Three UC San Diego Scientists Garner ENCODE GrantsRecently, the ENCyclopedia Of DNA Elements, otherwise known as ENCODE,  made national news with the single-day publication in multiple journals of dozens of related papers intended to more fully flesh out the functional components of the human genome. The findings were a big step, but the blueprint of human biology remains incomplete.  This week, the National Human Genome Research Institute, part of the National Institutes of Health, announced new grants worth $30.3 million this year alone to expand and deepen the effort.Three scientists at UC San Diego were among the recipients. Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UCSD, and colleagues have been awarded $11.4 million over four years (roughly $2.86 million per year) to continue their work developing a working catalog of the mouse genome.“The goal is to enhance use of this model organism in studying a wide range of tissues not readily accessible in the human (genome), and to tap into the power of comparative genomic analysis to increase understanding of the function of the human genome,” said an NHGRI official. Earlier this year, Ren and colleagues published a paper in Nature that described mapping for the first time a significant portion of the functional sequences of the mouse genome. Specifically, they looked at genome regions containing cis-regulatory elements, key stretches of DNA that appear to regulation the transcription of genes. Misregulation of genes can result in diseases like cancer.In addition to Ren’s grant, Gene Yeo, PhD, assistant professor of cellular and molecular medicine, and Xiang-Dong Fu, PhD, professor of cellular and molecular medicine (both, along with Ren, are members of the Institute of Genomic Medicine) are part of a team headed by Brenton Graveley, PhD, of the University of Connecticut Health Center that was awarded a four-year, $9.3 million grant to analyze human RNA transcripts to identify protein-binding sites and investigate their function. Proteins that bind to RNA can directly regulate protein production from RNA molecules, as well as affect protein production by regulating degradation of RNA molecules. The project is ENCODE’s first production scale effort to map protein-binding sites in RNA.
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Three UC San Diego Scientists Garner ENCODE Grants

Recently, the ENCyclopedia Of DNA Elements, otherwise known as ENCODE,  made national news with the single-day publication in multiple journals of dozens of related papers intended to more fully flesh out the functional components of the human genome.

The findings were a big step, but the blueprint of human biology remains incomplete.  This week, the National Human Genome Research Institute, part of the National Institutes of Health, announced new grants worth $30.3 million this year alone to expand and deepen the effort.

Three scientists at UC San Diego were among the recipients. Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UCSD, and colleagues have been awarded $11.4 million over four years (roughly $2.86 million per year) to continue their work developing a working catalog of the mouse genome.

“The goal is to enhance use of this model organism in studying a wide range of tissues not readily accessible in the human (genome), and to tap into the power of comparative genomic analysis to increase understanding of the function of the human genome,” said an NHGRI official.

Earlier this year, Ren and colleagues published a paper in Nature that described mapping for the first time a significant portion of the functional sequences of the mouse genome. Specifically, they looked at genome regions containing cis-regulatory elements, key stretches of DNA that appear to regulation the transcription of genes. Misregulation of genes can result in diseases like cancer.

In addition to Ren’s grant, Gene Yeo, PhD, assistant professor of cellular and molecular medicine, and Xiang-Dong Fu, PhD, professor of cellular and molecular medicine (both, along with Ren, are members of the Institute of Genomic Medicine) are part of a team headed by Brenton Graveley, PhD, of the University of Connecticut Health Center that was awarded a four-year, $9.3 million grant to analyze human RNA transcripts to identify protein-binding sites and investigate their function. Proteins that bind to RNA can directly regulate protein production from RNA molecules, as well as affect protein production by regulating degradation of RNA molecules. The project is ENCODE’s first production scale effort to map protein-binding sites in RNA.

Binding Sites for LIN28 Protein Found in Thousands of Human Genes

Protein expression also causes changes in gene splicing

A study led by researchers at the UC San Diego Stem Cell Research program and funded by the California Institute for Regenerative Medicine (CIRM) looks at an important RNA binding protein called LIN28, which is implicated in pluripotency and reprogramming as well as in cancer and other diseases.  According to the researchers, their study – published in the September 6 online issue of Molecular Cell – will change how scientists view this protein and its impact on human disease.

Studying embryonic stem cells and somatic cells stably expressing LIN28, the researchers defined discrete binding sites of LIN28 in 25 percent of human transcripts.  In addition, splicing-sensitive microarrays demonstrated that LIN28 expression causes widespread downstream alternative splicing changes –variations in gene products that can result in cancer or other diseases.

“Surprisingly, we discovered that LIN28 not only binds to the non-coding microRNAs, but can also bind directly to thousands of messenger RNAs,” said first author Melissa Wilbert, a doctoral student in the UC San Diego Biomedical Sciences graduate program. 

Messenger RNA or mRNA, are RNA molecules that encode a chemical “blueprint” for the synthesis of a protein.  MicroRNAs (miRNAs) are short snippets of RNA that are crucial regulators of cell growth, differentiation, and death.  While they don’t encode for proteins, miRNAs are important for regulating protein production in the cell by repressing or “turning off” genes.

“The LIN28 protein is linked to growth and development and is important very early in human development,” said principal investigator Gene Yeo, PhD, MBA, of the Department of Cellular and Molecular Medicine, the Stem Cell Research Program and the Institute for Genomic Medicine at UC San Diego. “It is usually turned off in adult tissue, but can be reactivated, for instance, in certain cancers or metabolic disorders, such as obesity.”

Using genome-wide biochemical methods to look at the set of all RNA molecules across the transcriptome, the researchers found that LIN28 recognizes and binds to a known hairpin-like structure found on the let-7 family of miRNA, but surprisingly, this same structure is also found on mRNAs, allowing LIN28 to directly regulate thousands of targets.

“One of these targets actually encodes for the LIN28 protein itself. In other words, LIN28 helps to make more of itself,” said Yeo.  This process, known as autoregulation, helps to maintain a so-called “steady-state” system in which a protein positively regulates its own production by binding to a regulatory element of the mRNA for the gene coding it. 

“Since these mRNA targets include those known to be involved in gene splicing, we also implicate LIN28 in the regulation of alternative splicing,” said Wilbert, adding that abnormal variations in splicing are often implicated in cancer and other disorders.   

In the splicing process, fragments that do not typically code for protein, called introns, are removed from gene transcripts, and the remaining sequences, called exons, are reconnected.  The splicing factor proteins themselves, as well as the location where these proteins bind, dictate which pieces of the RNA are included or excluded in the final gene transcript – in much the same way that removing and inserting scenes, or splicing, can alter the plot of a movie.

The discovery of thousands of precise binding sites for LIN28 within human genes offers a novel look at the role this protein plays in development and disease processes.  For example, scientists had looked at targeting a particular miRNA called let-7 to halt cancer growth.  “But we now see that LIN28 can, in essence, bypass let-7 and find many, many other binding sites – perhaps with the same adverse effect of uncontrolled cell overgrowth,” said Yeo.  “This suggests that LIN28 itself should be the therapeutic target for diseases, rather than let-7 or other miRNAs.”

Parsing a process of life Transcription is the first step in gene expression, the process by which information contained in a gene is used to make functional products, such as proteins. It’s fundamental to life and, not surprisingly, extraordinarily complicated.            In the July 22, 2012 issue of Nature Structural & Molecular Biology, Dong Wang, PhD, assistant professor in the Skaggs School of Pharmacy and Pharmaceutical Science, and colleagues further elucidate how transcription is altered by some forms of cytosine. Cytosine, of course, is one of the four main bases that comprise DNA and RNA (along with adenine, guanine and thymine; uracil replacing thymine in RNA). There are at least five forms of cytosine in human DNA. Wang and colleagues have discovered that two recently identified forms of cytosine, known as 5fC and 5caC, significantly reduce the transcription rate in vitro. The finding, said Wang, suggests that some forms of cytosine (and perhaps other players yet-to-be-identified) may provide another layer of regulation and fine-tuning to the transcription process. By slowing the activity of RNA polymerase II, a major transcriptional enzyme, 5fC and 5caC may make it easier for other enzymes, proteins and factors to play their parts in the larger act of gene expression. Photo: Structure of RNA Polymerase II, a key enzyme in mammalian cells that catalyzes the transcription of DNA into messenger RNA, the molecule that in turn dictates the order of amino acids in proteins. Courtesy of National Institute of General Medical Sciences.
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Parsing a process of life

Transcription is the first step in gene expression, the process by which information contained in a gene is used to make functional products, such as proteins. It’s fundamental to life and, not surprisingly, extraordinarily complicated.
           
In the July 22, 2012 issue of Nature Structural & Molecular Biology, Dong Wang, PhD, assistant professor in the Skaggs School of Pharmacy and Pharmaceutical Science, and colleagues further elucidate how transcription is altered by some forms of cytosine.

Cytosine, of course, is one of the four main bases that comprise DNA and RNA (along with adenine, guanine and thymine; uracil replacing thymine in RNA). There are at least five forms of cytosine in human DNA. Wang and colleagues have discovered that two recently identified forms of cytosine, known as 5fC and 5caC, significantly reduce the transcription rate in vitro.

The finding, said Wang, suggests that some forms of cytosine (and perhaps other players yet-to-be-identified) may provide another layer of regulation and fine-tuning to the transcription process. By slowing the activity of RNA polymerase II, a major transcriptional enzyme, 5fC and 5caC may make it easier for other enzymes, proteins and factors to play their parts in the larger act of gene expression.

Photo: Structure of RNA Polymerase II, a key enzyme in mammalian cells that catalyzes the transcription of DNA into messenger RNA, the molecule that in turn dictates the order of amino acids in proteins. Courtesy of National Institute of General Medical Sciences.

A photomicrograph of superficial keratinocytes or skin cells. Image courtesy of Thomas Deerinck, National Center for Microscopy and Imaging Research, UC San Diego. What Happens When We SunburnResearchers describe inflammatory mechanism for first time The biological mechanism of sunburn – the reddish, painful, protective immune response from ultraviolet (UV) radiation – is a consequence of RNA damage to skin cells, report researchers at the University of California, San Diego School of Medicine and elsewhere in the July 8, 2012 Advance Online Publication of Nature Medicine. The findings open the way to perhaps eventually blocking the inflammatory process, the scientists said, and have implications for a range of medical conditions and treatments. “For example, diseases like psoriasis are treated by UV light, but a big side effect is that this treatment increases the risk of skin cancer,” said principal investigator Richard L. Gallo, MD, PhD, professor of medicine at UC San Diego School of Medicine and Veterans Affairs San Diego Healthcare System. “Our discovery suggests a way to get the beneficial effects of UV therapy without actually exposing our patients to the harmful UV light. Also, some people have excess sensitivity to UV light, patients with lupus, for example. We are exploring if we can help them by blocking the pathway we discovered.” Using both human skin cells and a mouse model, Gallo, first author Jamie J. Bernard, a post-doctoral researcher, and colleagues found that UVB radiation fractures and tangles elements of non-coding micro-RNA – a special type of RNA inside the cell that does not directly make proteins. Irradiated cells release this altered RNA, provoking healthy, neighboring cells to start a process that results in an inflammatory response intended to remove sun-damaged cells. We see and feel the process as sunburn. More here
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A photomicrograph of superficial keratinocytes or skin cells. Image courtesy of Thomas Deerinck, National Center for Microscopy and Imaging Research, UC San Diego.

What Happens When We Sunburn
Researchers describe inflammatory mechanism for first time

The biological mechanism of sunburn – the reddish, painful, protective immune response from ultraviolet (UV) radiation – is a consequence of RNA damage to skin cells, report researchers at the University of California, San Diego School of Medicine and elsewhere in the July 8, 2012 Advance Online Publication of Nature Medicine.

The findings open the way to perhaps eventually blocking the inflammatory process, the scientists said, and have implications for a range of medical conditions and treatments.

“For example, diseases like psoriasis are treated by UV light, but a big side effect is that this treatment increases the risk of skin cancer,” said principal investigator Richard L. Gallo, MD, PhD, professor of medicine at UC San Diego School of Medicine and Veterans Affairs San Diego Healthcare System. “Our discovery suggests a way to get the beneficial effects of UV therapy without actually exposing our patients to the harmful UV light. Also, some people have excess sensitivity to UV light, patients with lupus, for example. We are exploring if we can help them by blocking the pathway we discovered.”

Using both human skin cells and a mouse model, Gallo, first author Jamie J. Bernard, a post-doctoral researcher, and colleagues found that UVB radiation fractures and tangles elements of non-coding micro-RNA – a special type of RNA inside the cell that does not directly make proteins. Irradiated cells release this altered RNA, provoking healthy, neighboring cells to start a process that results in an inflammatory response intended to remove sun-damaged cells.

We see and feel the process as sunburn.

More here

The art depicts RNAs wound in an undecipherable knot bound by hnRNP proteins, describing the intractable problem of RNA regulation as a “Gordian Knot.” As Alexander the Great discovered, the best way to unravel such a knot is a brute force approach, and thus Huelga et al. attack this puzzle through multiple, genome-wide swords (splicing arrays, CLIP-seq, and RNA-seq). The Splice of Life: Proteins Cooperate to Regulate Gene Splicing Understanding how RNA binding proteins control the genetic splicing code is fundamental to human biology and disease – much like editing film can change a movie scene. Abnormal variations in splicing are often implicated in cancer and genetic neurodegenerative disorders. In a step toward deciphering the “splicing code” of the human genome, researchers at the University of California, San Diego School of Medicine have comprehensively analyzed six of the more highly expressed RNA binding proteins collectively known as heterogeneous nuclear ribonucleoparticle (hnRNP) proteins.  This study, published online Feb 16 in Cell Press’ new open-access journal Cell Reports, describes how multiple RNA binding proteins cooperatively control the diversity of proteins in human cells by regulating the alternative splicing of thousands of genes.  In the splicing process, fragments that do not typically code for protein, called introns, are removed from gene transcripts, and the remaining sequences, called exons, are reconnected.  The proteins that bind to RNA are important for the control of the splicing process, and the location where they bind dictates which pieces of the RNA are included or excluded in the final gene transcript — in much the same fashion that removing and inserting scenes, or splicing, can alter the plot of a movie. “By integrating vast amounts of information about these key binding proteins, and making this data widely available, we hope to provide a foundation for building predictive models for splicing and future studies in other cell types such as embryonic stem cells,” said principal investigator Gene Yeo, PhD, assistant professor in the Department of Cellular and Molecular Medicine and the Institute for Genomic Medicine at UC San Diego, and a visiting professor at the Molecular Engineering Laboratory in Singapore. “If we can understand how these proteins work together and affect one another to regulate alternative splicing, it may offer important clues for rational drug design.” More here
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The art depicts RNAs wound in an undecipherable knot bound by hnRNP proteins, describing the intractable problem of RNA regulation as a “Gordian Knot.” As Alexander the Great discovered, the best way to unravel such a knot is a brute force approach, and thus Huelga et al. attack this puzzle through multiple, genome-wide swords (splicing arrays, CLIP-seq, and RNA-seq).

The Splice of Life: Proteins Cooperate to Regulate Gene Splicing

Understanding how RNA binding proteins control the genetic splicing code is fundamental to human biology and disease – much like editing film can change a movie scene. Abnormal variations in splicing are often implicated in cancer and genetic neurodegenerative disorders.

In a step toward deciphering the “splicing code” of the human genome, researchers at the University of California, San Diego School of Medicine have comprehensively analyzed six of the more highly expressed RNA binding proteins collectively known as heterogeneous nuclear ribonucleoparticle (hnRNP) proteins.
 
This study, published online Feb 16 in Cell Press’ new open-access journal Cell Reports, describes how multiple RNA binding proteins cooperatively control the diversity of proteins in human cells by regulating the alternative splicing of thousands of genes. 

In the splicing process, fragments that do not typically code for protein, called introns, are removed from gene transcripts, and the remaining sequences, called exons, are reconnected.  The proteins that bind to RNA are important for the control of the splicing process, and the location where they bind dictates which pieces of the RNA are included or excluded in the final gene transcript — in much the same fashion that removing and inserting scenes, or splicing, can alter the plot of a movie.

“By integrating vast amounts of information about these key binding proteins, and making this data widely available, we hope to provide a foundation for building predictive models for splicing and future studies in other cell types such as embryonic stem cells,” said principal investigator Gene Yeo, PhD, assistant professor in the Department of Cellular and Molecular Medicine and the Institute for Genomic Medicine at UC San Diego, and a visiting professor at the Molecular Engineering Laboratory in Singapore. “If we can understand how these proteins work together and affect one another to regulate alternative splicing, it may offer important clues for rational drug design.”

More here

Non-Coding RNA Relocates Genes When It’s Time To Go To Work

Cells develop and thrive by turning genes on and off as needed in a precise pattern, a process known as regulated gene transcription. In a paper published in the November 9 issue of The Journal of Neuroscience, researchers at the University of California, San Diego School of Medicine say this process is even more complex than previously thought, with regulated genes actually relocated to other, more conducive places in the cell nucleus.

“When regulated gene transcription goes awry, many human diseases result, such as diabetes, atherosclerosis, cancer and growth defects in children,” said Michael G. Rosenfeld, MD, a professor in the UC San Diego Department of Medicine, Howard Hughes Medical Institute investigator and senior author of the study. “We’ve shown that rather than being activated at certain, random locations within the cell nucleus, regulated genes can dynamically relocate. The discovery provides a more comprehensive picture of the interaction between regulated genes and human disease.”

Specifically, Rosenfeld and colleagues found that genes regulating cell proliferation responded to growth signals by moving targeted genes from a “silencing environment” in the nucleus called Polycomb bodies to another nuclear compartment called interchromatin granules, which is enriched with activating transcription factors. The movement was precisely guided by two non-coding RNA (ncRNA) molecules called TUG1 and NEAT2.

More here

Researchers have discovered that expression of the ataxin-7 gene – the cause of the neurological disorder spinocerebellar ataxia type 7 – has two regulators: a highly conserved, multi-tasking protein called CTCF and, surprisingly, an adjacent promoter containing non-coding RNA.  Illustration courtesy of Christina Takamatsu-Butler, UC San Diego. Non-coding RNA Has Role in Inherited Neurological Disorder – And Maybe Other Brain Diseases Too
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Researchers have discovered that expression of the ataxin-7 gene – the cause of the neurological disorder spinocerebellar ataxia type 7 – has two regulators: a highly conserved, multi-tasking protein called CTCF and, surprisingly, an adjacent promoter containing non-coding RNA.  Illustration courtesy of Christina Takamatsu-Butler, UC San Diego.

Non-coding RNA Has Role in Inherited Neurological Disorder – And Maybe Other Brain Diseases Too