Brian Strahl’s lab pinpoints new role for enzyme in DNA repair

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.

Original story published on news.unchealthcare.org

(Mark Derewicz, writer and Max Englund, graphic designer)

 

Brian Strahl, Ph.D.

Brian Strahl Promoted to Full Professor

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

Brian Strahl receives NIH and NSF grants to study gene expression

Congratulations to Dr. Brian Strahl, Professor of Biochemistry and Biophysics for receiving grants from the NIH and NSF

The National Institutes of Health and the National Science Foundation have given Dr. Brian Strahl grants to study the basic functions of gene regulation in the context of chromatin (DNA that is compacted by the action of histone proteins).  One grant is centered on the role of histone chaperones, which are proteins that insert or remove histones in the chromatin environment, and the other is on how enzymes that modify histones with chemical “tags” or post-translational modifications regulate the opening and closing of chromatin to make the DNA assessable for gene transcription.  These grants will significantly advance our understanding of gene expression.

Brian Strahl obtained his PhD in 1998 from North Carolina State University before performing his postdoctoral studies with Dr. C. David Allis at the University of Virginia. In 2001, Brian joined the faculty at the University of North Carolina at Chapel Hill, where his group has been addressing how the chemical “tags” on histones influence the structure and function of chromatin.  Dr. Strahl’s scientific contributions have been recognized with a number of awards, including a Presidential Early Career Award for Scientists and Engineers (PECASE) and the ASBMB Schering-Plough Research Institute Award for outstanding research contributions to biochemistry and molecular biology.

Link to Strahl Lab.

 

Brian Strahl Promoted to Full Professor

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 Dr. 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).

 

Brian Strahl featured in history of epigenetics story

Dr. Brian Strahl, associate professor of biochemistry & biophysics at UNC-Chapel Hill, is featured in a video and story about the history of epigenetics in the Jan 15, 2014 (Vol. 34, No. 2) issue of GEN (Genetic Engineering & Biotechnology News). The video and related featured story can be found here.

Drs. David Allis and Brian Strahl formally proposed the ‘histone code’ about 14 years ago. At that time, Dr. Strahl was a postdoctoral fellow in David Allis’ lab. This hypothesis provided an explanation for how distinct histone modifications, such as acetylation and methylation, could regulate epigenetic inheritance, gene expression and the control of cell growth and differentiation. However, limited experimental support exists for this hypothesis, and to date, it is unclear whether the binding of DNA-associated proteins to combinatorially-modified histones is a universal phenomenon of these regulators or is restricted to a subset of histone-binding proteins.

To address this long-standing question, Dr. Strahl’s lab (as well as others) are investigating how DNA-associated proteins bind to one or more histone modifications to regulate cellular function.  With his colleagues, the Strahl lab has been utilizing high-density histone peptide microarrays to determine how proteins with specialized histone interaction domains associate with multiple histone modifications to regulate chromatin structure and function.  Recent work has uncovered how the E3 ubiquitin ligase UHRF1 binds to histone H3 in a combinatorial manner – a binding event that governs the epigenetic inheritance of DNA methylation. To learn more, visit Brian Strahl’s page.

Brian Strahl and colleagues identify another piece of the ‘histone code’ puzzle

UNC-CHAPEL HILL – DNA is often called the blueprint of life, but the four letter combinations that make up the genetic code are just part of the story.  Built upon the DNA lies additional ‘epigenetic’ information in the form of a complex ensemble of chemical tags attached to the DNA itself and on proteins that package our DNA – called histones – which ultimately control how our genetic code is accessed and used.  Interestingly, histones are decorated with many types of chemical tags, and their particular combinations have been referred to as the ‘histone code’.  But understanding how this ‘code’ is interpreted by the cell has proven challenging due its sheer complexity and a lack of tools to study the ‘code’ inside the cell.

Now research from the University of North Carolina at Chapel Hill School of Medicine has shown how a protein called UHRF1 “reads” the ‘histone code’ in a specific way to perform an important cellular function. “Because the protein has been found to be defective in cancer, the finding not only lends new insight into functions downstream of the ‘histone code’ but could also point the way toward novel strategies for cancer treatment and prevention,” said senior study author Brian Strahl, PhD, associate professor of biochemistry and biophysics and member of the UNC Lineberger Comprehensive Cancer Center.

The research, which appears June 1^st, 2013, in the journal Genes and Development, is the latest of many studies to investigate the ‘histone code’ hypothesized more than ten years ago by Strahl and his former postdoctoral advisor C. David Allis. The hypothesis suggests that distinct combinations of histone modifications work together to form a ‘code,’ akin to the classic genetic code, in which three-letter combinations of nucleotides make an amino acid. These histone modifications – chemical changes like phosphorylation, acetylation and methylation — generate an epigenetic language that is interpreted through the ability to recruit proteins to DNA and histones that in turn modulate cellular functions.

“This study provides important support for the ‘histone code’ hypothesis, and also reiterates how difficult it will be to crack this ‘code.’ It is not enough to understand how one tag works in isolation, we now have to look at all different combinations of tags on both histones and DNA to piece together the puzzle encrypting this second layer of information,” said Strahl.

Over the last decade, researchers have pinpointed a number of different “domains” that proteins use to interact with, or read, the ‘histone code’. Scott Rothbart, PhD, a postdoctoral research fellow in Strahl’s laboratory, previously showed that one such domain on the protein UHFR1 – called the tandem Tudor — helps it bind to a histone in the cell that is methylated at a specific place. Adjacent to the Tudor was another domain called a PHD finger that helped the protein also bind the unmodified end of a histone. Rothbart and Strahl wondered if these neighboring domains might function together to help UHRF1 to read the ‘histone code’ and, subsequently, influence its ability to function in the cell.

To investigate this question, the researchers used a highly sophisticated peptide microarray technology developed in the Strahl lab. Just as DNA microarrays contain sections of DNA sequence spotted on glass slides, these peptide arrays contained sections of modified histone proteins. When the researchers applied the UHRF1 protein to the array, they found it bound the histone differently when it contained the linked Tudor and PHD domains than when it contained the domains in isolation. They then used biochemical techniques to show that the two domains of UHRF1 functioned together in cells – whereby each domain is making a key contribution to promote binding to the histone protein in a specific way.

One of the main functions of UHRF1 is the maintenance of a critical modification known as DNA methylation. The researchers showed that when these domains of UHRF1 were not functioning together to read the ‘histone code’, DNA methylation patterns in the cell were eventually lost.

“Abnormalities in the patterning of DNA methylation are a hallmark of many cancers. In addition, UHRF1 has been found to be defective in a number of cancers including prostate, breast, kidney, and lung cancer,” said Scott Rothbart, PhD, who is lead author of the study.

“UHRF1’s function in maintaining DNA methylation seems to be reversible – if you take it out of the cell you lose DNA methylation, but if you add it back you restore DNA methylation. We therefore think that by using small molecules to disrupt the recognition of the ‘histone code’ by UHRF1, we may be able to reprogram DNA methylation patterns in cancer cells.”

The research was supported in part by the National Institutes of Health, the Carolina Partnership and the University Cancer Research Fund, the Natural Sciences and Engineering Research Council of Canada, and the American Cancer Society.

Study co-authors from UNC were Bradley M. Dickson, PhD, postdoctoral research associate; Krzysztof Krajewski, PhD, research assistant professor; and Dmitri B. Kireev, PhD, research professor.  Other collaborators on the story were Cheryl Arrowsmith, PhD, professor; Michelle Ong, postdoctoral research associate; and Scott Houliston from the University of Toronto.

Media contacts:  Tom Hughes, (919) 966-6047, tahughes@unch.unc.edu

UNC scientists Marcey Waters, Brian Strahl & Xian Chen receive a W.M. Keck Foundation award to study protein methylation

Three scientists at the University of North Carolina (UNC) at Chapel Hill have received a grant from the W.M. Keck Foundation’s Medical Research Program to study a widespread but largely unexplored phenomenon that may be implicated in many diseases, including cancer.

The phenomenon, called protein methylation, has added a new dimension in our understanding of how genes and other aspects of the cell are regulated, explained Marcey L. Waters, principal investigator of the project and professor in the department of chemistry in UNC’s College of Arts and Sciences. Proteins are modified with these chemical tags, which in turn change their behavior in ways that are important for turning on or off their functions.

“However, protein methylation is challenging to study,” said Waters, “largely because we lack the right tools to study it. The goal of this grant is to help us develop the tools to better characterize this phenomenon – how many proteins are methylated in different cells, what happens when protein methylation goes awry, and how this influences other chemical interactions that regulate gene expression.”

The new tools will provide researchers with a map of these chemical tags and the patterns with which these tags decorate the surface of different proteins. A visual and/or chemical representation of these patterns may provide breakthrough insights into why certain cells become diseased while others stay healthy. Furthermore, Waters and her co-principal investigators, Drs. Brian D. Strahl and Xian Chen, associate professors in the department of biochemistry and biophysics in UNC’s School of Medicine, plan to use these new tools to pinpoint precisely which molecular interactions within cells break down and lead to disease. This could open the door to the development of highly specific and targeted therapies. Drs. Xian Chen and Brian Strahl are also members of the UNC Lineberger Comprehensive Cancer Center.

More information on the W.M. Keck Foundation can be found here.

College of Arts and Sciences contact: Dee Reid, (919) 843-6339, deereid@unc.eduUNC News Services contact: Thania Benios, (919) 962-8596, thania_benios@unc.edu

A recent paper by Dr. Brian Strahl and colleagues on H3K9me and DNA methylation is selected as nature structural & molecular biology’s “article of the month”.

A recent paper by UNC researcher Dr. Brian D Strahl has been selected as the November 2012 article of the month by .  In this paper, Dr. Strahl and colleagues show how UHRF1, an E3 ubiquitin ligase, links H3K9 methylation to DNA methylation maintenance in humans.

UNC Professor Dr. Brian Strahl interviewed in Science Magazine

In the latest issue of Science Magazine (Vol. 338 no 6106 p549 October 26, 2012), science writer Jeffrey Perkel explores the recent Epigenomics roadmap initiative funded by the National Institutes of Health (NIH).  In the article, Jeffrey interviews Brian D. Strahl, Associate Professor at UNC Chapel Hill, about the grant he recevied from the roadmap initiatve, and how his studies fit into the overall efforts of the epigenomics program. The article highlights how the initiave started, and how the new technologies it funded have led to fundamental insights into the function of chromatin. To learn more, click on the link below.

http://www.sciencemag.org/site/products/lst_20121026.xhtml

New research from the Strahl lab at UNC has established a link between histone H3 lysine 9 methylation and DNA methylation in humans

Mouse embryonic stem cells (blue, green) lose DNA methylation (red) in the absence of UHRF1. Source: Brian D Strahl Lab, UNC School of Medicine

CHAPEL HILL, N.C. – Over the last two decades, scientists have come to understand that the genetic code held within DNA represents only part of the blueprint of life. The rest comes from specific patterns of chemical tags that overlay the DNA structure, determining how tightly the DNA is packaged and how accessible certain genes are to be switched on or off.

As researchers have uncovered more and more of these “epigenetic” tags, they have begun to wonder how they are all connected. Now, research from Brian D. Strahl’s group at UNC has established a new link between two epigenetic modifications — histone H3 lysine 9 methylation and DNA methylation — in humans.

The study, which was published Sept. 30, 2012 by the journal Nature Structural & Molecular Biology, implicates a protein called UHRF1 in the maintenance of these epigenetic tags. Because the protein has been found to be defective in cancer, the finding could help scientists understand not only how microscopic chemical changes can ultimately affect the epigenetic landscape but also give clues to the underlying causes of disease and cancer.

“There’s always been the suspicion that regions marked by DNA methylation might be maintained by H3 lysine 9 methylation, and that has even been shown to be true in model organisms like fungus and plants,” said senior study author Brian D Strahl, PhD, associate professor of biochemistry and biophysics in the University of North Carolina School of Medicine and a member of UNC Lineberger Comprehensive Cancer Center. “But no one has been able to make that leap in human cells. It’s been controversial in terms of whether or not there’s really a connection. We have shown there is.”

Brian Strahl, along with his postdoctoral fellow Scott Rothbart, honed in on this discovery by using a highly sophisticated technique developed in his lab known as next generation peptide arrays. First the Strahl lab generated specific types of histone modifications and dotted them on tiny glass slides called “arrays.” They then used these “arrays” to see how histone modifications affected the docking of different proteins. One protein – UHRF1 – stood out because it bound a specific histone modification (lysine 9 methylation on histone H3) in cases where others could not.

Strahl and his colleagues focused the rest of their experiments on understanding the role of UHRF1 binding to this histone modification. They found that while other proteins that dock on this epigenetic tag are ejected during a specific phase of the cell cycle, mitosis, UHRF1 sticks around. Importantly, the protein’s association with histones throughout the cell cycle appears to be critical to maintaining another epigenetic tag called DNA methylation.  The result was surprising because researchers had previously believed that the maintenance of DNA methylation occurred exclusively during a single step of the cell cycle called DNA replication.

“This role of UHRF1 outside of DNA replication is certainly unexpected, but I think it is just another way of making sure we don’t lose information about our epigenetic landscape,” said Strahl.

The research was funded by the National Institutes of Health and the North Carolina Biotechnology Center.

Study co-authors from UNC were Scott B. Rothbart, PhD, a postdoc in Brian D. Strahl’s lab at UNC; Krzysztof Krajewski, PhD, research assistant professor; and Jorge Y. Martinez, a former student in Strahl’s lab.

Media contact: Tom Hughes, (919) 966-6047, tahughes@unch.unc.edu