journal Science, the study also someday may help clarify the mechanism of high-temperature superconductivity, the frictionless transmission of electricity.

The researchers tested the frustrated magnets — so-named because they should be magnetic at low temperatures but aren’t — to see if they exhibit a behavior called the Hall Effect. When a magnetic field is applied to an electric current flowing in a conductor such as a copper ribbon, the current deflects to one side of the ribbon. This deflection, first observed in 1879 by E.H. Hall, is used today in sensors for devices such as computer printers and automobile anti-lock braking systems.

Because the Hall Effect happens in charge-carrying particles, most physicists thought it would be impossible to see such behavior in non-charged, or neutral, particles like those in frustrated magnets. “To talk about the Hall Effect for neutral particles is an oxymoron, a crazy idea,” said N. Phuan Ong, Princeton’s Eugene Higgins Professor of Physics.

Nevertheless, some theorists speculated that the neutral particles in frustrated magnets might bend to the Hall rule under extremely cold conditions, near absolute zero, where particles behave according to the laws of quantum mechanics rather than the classical physical laws we observe in our everyday world. Harnessing quantum behavior could enable game-changing innovations in computing and electronic devices.

Ong and colleague Robert Cava, Princeton’s Russell Wellman Moore Professor of Chemistry, and their graduate students Max Hirschberger and Jason Krizan decided to see if they could settle the debate and demonstrate conclusively that the Hall Effect exists for frustrated magnets.

To do so, the research team turned to a class of the magnets called pyrochlores. They contain magnetic moments that, at very low temperatures near absolute zero, should line up in an orderly manner so that all of their “spins,” a quantum-mechanical property, point in the same direction. Instead, experiments have found that the spins point in random directions. These frustrated materials are also referred to as “quantum spin ice.”

“These materials are very interesting because theorists think the tendency for spins to align is still there, but, due to a concept called geometric frustration, the spins are entangled but not ordered,” Ong said. Entanglement is a key property of quantum systems that researchers hope to harness for building a quantum computer, which could solve problems that today’s computers cannot handle.

A chance conversation in a hallway between Cava and Ong revealed that Cava had the know-how and experimental infrastructure to make such materials. He tasked chemistry graduate student Krizan with growing the crystals while Hirschberger, a graduate student in physics, set up the experiments needed to look for the Hall Effect.

Graduate student Max Hirschberger lowers the assembled experimental setup into a high-field magnet system, capable of creating fields as strong as 250,000 times the earth's magnetic field.  (Image credit: Jason Krizan.)

Graduate student Max Hirschberger lowers the assembled experimental setup into a high-field magnet system, capable of creating fields as strong as 250,000 times the earth’s magnetic field. (Image credit: Jason Krizan.)

“The main challenge was how to measure the Hall Effect at an extremely low temperature where the quantum nature of these materials comes out,” Hirschberger said. The experiments were performed at temperatures of 0.5 degrees Kelvin, and required Hirschberger to resolve temperature differences as small as a thousandth of a degree between opposite edges of a crystal.

To grow the crystals, Krizan first synthesized the material from terbium oxide and titanium oxide in a furnace similar to a kiln. After forming the pyrochlore powder into a cylinder suitable for feeding the crystal growth, Krizan suspended it in a chamber filled with pure oxygen and blasted it with enough focused light from four 1000-Watt halogen light bulbs to heat a small region to 1800 degrees Celsius. The final products were thin, flat transparent or orange slabs about the size of a sesame seed.

To test each crystal, Hirschberger attached tiny gold electrodes to either end of the slab, using microheaters to drive a heat current through the crystal. At such low temperatures, this heat current is analogous to the electric current in the ordinary Hall Effect experiment.

At the same time, he applied a magnetic field in the direction perpendicular to the heat current. To his surprise, he saw that the heat current was deflected to one side of the crystal. He had observed the Hall Effect in a non-magnetic material.

Surprised by the results, Ong suggested that Hirschberger repeat the experiment, this time by reversing the direction of the heat current. If Hirschberger was really seeing the Hall Effect, the current should deflect to the opposite side of the crystal. Reconfiguring the experiment at such low temperatures was not easy, but eventually he demonstrated that the signal did indeed reverse in a manner consistent with the Hall Effect.

“All of us were very surprised because we work and play in the classical, non-quantum world,” Ong said. “Quantum behavior can seem very strange, and this is one example where something that shouldn’t happen is really there. It really exists.”

The use of experiments to probe the quantum behavior of materials is essential for broadening our understanding of fundamental physical properties and the eventual exploitation of this understanding in new technologies, according to Cava. “Every technological advance has a basis in fundamental science through our curiosity about how the world works,” he said.

Further experiments on these materials may provide insights into how superconductivity occurs in certain copper-containing materials called cuprates, also known as “high-temperature” superconductors because they work well above the frigid temperatures required for today’s superconductors, such as those used in MRI machines.

One of the ideas for how high-temperature superconductivity could occur is based on the possible existence of a particle called the spinon. Theorists, including the Nobel laureate Philip Anderson, Princeton’s Joseph Henry Professor of Physics, Emeritus and a senior physicist, and others have speculated that spinons could be the carrier of a heat current in a quantum system such as the one explored in the present study.

Although the team does not claim to have observed the spinon, Ong said that the work could lead in such a direction in the future. “This work sets the stage for hunting the spinon,” Ong said. “We have seen its tracks, so to speak.”

 

The research was funded by the Army Research Office (ARO W911NF-11-1-0379, ARO W911NF-12-1-0461), the U.S. National Science Foundation (DMR 1420541), and the U.S. Department of Energy’s Division of Basic Energy Sciences, (DE-FG-02-08ER46544).

Citation:

Max Hirschberger, Jason W. Krizan, R. J. Cava, N. P. Ong. Large thermal Hall conductivity of neutral spin excitations in a frustrated quantum magnet. Science. 10.1126/science.1257340

Revisiting the mechanics of the action potential (Nature Communications)

By Staff

AW_Pic

The action potential (AP) and the accompanying action wave (AW) constitute an electromechanical pulse traveling along the axon.

The action potential is widely understood as an electrical phenomenon. However, a long experimental history has documented the existence of co-propagating mechanical signatures.

In a new paper in the journal Nature Communications, two Princeton University researchers have proposed a theoretical model to explain these mechanical signatures, which they term “action waves.” The research was conducted by Ahmed El Hady, a visiting postdoctoral research associate at the Princeton Neuroscience Institute and a postdoctoral fellow at the Howard Hughes Medical Institute, and Benjamin Machta, an associate research scholar at the Lewis-Sigler Institute for Integrative Genomics and a lecturer in physics and the Lewis-Sigler Institute for Integrative Genomics.

In the model, the co-propagating waves are driven by changes in charge separation across the axonal membrane, just as a speaker uses charge separation to drive sound waves through the air. The researchers argue that these forces drive surface waves involving both the axonal membrane and cytoskeleton as well as its surrounding fluid. Their model may help shed light on the functional role of the surprisingly structured axonal cytoskeleton that recent super-resolution techniques have uncovered, and suggests a wider role for mechanics in neuronal function.

Read the paper.

Ahmed El Hady & Benjamin B. Machta. Mechanical surface waves accompany action potential propagation. Nature Communications 6, No. 6697 doi:10.1038/ncomms7697

Do biofuel policies seek to cut emissions by cutting food? (Science)

By Catherine Zandonella, Office of the Dean for Research

2015_03_27_cornfieldA study published today in the journal Science found that government biofuel policies rely on reductions in food consumption to generate greenhouse gas savings.

Shrinking the amount of food that people and livestock eat decreases the amount of carbon dioxide that they breathe out or excrete as waste. The reduction in food available for consumption, rather than any inherent fuel efficiency, drives the decline in carbon dioxide emissions in government models, the researchers found.

“Without reduced food consumption, each of the models would estimate that biofuels generate more emissions than gasoline,” said Timothy Searchinger, first author on the paper and a research scholar at Princeton University’s Woodrow Wilson School of Public and International Affairs and the Program in Science, Technology, and Environmental Policy.

Searchinger’s co-authors were Robert Edwards and Declan Mulligan of the Joint Research Center at the European Commission; Ralph Heimlich of the consulting practice Agricultural Conservation Economics; and Richard Plevin of the University of California-Davis.

The study looked at three models used by U.S. and European agencies, and found that all three estimate that some of the crops diverted from food to biofuels are not replaced by planting crops elsewhere. About 20 percent to 50 percent of the net calories diverted to make ethanol are not replaced through the planting of additional crops, the study found.

The result is that less food is available, and, according to the study, these missing calories are not simply extras enjoyed in resource-rich countries. Instead, when less food is available, prices go up. “The impacts on food consumption result not from a tailored tax on excess consumption but from broad global price increases that will disproportionately affect some of the world’s poor,” Searchinger said.

The emissions reductions from switching from gasoline to ethanol have been debated for several years. Automobiles that run on ethanol emit less carbon dioxide, but this is offset by the fact that making ethanol from corn or wheat requires energy that is usually derived from traditional greenhouse gas-emitting sources, such as natural gas.

Both the models used by the U.S. Environmental Protection Agency and the California Air Resources Board indicate that ethanol made from corn and wheat generates modestly fewer emissions than gasoline. The fact that these lowered emissions come from reductions in food production is buried in the methodology and not explicitly stated, the study found.

The European Commission’s model found an even greater reduction in emissions. It includes reductions in both quantity and overall food quality due to the replacement of oils and vegetables by corn and wheat, which are of lesser nutritional value. “Without these reductions in food quantity and quality, the [European] model would estimate that wheat ethanol generates 46% higher emissions than gasoline and corn ethanol 68% higher emissions,” Searching said.

The paper recommends that modelers try to show their results more transparently so that policymakers can decide if they wish to seek greenhouse gas reductions from food reductions. “The key lesson is the trade-offs implicit in the models,” Searchinger said.

The research was supported by The David and Lucile Packard Foundation.

Read the abstract.

T. Searchinger, R. Edwards, D. Mulligan, R. Heimlich, and R. Plevin. Do biofuel policies seek to cut emissions by cutting food? Science 27 March 2015: 1420-1422. DOI: 10.1126/science.1261221.

When attention is a deficit: How the brain switches strategies to find better solutions (Neuron)

By Catherine Zandonella, Office of the Dean for Research

2015_03_26_JW_Schuck_NYC3Sometimes being too focused on a task is not a good thing.

During tasks that require our attention, we might become so engrossed in what we are doing that we fail to notice there is a better way to get the job done.

For example, let’s say you are coming out of a New York City subway one late afternoon and you want to find out which way is west. You might begin to scan street signs and then suddenly realize that you could just look for the setting sun.

A new study explored the question of how the brain switches from an ongoing strategy to a new and perhaps more efficient one. The study, conducted by researchers at Princeton University, Humboldt University of Berlin, the Bernstein Center for Computational Neuroscience in Berlin, and the University of Milan-Bicocca, found that activity in a region of the brain known as the medial prefrontal cortex was involved in monitoring what is happening outside one’s current focus of attention and shifting focus from a successful strategy to one that is even better. They published the finding in the journal Neuron.

“The human brain at any moment in time has to process quite a wealth of information,” said Nicolas Schuck, a postdoctoral research associate in the Princeton Neuroscience Institute and first author on the study. “The brain has evolved mechanisms that filter that information in a way that is useful for the task that you are doing. But the filter has a disadvantage: you might miss out on important information that is outside your current focus.”

Schuck and his colleagues wanted to study what happens at the moment when people realize there is a different and potentially better way of doing things. They asked volunteers to play a game while their brains were scanned with magnetic resonance imaging (MRI). The volunteers were instructed to press one of two buttons depending on the location of colored squares on a screen. However, the game contained a hidden pattern that the researchers did not tell the participants about, namely, that if the squares were green, they always appeared in one part of the screen and if the squares were red, they always appeared in another part. The researchers refrained from telling players that they could improve their performance by paying attention to the color instead of the location of the squares.

Volunteers played a game where they had to press one button or another depending on the location of squares on a screen. Participants that switched to a strategy based on the color of the square were able to improve their performance on the game. (Image source: Schuck, et al.)

Volunteers played a game where they had to press one button or another depending on the location of squares on a screen. Participants that switched to a strategy based on the color of the squares were able to improve their performance on the game. (Image source: Schuck, et al.)

Not all of the players figured out that there was a more efficient way to play the game. However, among those that did, their brain images revealed specific signals in the medial prefrontal cortex that corresponded to the color of the squares. These signals arose minutes before the participants switched their strategies. This signal was so reliable that the researchers could use it to predict spontaneous strategy shifts ahead of time, Schuck said.

“These findings are important to better understand the role of the medial prefrontal cortex in the cascade of processes leading to the final behavioral change, and more generally, to understand the role of the medial prefrontal cortex in human cognition,” said Carlo Reverberi, a researcher at the University of Milan-Bicocca and senior author on the study. “Our findings suggest that the medial prefrontal cortex is ‘simulating’ in the background an alternative strategy, while the overt behavior is still shaped by the old strategy.”

The study design – specifically, not telling the participants that there was a more effective strategy – enabled the researchers to show that the brain can monitor background information while focused on a task, and choose to act on that background information.

“What was quite special about the study was that the behavior was completely without instruction,” Schuck said. “When the behavior changed, this reflected a spontaneous internal process.”

Before this study, he said, most researchers had focused on the question of switching strategies because you made a mistake or you realized that your current approach isn’t working. “But what we were able to explore,” he said, “is what happens when people switch to a new way of doing things based on information from their surroundings.” In this way, the study sheds light on how learning and attention can interact, he said.

The study has relevance for the question of how the brain balances the need to maintain attention with the need to incorporate new information about the environment, and may eventually help our understanding of disorders that involve attention deficits.

Schuck designed and conducted the experiments while a graduate student at Humboldt University and the International Max Planck Research School on the Life Course (LIFE) together with the other authors, and conducted the analysis at Princeton University in the laboratory of Yael Niv, assistant professor of psychology and the Princeton Neuroscience Institute in close collaboration with Reverberi.

The research was supported through a grant from the U.S. National Institutes of Health, the International Max Planck Research School LIFE, the Italian Ministry of University, the German Federal Ministry of Education and Research, and the German Research Foundation.

Read the abstract.

Nicolas W. Schuck, Robert Gaschler, Dorit Wenke, Jakob Heinzle, Peter A. Frensch, John-Dylan Haynes, and Carlo Reverberi. Medial Prefrontal Cortex Predicts Internally Driven Strategy Shifts, Neuron (2015) http://dx.doi.org/10.1016/j.neuron.2015.03.015.

 

 

Cytomegalovirus hijacks human enzyme for replication (Cell Reports)

DiagramBy: Tien Nguyen, Department of Chemistry

More than 60 percent of the world’s population is infected with a type of herpes virus called human cytomegalovirus. The virus replicates by commandeering the host cell’s metabolism but the details of this maneuver are unclear.

Researchers at Princeton University have discovered that cytomegalovirus manipulates a process called fatty acid elongation, which makes the very-long-chain fatty acids necessary for virus replication. Published in the journal Cell Reports on March 3, the research team identified a specific human enzyme—elongase enzyme 7—that the virus induces to turn on fatty acid elongation.

“Elongase 7 was just screaming, ‘I’m important, study me,’” said John Purdy, a postdoctoral researcher in the Rabinowitz lab and lead author on the study.

He found that once a cell was infected by cytomegalovirus, the level of elongase 7 RNA increased over 150-fold. Purdy then performed a genetic knockdown experiment to silence elongase 7 and established that in its absence the virus was unable to efficiently replicate.

“Elongases are a family of seven related proteins. The particular importance of elongase 7 for cytomegalovirus replication was a pleasant surprise, and enhances its appeal as a drug target,” said Joshua Rabinowitz, a professor of chemistry and the Lewis-Sigler Institute for Integrative Genomics at Princeton and co-author on the paper.

Activation of the elongase enzyme led to an increase in very-long-chain fatty acids, which are used by the virus to build its viral envelope and replicate. The researchers fed infected cells a sugar called heavy isotope-labeled carbon-13 glucose, which is metabolized by the cell to form substrates for fatty acid elongation. The heavy isotope carbon-13 atoms were incorporated into new products that were detected and identified by their mass using a mass spectrometry method. This powerful technique provided insight into the amount of fatty acids produced and how they are constructed.

Cytomegalovirus infection mostly threatens populations with compromised immune systems and developing fetuses, and is the leading cause of hearing loss in children. Current treatments target the DNA replication step of the virus and are not very effective. These findings have advanced the understanding of the virus’s operations and identified fatty acid elongation as a key process that warrants further study.

This work was funded by National Institute of Health grants AI78063, CA82396, and GM71508 and an American Heart Association postdoctoral fellowship to J.G.P. (12POST9190001).

Read the full article here:

Purdy, J. G.; Shenk, T.; Rabinowitz, J. D. “Fatty Acid Elongase 7 Catalyzes the Lipidome Remodeling Essential for Human Cytomegalovirus Replication.” Cell Reports, 2015, 10, 1375.

 

Letting go of the (genetic) apron strings (Cell)

Researchers explore the shift from maternal genes to the embryo’s genes during development

By Catherine Zandonella, Office of the Dean for Research

Fruit fly embryo

Cells in an early-stage fruit fly embryo. (Image courtesy of NIGMS image gallery).

A new study from Princeton University researchers sheds light on the handing over of genetic control from mother to offspring early in development. Learning how organisms manage this transition could help researchers understand larger questions about how embryos regulate cell division and differentiation into new types of cells.

The study, published in the March 12 issue of the journal Cell, provides new insight into the mechanism for this genetic hand-off, which happens within hours of fertilization, when the newly fertilized egg is called a zygote.

“At the beginning, everything the embryo needs to survive is provided by mom, but eventually that stuff runs out, and the embryo needs to start making its own proteins and cellular machinery,” said Princeton postdoctoral researcher in the Department of Molecular Biology and first author Shelby Blythe. “We wanted to find out what controls that transition.”

Blythe conducted the study with senior author Eric Wieschaus, Princeton’s Squibb Professor in Molecular Biology, Professor of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, a Howard Hughes Medical Institute investigator, and a Nobel laureate in physiology or medicine.

Researchers have known that in most animals, a newly fertilized egg cell divides rapidly, producing exact copies of itself using gene products supplied by the mother. After a short while, this rapid cell division pauses, and when it restarts, the embryonic DNA takes control and the cells divide much more slowly, differentiating into new cell types that are needed for the body’s organs and systems.

To find out what controls this maternal to zygotic transition, also called the midblastula transition (MBT), Blythe conducted experiments in the fruit fly Drosophila melanogaster, which has long served as a model for development in higher organisms including humans.

These experiments revealed that the slower cell division is a consequence of an upswing in DNA errors after the embryo’s genes take over. Cell division slows down because the cell’s DNA-copying machinery has to stop and wait until the damage is repaired.

Blythe found that it wasn’t the overall amount of embryonic DNA that caused this increase in errors. Instead, his experiments indicated that the high error rate was due to molecules that bind to DNA to activate the reading, or “transcription,” of the genes. These molecules stick to the DNA strands at thousands of sites and prevent the DNA copying machinery from working properly.

To discover this link between DNA errors and slower cell replication, Blythe used genetic techniques to create Drosophila embryos that were unable to repair DNA damage and typically died shortly after beginning to use their own genes. He then blocked the molecules that initiate the process of transcription of the zygotic genes, and found that the embryos survived, indicating that these molecules that bind to the DNA strands, called transcription factors, were triggering the DNA damage. He also discovered that a protein involved in responding to DNA damage, called Replication Protein A (RPA), appeared near the locations where DNA transcription was being initiated. “This provided evidence that the process of awakening the embryo’s genome is deleterious for DNA replication,” he said.

The study also demonstrates a mechanism by which the developing embryo ensures that cell division happens at a pace that is slow enough to allow the repair of damage to DNA during the switchover from maternal to zygotic gene expression. “For the first time we have a mechanistic foothold on how this process works,” Blythe said.

The work also enables researchers to explore larger questions of how embryos regulate DNA replication and transcription. “This study allows us to think about the idea that the ‘character’ of the DNA before and after the MBT has something to do with the DNA acquiring the architectural features of chromatin [the mix of DNA and proteins that make up chromosomes] that allow us to point to a spot and say ‘this is a gene’ and ‘this is not a gene’,” Blythe said. “Many of these features are indeed absent early in embryogenesis, and we suspect that the absence of these features is what allows the rapid copying of the DNA template early on. Part of what is so exciting about this is that early embryos may represent one of the only times when this chromatin architecture is missing or ‘blank’. Additionally, these early embryos allow us to study how the cell builds and installs these features that are so essential to the fundamental processes of cell biology.”

This work was supported in part by grant 5R37HD15587 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development.

Read the abstract

Blythe, Shelby A. & Eric R. Wieschaus. Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition. Cell. Published online on March 5, 2015. doi:10.1016/j.cell.2015.01.050. http://www.sciencedirect.com/science/article/pii/S0092867415001282