July 23, 2015
CHAPEL HILL, NC – For years, a crisis has been brewing in molecular biology. The problem is that antibodies – research tools used to identify key proteins at work in a cell – aren’t always what they seem. Unreliable antibodies have led to numerous instances of false findings, failed experiments, and wasted money and samples.
Enter the Histone Antibody Specificity Database (www.histoneantibodies.com), a newly launched online portal that lets scientists find the right antibodies for their research with a much higher degree of confidence than ever before. Rather than relying on the claims of antibody manufacturers, the database is populated with validated test results, allowing researchers to access and compare real-world data and pick the most reliable antibody for each experiment.
A paper published today in the journal Molecular Cell describes the database and the science behind it.
“I can’t think of any field of biomedical research that doesn’t rely on antibodies; they’re typically the linchpin in many studies,” said Brian D. Strahl, PhD, professor of biochemistry and biophysics in the University of North Carolina School of Medicine and the study’s co-senior author. “But how reliable are these tools? There’s been a real awakening in the biological community that we need better ways to know if the antibodies are recognizing what they’re intended to recognize. That’s what we aim to accomplish with this portal.”
The web portal focuses on histone antibodies, a subset of antibodies that are central to the fast-growing field of epigenetics. Epigenetics researchers examine how layers of information outside the genome control the ‘on’ and ‘off’ state of genes, much like a light switch, that in turn affect all aspects of human health. Scientists use histone antibodies to track the roles of various proteins in this vital process of gene regulation.
“Epigenetic regulation of our genome is at the core of all aspects of biology, and basic research in this area is uncovering key mechanisms that contribute to human health and disease,” said Scott B. Rothbart, PhD, assistant professor in the Center for Epigenetics at Van Andel Research Institute (VARI) and co-corresponding author of the study. “Drugs targeting the epigenetic machinery are being tested in oncology clinics now, and a better understanding of what the antibodies are recognizing will help researchers define more precisely how epigenetics works and ultimately lead to better, stronger conclusions that can make a difference for drug discovery and future therapeutic interventions.”
Initially developed in the 1970s, laboratory-produced antibodies have been commercially available to scientists for decades. Since then, many researchers have simply ordered antibodies from among the hundreds of thousands on the market, taking their labels at face value. But a growing body of evidence has revealed that an alarming number of antibodies do not perform as advertised.
Each histone antibody is supposed to bind to a specific protein target, allowing scientists to track where and how that protein is being regulated in healthy and diseased cells. However, some antibodies have been observed binding to other proteins in addition to their primary target while other antibodies have been shown to bind to just one target, but not the target indicated on the product label. In some cases, an antibody’s accuracy and specificity vary from one lot to the next, suggesting quality-control issues in the manufacturing process.
All of these errors muddy – and in some cases, completely undermine – research results.
While some vendors have stepped up their testing and quality control efforts, others have not, and few researchers have the resources or time to do the battery of tests recommended to ensure their antibodies are performing as indicated.
The new database offers an easy way to access detailed information about the accuracy and specificity of more than 100 commonly used and commercially available histone antibodies.
The testing method used to populate the database is based on custom-designed peptide microarrays that Strahl and his colleagues developed. The arrays present a library of all of the chemical modifications or “tags” known to occur on histone proteins. Analyzing antibodies that are developed to target these different tags on the arrays quickly illuminates the types of tags to which each antibody is capable of binding. This matters a lot. Each tag is thought to have a different function. For example, turning a gene ‘on’ or ‘off’.
Once word got out about the team’s peptide array platform, Strahl and his colleagues started fielding calls from other scientists asking for advice on antibody selection. Such interest from the scientific community sparked the team’s idea to buy all of the most common histone antibodies, test them on the array, and publish the results in an online portal accessible to everyone.
“We wanted it to be much more than a simple search-and-go database,” Strahl said. “Peptide arrays like the ones we developed are now available commercially, so any researcher, antibody manufacturer, or pharmaceutical company can run these tests. We built the portal so that people can easily upload their own results and the database can continue to grow.”
The portal allows users to search for antibodies using multiple parameters. A quality-control plan is in place to ensure the validity of user-submitted data.
Strahl said he hoped the database would enable more accurate and reproducible epigenetic findings.
“You don’t expect every antibody to be 100% perfect, but we think it’s important for researchers to be able to know what the flaws are,” Strahl said. “That way, at least people can interpret their results with the right amount of caution based on what the antibodies see – or don’t see.”
This work was supported by grants from the NIH and the W.M. Keck Foundation
Additional UNC coauthors include Terry R. Magnuson, PhD, the Sarah Graham Kenan Professor and chair of the department of genetics in the UNC School of Medicine; Erin Shanle, PhD, a postdoctoral research associate in Strahl’s lab; Jesse R. Raab, PhD, a postdoctoral fellow in Magnuson’s lab; Krzysztof Krajewski, PhD, research assistant professor; and Angela H. Guo, an undergraduate researcher in Strahl’s lab. Other coauthors include Bradley M. Dickson, PhD, a computational biophysicist in Rothbart’s lab at VARI, graduate student Adrian T. Grzbowski and Alexander J. Ruthenburg, PhD, of the University of Chicago; Steven Z. Josefowicz, PhD, and David Allis, PhD, of The Rockefeller University; and Stephen M. Fuchs, PhD, of Tufts University.
Van Andel Institute (VAI) is an independent biomedical research and science education organization committed to improving the health and enhancing the lives of current and future generations. Established by Jay and Betty Van Andel in 1996 in Grand Rapids, Michigan, VAI has grown into a premier research and educational institution that supports the work of more than 270 scientists, educators and staff. Van Andel Research Institute (VARI), VAI’s research division, is dedicated to determining the epigenetic, genetic, molecular, and cellular origins of cancer, Parkinson’s, and other diseases, and translating those findings into effective therapies. The Institute’s scientists work in on-site laboratories and participate in collaborative partnerships that span the globe. Learn more about Van Andel Institute or donate by visiting www.vai.org. 100% To Research, Discovery & Hope®
UNC has launched a new program that aims to address the fundamental gaps in knowledge surrounding epigenetic regulation, with a long-term goal of developing novel therapeutic approaches towards treating human disease. The program is centered around a highly collaborative and team science environment that has a dedicated goal of solving fundamental and challenging problems in chromatin biology – with an emphasis on developing novel approaches towards treating human disease. The large number of research faculty at UNC specializing in different areas of epigenetic research are optimally positioned to meet this challenge.
Faculty at UNC are focused on the basic mechanisms of epigenetic regulation using a variety of model organisms, high-throughput drug discovery efforts to target epigenetic machinery and clinical research that emphasizes epigenetic translational science employing the knowledge gained by basic research and drug discovery efforts. These researchers employ a range of cutting edge technologies, such as genomic and proteomic techniques, to address a vast number of epigenetic problems – and this research is supported by top-notch core facilities. The Chromatin and Epigenetics Program currently encompasses 34 faculty members, and participation of several laboratories from the National Institute of Environmental Health.
Along with the many resources and events associated with this new program, a highlight is the Chromatin and Epigenetics Certificate Program. Doctoral students interested in being formally part of the Program in Chromatin and Epigenetics can apply for entrance into a certificate program. The goal of this program is to provide students with more emphasis on epigenetic mechanisms and further exposure to approaches and techniques used in epigenetic research.
The leadership behind the program are Terry Magnuson, PhD, and Brian Strahl, PhD. Magnuson is a professor and chair of Genetics at UNC and the Executive Associate Dean for Research for the School of Medicine. Work in the Magnuson lab focuses on the role of mammalian genes in unique epigenetic phenomena such as genomic imprinting, X-chromosome inactivation, stem cell pluripotency and the tumor suppressor role of chromatin remodeling complexes. Strahl is a professor and director of graduate studies of Biochemistry and Biophysics at UNC. The Strahl lab addresses how histone post-translational modifications, and the combinatorial codes they create, contribute to the structure and function of chromatin.
Scientists from UNC-Chapel Hill have created a new way to investigate epigenetic mechanisms important in diseases ranging from Alzheimer’s to cancers.
Robert Duronio, PhD; Daniel McKay, PhD; Greg Matera, PhD; Brian Strahl, PhD.
CHAPEL HILL, NC –University of North Carolina scientists have created a new research tool, based on the fruit fly, to help crack the histone code. This research tool can be used to better understand the function of histone proteins, which play critical roles in the regulation of gene expression in animals and plants.
This work, published in the journal Developmental Cell, opens the door to experiments that are expected to uncover new biology important for a host of conditions, such as neurological diseases, diabetes, obesity, and especially cancer, which has become a hotbed of epigenetic research.
“People think cancer is a disease of uncontrolled proliferation, but that’s just one aspect of it,” said Robert Duronio, PhD, professor of biology and genetics and co-senior author. “Cancer is actually a disease of development in which the cells don’t maintain their proper functions; they don’t do what they’re supposed to be doing.” Somehow, the gene regulation responsible for proper cell development goes awry.
One aspect of gene regulation involves enzymes placing chemical tags or modifications on histone proteins – which control a cell’s access to the DNA sequences that make up a gene. Properly regulated access allows cells to develop, function, and proliferate normally. The chemical modification of histones is thought to be a form of epigenetic information – information separate from our DNA – that controls gene regulation. This idea is based on the study of the enzymes that chemically modify histones. However, there is a flaw in this argument.
“In complex organisms, such as fruit flies, mice, and humans, scientists have only been able to infer how these enzymes mechanistically accomplish their tasks,” said Daniel McKay, PhD, assistant professor of genetics and biology and first author of the paper. “It’s been technically impossible to directly study the role of histone modifications. Now, through our collaboration between UNC biologists, we’ve been able to develop a tool in fruit flies to directly test the function of histones independently of the enzymes that modify them.”
This is crucial because therapies, such as cancer drugs, can target histones. With this new research tool, scientists will be able to better study thousands of enzyme-histone interactions important for human health.
“If you think of the genome as a recipe book, then you could say we’ve made it possible to know that there are hidden ingredients that help explain how specific recipes turn out correctly or not,” said Greg Matera, PhD, professor of biology and genetics and co-senior author of the paper. “That’s the first step in scientific discovery – knowing that there are things we need to look for and then searching for them.”
Before now, a lot of this epigenetic research had been done in yeast – single cell organisms that also use enzymes to lay chemical tags on histone proteins. This work has yielded many interesting findings and has led to the development of therapeutics. But some of this work has led to an oversimplification of human biology, leaving many questions about human health unanswered.
For instance, in complex organisms, enzymes in cells typically do more than one thing. One likely reason for this is that animals undergo cellular differentiation; human life begins as a single cell that differentiates into the various cell types needed for different organs, body parts, blood, the immune system, etc. This differentiation has to be maintained throughout life.
“Because of this, animals likely have a greater requirement for epigenetic regulation than yeast do,” Matera said. “Animal cells have to ‘remember’ that they must express genes in specific ways.” When cancer cells start dividing rapidly to form tumors, these cells are actually reverting to an earlier time in their development when they were supposed to divide rapidly. The gene regulation that was supposed to rein them in has gone haywire.
Whereas in yeast, a histone-modifying enzyme might have a single regulatory task, the human version of that same enzyme might have other regulatory tasks that involve additional proteins.
“In fact, maybe the really critical target of that one modifying enzyme is some other protein that we don’t know about yet,” Matera said. “And we need to know about it.”
The best way to figure that out would be to make it impossible for the enzyme to modify a histone by changing – or mutating – the histone protein. If a histone protein could be disabled in this way and cells still behaved normally, then that would mean there was some other protein that the enzyme acted on. To do this, however, would require replacing a histone gene with a genetically engineered one that could not be modified by an enzyme.
The problem is that in animals, such as mice and humans, there are many histone genes and they are scattered throughout the genome. This makes replacing them with ‘designer’ histone genes difficult. In addition, other genes are located in between the histone genes. Therefore, deleting the portion of the chromosome with histone genes in order to replace them with a modified one would wind up deleting other genes vital for survival. This would make such an approach in, say, a mouse, useless.
“It has been technically impossible to do this kind of research in complex organisms,” Duronio said. “But fruit flies have all their histone genes in one place on the chromosome; this makes it feasible to delete the normal genes and replace them with designer genes.”
Matera, Duronio, and McKay led an effort to delete the histone genes in fruit flies and replace them with specific designer histone genes they created. These new genes were created so they could not be the repositories of epigenetic tags or modifications. That is, the modifying enzyme would not be able to do its job on that particular protein.
As shown in the Developmental Cell paper, the researchers put their new tool to the test. They “broke” one histone protein that had been identified to interact in a specific way with a modifying enzyme, and they got the outcome in fruit flies they expected. But for another enzyme-histone interaction, the researchers got an unexpected result.
Previously, in mammalian cells, other researchers had discovered that when you mutate a specific modifying enzyme, the result is death because the cells can’t replicate.
With their new fruit fly research model, the UNC researchers altered the histone gene so that this particular enzyme could not modify its histone protein target. The result was not death. In fact, the flies lived and flew as normal flies do. This meant that the enzyme, which was previously proven to be vital to life, must do something else very important.
“There must be another target for that modifying enzyme,” Matera said. “There must be another hidden carrier of epigenetic information that we don’t know about.”
McKay added, “This is a demonstration of the potential of our epigenetic platform. Going forward, we’re going to do a lot more experiments to identify more discrepancies and hopefully other targets of these enzymes. We’re on the ground floor of a long-term project.”
This research shows that the epigenetic recipe book for yeast is thin. The recipe book for humans, which is genetically akin to the one for fruit flies, is much thicker, more complex, and full of hidden ingredients scientists have yet to discover.
Now, scientists have a tool to test the recipes.
Brian Strahl, PhD, professor of biochemistry and Biophysics in the School of Medicine, is also a principal investigator of this study.
Duronio, Matera, and McKay are professors in the UNC School of Medicine and the College of Arts and Sciences.
Strahl, Duronio, and Matera are members of the UNC Lineberger Comprehensive Cancer center. Matera, Duronio, and McKay are members of the Integrative Program for Biological and Genome Sciences. Duronio is the director of the program.
National Institutes of Health and the University of North Carolina funded this research.
Media Contact: Mark Derewicz, 919-923-0959, email@example.com
February 9, 2015
Brian Strahl, PhD, and his band of biochemists unravel the complicated mysteries of the epigenetic code to find a culprit in cancer development.
By Mark Derewicz
Every single human cell contains every single human gene. But depending on the cell, only some of these genes need to be expressed or “turned on.” For instance, a heart cell has all the genes needed for, say, proper kidney function. But that heart cell won’t express those genes. In a heart cell, those genes are “turned off.” When one of these “wrong” genes is turned on by mistake, the result can be rampant cell growth – cancer.
How this happens used to be the stuff of science fiction. Now, scientists know that there are tiny proteins –epigenetic proteins – that sit atop the genetic code inside cells. These proteins are responsible for turning on or off the genes.
Now, UNC researchers discovered that one gene-regulating protein called Bre1 must be maintained in the proper amount for other epigenetic players to do their jobs properly. It’s a key coordinator in the sort of cellular scenes that can turn a healthy cell into a cancer cell.
Setting the scene
Within each cell of the body is an ongoing and intricate performance with genes playing some of the leading roles. As with all performances, the actors do not act alone, but instead, rely on support from behind the scenes. This supporting staff provides the script and cues for what the genes are supposed to say and do – how genes are accessed and used. Important members of the support staff are histones – the proteins that package genes inside cells and allow them to be used for various cellular functions that keep us healthy; they allow the plot to unfold perfectly.
Unfortunately, sometimes cues are missed or lines are forgotten and the show doesn’t go as planned. This causes the actors to speak when they should be quiet or stay quiet when they should speak. And if one of these actor genes happens to be essential for, say, cell growth, then the result can be disastrous. The actors take the story in an unintended direction.
All this supporting staff is part of epigenetics – epi meaning on or above – a field that focuses on the environment and the players that allow our genes to act.
“I think epigenetics is a new frontier of cancer research,” says Brian Strahl, Ph.D., a professor of biochemistry and biophysics in the UNC School of Medicine. “We can now sequence the entire genome of a cancer cell, and what we’re finding is that many cancers have mutations in the epigenetic machinery. We’re not just finding this in cancer cell lines in the lab but in cancer patients.”
The director’s cut
Strahl, who’s a member of the UNC Lineberger Comprehensive Cancer Center, said major questions surround how histones wrap up the DNA into chromatin – a structure that allows or denies access to the genetic information inside our cells.
This is what Strahl studies. His goal is to figure out precisely how histones contribute to basic biological functions and, in turn, contribute to cancers and other diseases. Adding a twist to this idea, however, is the fact that not every histone is the same.
“We’ve already learned that the histone proteins found at the sites of genes can be chemically modified with a variety of small chemical “tags” that either promote or further prevent access to our genetic information – our DNA. And this access or denial ultimately affects genes so they are either activated or not.”
These chemical tags come from a variety of sources – mainly the food we eat, the chemicals in the environment that gets inside us through our skin and lungs, for example, and the various biological chemicals that simply make us tick. Proper nutrients, for instance, allow for the formation of chemical tags to direct the histones to activate genes in the proper ways. Nasty environmental stuff, such as cigarette smoke, can mess up the epigenetic machinery.
Yet, these chemical tags are not ultimately in charge of the genes. Another layer of proteins above the histones are responsible for putting on the chemical tags.
“Something has to ensure that these chemical tags on histones are regulated properly, to ensure that the tags are only present on the right genes at the right time,” Strahl said.
Strahl and graduate student Glenn Wozniak focused on one of the proteins that add these chemical tags – a protein called Bre1, which keeps one tag – ubiquitin – in check.
In a sense, Bre1 hires ubiquitin; it allows ubiquitin to do its job.
Ubiquitin is known to help a histone open up the cell’s chromatin to expose genes for activation. When ubiquitin is finished, it is removed from the histones, and the genes become inactivated.
If this process goes awry – if the genes are allowed to remain active indefinitely – then normal cells can turn into cancer cells. And the entire cellular performance collapses.
The Goldilocks effect
Until now, how this happened was unclear. Through a series of experiments, Strahl and Wozniak found that, like the chemical tags themselves, a precise amount of Bre1 must be maintained to ensure that just the right amount of ubiquitin is added to histones.
“We found that if there’s too little Bre1, then the gene doesn’t turn on,” Strahl said. “If there’s too much, the gene doesn’t shut off. We call it the Goldilocks effect.”
Wozniak added, “We also found that when Bre1 is not needed or when it doesn’t perform its function, it’s removed as a control mechanism. There won’t be as much ubiquitin on histones because Bre1 is not there.”
Strahl and Wozniak’s finding illuminates what had been an epigenetic mystery. Scientific literature on Bre1 had been mixed.
“Some studies indicated that Bre1 had a role as a tumor suppressor,” Strahl said. “Other studies showed that it’s a cancer promoter. So there’s been conflicting evidence about all of this. Now we know. If there’s too little Bre1, the gene won’t turn on.” This could turn off the genes that protect the cell from cancer. “If there’s too much,” Strahl said. “Then the genes might not turn off.” This could also trigger cancer development.
“When you think about it, Bre1 could be a really good target for a cancer drug,” Strahl said. “Cancer cells divide rapidly. A lot of chemotherapies involve creating DNA damage within all rapidly dividing cells. But if you just target the Bre1 protein and maybe shut it off, you could have very bad outcomes specifically for rapidly dividing cancer cells. They wouldn’t be able to transcribe genes anymore.”
Strahl and Wozniak’s study appeared in the journal Genes and Development. The National Science Foundation funded this work
Illustration by Max Englund/UNC Health Care
The discovery, from the lab of Brian Strahl, PhD, offers insights for the creation of better, more targeted therapies for various forms of cancer.
Twelve years ago, UNC School of Medicine researcher Brian Strahl, PhD, found that a protein called Set2 plays a role in how yeast genes are expressed – specifically how DNA gets transcribed into messenger RNA. Now his lab has found that Set2 is also a major player in DNA repair, a complicated and crucial process that can lead to the development of cancer cells if the repair goes wrong. “We found that if Set2 is mutated, DNA repair does not properly occur” said Strahl, a professor of biochemistry and biophysics. “One consequence could be that if you have broken DNA, then loss of this enzyme could lead to downstream mutations from inefficient repair. We believe this finding helps explain why the human version of Set2 – which is called SETD2 – is frequently mutated in cancer.”
The finding, published online June 9 in the journal Nature Communications, is the first to show Set2’s role in DNA repair and paves the way for further inquiry and targeted approaches to treating cancer patients. In previous studies, including recent genome sequencing of cancer patients, human SETD2 has been implicated in several cancer types, especially in renal cell carcinoma – the most common kind of kidney cancer. SETD2 plays such a critical role in DNA transcription and repair that Strahl is now teaming up with fellow UNC Lineberger Comprehensive Cancer Center members Stephen Frye, PhD, director of the UNC Center for Integrative Chemical Biology and Drug Discovery (CICBDD), Jian Jin, PhD, also with the CICBDD, and Kim Rathmell, MD, PhD, an associate professor in the department of genetics. Their hope is to find compounds that can selectively kill cells that lack SETD2. Such personalized medicine is a goal of cancer research at UNC and elsewhere.
In recent years, scientists have discovered the importance of how DNA is packaged inside nuclei. It is now thought that the “mis-regulation” of this packaging process can trigger carcinogenesis. This realm of research is called epigenetics, and at the heart of it is chromatin – the nucleic acids and proteins that package DNA to fit inside cells.
Proper packaging allows for proper DNA replication, prevents DNA damage, and controls how genes are expressed. Typically, various proteins tightly regulate how these complex processes happen, including how specific enzyme modifications occur during these processes. Some proteins are involved in turning “on” or turning “off” these modifications. For instance, protein and DNA modifications involved in gene expression in kidneys must at some point be turned off.
In 2002, Brian Strahl found that Set2 in yeast played a role as an off switch in gene expression – particularly when DNA is copied to make RNA. Now, Brian Strahl’s team found that Set2 also regulates how the broken strands of DNA – the most severe form of DNA damage in cells – are repaired. If DNA isn’t repaired correctly, then that can result in disastrous consequences for cells, one of them being increased mutation that can lead to cancer.
Through a series of biochemical and genetic experiments, Deepak Jha, a graduate student in Strahl’s lab, was able to see what happens when cells experience a break in the double-strand of DNA. “We found that Set2 is required when cells decide how to repair the break in DNA,” said Jha, the first author of the Nature Communications paper. He said that the loss of Set2 keeps the chromatin in a more open state – not as compact as normal. This, Strahl said, leaves the DNA at greater risk of mutation. “This sort of genetic instability is a hallmark of cancer biology,” Jha said.
Strahl and Jha said they still don’t know the exact mechanism by which Set2 becomes mutated or why its mutation affects its function. But that’s the subject of their next inquiry. They are now collaborating with Rathmell and Ian Davis, also members of UNC Lineberger Comprehensive Cancer Center, to study how the human protein SETD2 is regulated and how its mutation contributes to cancer. Strahl said, “We think this work will lead to a greater understanding of cancer biology, and open the door to future therapeutic approaches for patients in need of better treatment options.”
This research was funded through a grant from the National Institutes of Health. Link to Strahl Lab.
(Mark Derewicz, writer and Max Englund, graphic designer)
Brian Strahl, Ph.D.
Congratulations to Dr. Brian Strahl who was promoted to full professor effective April 25, 2014.
Brian Strahl’s laboratory has been at the forefront of understanding how histones and their covalent modifications regulate chromatin structure and function, with a particular emphasis on how chromatin impacts gene regulation. His career began at the University of North Carolina (UNC) at Greensboro, where he majored in Biology and Chemistry. He then obtained his doctorate degree in Biochemistry from North Carolina State University in 1998, where he provided new insights into the transcriptional regulation of the Follicle Stimulating Hormone-ß (FSHß) gene. His curiosity in transcriptional regulation led him to pursue his postdoctoral studies in the laboratory of Dr. C. David Allis at the University of Virginia. In David’s lab, he made a number of seminal discoveries in the area of histone methylation and histone function. In particular, Dr. Strahl identified new sites of histone lysine methylation and linked this chromatin modification to gene regulation using the model organism Tetrahymena. His work also helped to identify the first lysine-specific histone methyltransferase in humans and several others in the budding yeast S. cerevisiae. Dr. Strahl, with David Allis, also coined the idea of the histone code – a highly influential review that has been cited well over 5000 times.
In December of 2001, Dr. Strahl initiated his lab at UNC-Chapel Hill, where he has now been promoted to the rank of Full Professor in the Department of Biochemistry & Biophysics. Dr. Strahl is also the Director of Graduate Studies and is the Faculty Director of the UNC High-Throughput Peptide Synthesis and Arraying Core Faculty.
With his colleagues, his group has been at the forefront of determining how small chemical additions or molecular “tags” on histone proteins regulate the accessibility of DNA and the genetic information it contains. Histones are central to the organization of our DNA in cells. These proteins come in a variety of types or isoforms – defined as histone H3, H4, H2A and H2B, and they associate with themselves as a means to package our DNA within the small nuclei of cells. Two copies each of each histone type come together to form what is called an octamer, which wraps approximately 147 base pairs of DNA around it. This structure (histones + DNA) makes up the fundamental building block of chromatin – the nucleosome. Strings of nucleosomes make up the chromatin fiber, and they organize into higher-order structures that are poorly defined but allow large genomes (e.g., ~3 billion base pairs making up the human genome) to fit in the confines of a 2-10 micron nucleus. With all this compaction, a fundamental question Brian Strahl’s group has been addressing is how our genome is made accessible at the right place and time for all of the fundamental processes that occurs with DNA (e.g., gene expression, DNA repair and replicating the genome).
Dr. Strahl’s UNC group has made a number of key contributions into the role of these chemical tags or modifications on histones (e.g., methylation and ubiquitylation), and more recently, DNA methylation. Using budding yeast as a model system, his lab has helped to show how histone-modifying enzymes “hitch a ride” with RNA polymerase II (RNAPII) during gene transcription, and how the modifications they put on histones contributes to the transcription process.
More recently, the Strahl group has focused on how patterns of histone modifications (i.e., the ‘histone code’) regulate the structure and function of chromatin. To understand how patterns of histone modifications function, they developed a high-throughput peptide microarray platform, where hundreds of synthetic histone peptides that are combinatorially modified with distinct chemical modifications are arrayed on glass slides. With this technology, the lab has been interrogating chromatin-associated proteins that are critical for cell growth and development, and/or are dysregulated in human cancer. One such protein his lab has recently been focused on is UHRF1, an E3 ubiquitin ligase essential for DNA methylation. Dr. Strahl’s lab showed that this protein binds to a particular pattern of histone modification to regulate the maintenance of DNA methylation in human cells. They are continuing these lines of studies to address how the chromatin-machinery engages histones and DNA, and how these factors influence fundamental processes in the cell such as gene transcription.
Work in Dr. Strahl’s lab is funded by the National Institutes of Health (NIH), the Keck Foundation and the National Science Foundation (NSF).
Learn more about the Strahl Lab here.
-Brian Strahl, PhD