All the Cell’s a Stage

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

f32e7726-fe1e-478f-a2dd-e6b4b8e5f492

Illustration by Max Englund/UNC Health Care

New story posted here

Brian Strahl

Brian Strahl, PhD

Posted in Uncategorized | Tagged , , , , | Leave a comment

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)

 ImageImageImage

Brian Strahl, Ph.D.

Posted in Uncategorized | Tagged , , , , | Leave a comment

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

Image

Posted in Uncategorized | Tagged , | Leave a comment

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_1

 

Posted in Uncategorized | Tagged , , , | Leave a comment

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).

 

Image

Posted in Uncategorized | Tagged , , | Leave a comment

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.Image

Posted in Uncategorized | Tagged , , | Leave a comment

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

Image

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 1st, 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

Posted in Uncategorized | Tagged , , , , , , , | Leave a comment