Gene silencing instructions acquired through ‘molecular memory’ tags on chromatin

Scientists at Indiana University have unlocked one of the mysteries of modern genetics: how acquired traits can be passed between generations in a process called epigenetic inheritance. The new work finds that cells don’t know to silence some genes based on information hardwired into their DNA sequences, but recognize heritable chemical marks that are added to the genes. These chemical tags serve as a form of molecular memory, allowing cells to recognize the genes and remember to silence them again in each new generation.The discovery made by a 12-member all-Indiana University team of scientists led by IU biologist and biochemist Craig Pikaard provides important new insight into how plant cells know to silence a genetic locus — that specific place on a chromosome where a gene is located — in every successive generation.Rather than rely on intrinsic, DNA sequence-based information, the cells instead must recall the need to silence specific loci by relying on chemical marks displayed on the complex of DNA and proteins called chromatin. Addition, or removal, of one-carbon (methyl) or two-carbon (acetyl) chemical tags are ways of modifying chromatin that can impart additional, epigenetic (literally, “above genetic”) information to a locus beyond the genetic information encoded in the DNA.The ability to perpetuate chromatin marks serves as a form of epigenetic memory that confers what Pikaard calls silent locus identity, a pre-established state that is needed for the cell to deliver to the loci the machinery that actually accomplishes silencing in a multi-step process known as RNA-directed DNA methylation (RdDM). RdDM involves short-interfering RNAs (siRNA), tiny RNA molecules that are 24 nucleotides long and that guide the addition of methyl groups to matching DNA strands, ultimately rendering the genes inactive.”Importantly, this work shows that silent locus identity is required for, but separable from, actual gene silencing,” Pikaard said. “We’ve found that epigenetic inheritance is a two-step process, with the heritable specification of silent locus identity occurring before actual silencing of the locus can occur.”Scientists are interested in epigenetic inheritance because it’s a process by which heritable modifications occur in gene function without changes in the base sequence of an organism’s DNA being required. Disease states such as cancer, which occur sporadically during an individual’s lifetime, are increasingly recognized as having an epigenetic basis. Pikaard said the new work not only sheds important new light on the mechanisms responsible for epigenetic inheritance, a topic of broad interest in the fields of genetics and chromosome biology, but it also helps explain the basis for the recruitment of two plant-specific gene silencing enzymes — the RNA polymerases Pol IV and Pol V — first identified by Pikaard in 1999.Specifically, the researchers tested and identified the relationship between histone deacetylase 6 (HDA6), an enzyme that removes acetyl groups from histones, and the CG DNA sequence maintenance methyltransferase, MET1, and discovered that their partnership in maintenance methylation can explain the perpetuation of epigenetic memory that accounts for silent locus identity.”Collectively, our results show that silent locus identity is perpetuated from generation to generation through the actions of HDA6 and MET1,” Pikaard said. “These activities are not sufficient to silence the loci but maintain a chromatin state that is required for Pol IV recruitment, siRNA biogenesis and RdDM, which is what ultimately silences the loci.” When the team removed the RdDM pathway in Pol IV and Pol V mutant strains of the model plant Arabidopsis thaliana (rockcress), all gene silencing was lost, but silent locus identity remained. They then removed the HDA6 and MET1-dependent process that specifies silent locus identity and, importantly, the epigenetic memory required for silent locus identity was lost and unable to be regained.Story Source:The above story is based on materials provided by Indiana University. …

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Success of new bug-fighting approach may vary from field to field

A new technique to fight crop insect pests may affect different insect populations differently, researchers report. They analyzed RNA interference (RNAi), a method that uses genetic material to “silence” specific genes — in this case genes known to give insect pests an advantage. The researchers found that western corn rootworm beetles that are already resistant to crop rotation are in some cases also less vulnerable to RNAi.The study is reported in the journal Pesticide Biochemistry and Physiology.”Our results indicate that the effectiveness of RNAi treatments could potentially vary among field populations depending on their genetic and physiological backgrounds,” the researchers wrote.The western corn rootworm will likely be one of the first crop pests to be targeted with RNAi technology, said Manfredo Seufferheld, a former University of Illinois crop sciences professor who led the study with crop sciences graduate student Chia-Ching Chu, entomology research associate Weilin Sun, Illinois Natural History Survey insect behaviorist Joseph Spencer and U. of I. entomology professor Barry Pittendrigh.Controlling the western corn rootworm costs growers more than $1 billion a year in the U.S. Current methods for keeping the bug in check — crop rotation and genetically modified corn — face challenges from populations of resistant western corn rootworms at various locations across the Corn Belt, Spencer said.Seufferheld and his colleagues recently discovered an important factor that helps rootworms overcome crop rotation, the practice of alternately planting soybeans and corn in the same field year to year. They found that microbes in the guts of rotation-resistant rootworms help those beetles that stray into soybean fields survive on soybean leaves for a few days — just long enough for the females to lay their eggs in soil that will be planted in corn the following year.Rather than studying a laboratory population of insects, in the new analysis the team tested RNAi on rootworm beetles collected from fields in three locations in the Midwest — two in Illinois with established rotation-resistant populations and the third from an area in Missouri with no evidence of rotation resistance.”After generations in the laboratory, insects gradually lose their natural diversity,” Seufferheld said. This makes it easier to control them, and may not accurately reflect actual insect responses in the field, he said. Seufferheld now works for Monsanto and is based in Buenos Aires, where he is in charge of insect resistance management.The team targeted two genes that are regulated differently in rotation-resistant and non-resistant rootworms. The first, DvRs5, codes for an enzyme that helps the rootworms digest plant proteins. …

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BPA linked to breast cancer tumor growth

UT Arlington biochemists say their newly published study brings researchers a step closer to understanding how the commonly used synthetic compound bisphenol-A, or BPA, may promote breast cancer growth.Subhrangsu Mandal, associate professor of chemistry/biochemistry, and Arunoday Bhan, a PhD student in Mandal’s lab, looked at a molecule called RNA HOTAIR. HOTAIR is an abbreviation for long, non-coding RNA, a part of DNA in humans and other vertebrates. HOTAIR does not produce a protein on its own but, when it is being expressed or functioning, it can suppress genes that would normally slow tumor growth or cause cancer cell death.High levels of HOTAIR expression have been linked to breast tumors, pancreatic and colorectal cancers, sarcoma and others.UT Arlington researchers found that when breast cancer and mammary gland cells were exposed to BPA in lab tests, the BPA worked together with naturally present molecules, including estrogen, to create abnormal amounts of HOTAIR expression. Their results were published online in February by the Journal of Steroid Biochemistry and Molecular Biology.”We can’t immediately say BPA causes cancer growth, but it could well contribute because it is disrupting the genes that defend against that growth,” said Mandal, who is corresponding author on the paper.”Understanding the developmental impact of these synthetic hormones is an important way to protect ourselves and could be important for treatment,” he said.Bhan is lead author on the new paper. Co-authors include Mandal lab members Imran Hussain and Khairul I Ansari, as well as Linda I. Perrotti, a UT Arlington psychology assistant professor, and Samara A.M. Bobzean, a member of Perrotti’s lab.”We were surprised to find that BPA not only increased HOTAIR in tumor cells but also in normal breast tissue,” said Bhan. He said further research is needed, but the results beg the question — are BPA and HOTAIR involved in tumor genesis in addition to tumor growth?BPA has been widely used in plastics, such as food storage containers, the lining of canned goods and, until recently, baby bottles. It belongs to a class of endocrine disrupting chemicals, or EDCs, which have been shown to mimic natural hormones. These endocrine disruptors interfere with hormone regulation and proper function of human cells, glands and tissue. …

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It slices, it dices, and it protects the body from harm: 3-D structure of enzyme that helps defend against bacteria

An essential weapon in the body’s fight against infection has come into sharper view. Researchers at Princeton University have discovered the 3D structure of an enzyme that cuts to ribbons the genetic material of viruses and helps defend against bacteria.The discovery of the structure of this enzyme, a first-responder in the body’s “innate immune system,” could enable new strategies for fighting infectious agents and possibly prostate cancer and obesity. The work was published Feb. 27 in the journal Science.Until now, the research community has lacked a structural model of the human form of this enzyme, known as RNase L, said Alexei Korennykh, an assistant professor of molecular biology and leader of the team that made the discovery.”Now that we have the human RNase L structure, we can begin to understand the effects of carcinogenic mutations in the RNase L gene. For example, families with hereditary prostate cancers often carry genetic mutations in the region, or locus, encoding RNase L,” Korennykh said. The connection is so strong that the RNase L locus also goes by the name “hereditary prostate cancer 1.” The newly found structure reveals the positions of these mutations and explains why some of these mutations could be detrimental, perhaps leading to cancer, Korennykh said. RNase L is also essential for insulin function and has been implicated in obesity.The Princeton team’s work has also led to new insights on the enzyme’s function.The enzyme is an important player in the innate immune system, a rapid and broad response to invaders that includes the production of a molecule called interferon. Interferon relays distress signals from infected cells to neighboring healthy cells, thereby activating RNase L to turn on its ability to slice through RNA, a type of genetic material that is similar to DNA. The result is new cells armed for destruction of the foreign RNA.The 3D structure uncovered by Korennykh and his team consists of two nearly identical subunits called protomers. The researchers found that one protomer finds and attaches to the RNA, while the other protomer snips it.The initial protomer latches onto one of the four “letters” that make up the RNA code, in particular, the “U,” which stands for a component of RNA called uridine. …

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As hubs for bees, pollinators, flowers may be crucial in disease transmission

Like a kindergarten or a busy airport where cold viruses and other germs circulate freely, flowers are common gathering places where pollinators such as bees and butterflies can pick up fungal, bacterial or viral infections that might be as benign as the sniffles or as debilitating as influenza.But “almost nothing is known regarding how pathogens of pollinators are transmitted at flowers,” postdoctoral researcher Scott McArt and Professor Lynn Adler at the University of Massachusetts Amherst write. “As major hubs of plant-animal interactions throughout the world, flowers are ideal venues for the transmission of microbes among plants and animals.”In a recent review in Ecology Letters with colleagues at Yale and the University of Texas at Austin, McArt and Adler survey the literature and identify promising areas for future research on how floral traits influence pathogen transmission.As the authors point out, “Given recent concerns about pollinator declines caused in part by pathogens, the role of floral traits in mediating pathogen transmission is a key area for further research.” They say their synthesis could help efforts to control economically devastating pollinator-vectored plant pathogens such as fire blight, which affects rose family fruits such as apples and pears, and mummyberry disease, which attacks blueberries.McArt adds, “Our intent with this paper is to stimulate interest in the fascinating yet poorly understood microbial world of flowers. We found several generalities in how plant pathogens are transmitted at flowers, yet the major take-home from our paper may be in pointing out that this is an important gap in our knowledge.”The authors identified 187 studies pertaining to plant pathogens published between 1947 and 2013 in which floral visitors were implicated in transmission and where transmission must have occurred at flowers or pathogen-induced pseudoflowers. These are flower-like structures made by a pathogen that can look and smell like a real flower, for example. Regarding animal pathogens, they identified 618 studies published before September 2013 using the same criteria.”In total, we found eight major groups of animal pathogens that are potentially transmitted at flowers, including a trypanosomatid, fungi, bacteria and RNA viruses,” they note. Their paper, “Arranging the bouquet of disease: Floral traits and the transmission of plant and animal pathogens,” was featured in the publisher’s “News Round-Up” of “most newsworthy research.”Traditionally, research on flower evolution has focused largely on selection by pollinators, but as McArt and colleagues point out, pollinators that also transmit pathogens may reduce the benefits to the plant of attracting them, depending on the costs and benefits of pollination. The researchers say more work is needed before scientists can know whether a flower’s chemical or physical traits determine the likelihood that pathogens are transmitted, for example, and whether infection by pathogens is an inevitable consequence of pollinator visitation.”Plant pathologists have made great strides in identifying floral traits that mediate host plant resistance to floral pathogens in individual systems; synthesizing this literature can provide generality in identifying traits that mediate plant-pathogen dynamics. From the pollinator’s perspective, there has been surprisingly little work elucidating the role of flowers and floral traits for pathogen transmission. Given recent concerns about pollinator declines caused in part by pathogens, understanding the role of floral traits in disease transmission is a key missing element,” say McArt and colleagues.Story Source:The above story is based on materials provided by University of Massachusetts at Amherst. Note: Materials may be edited for content and length.

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Cortical convolutions controlled in sections: Non-coding DNA sequence affects brain’s characteristic folding, study shows

Researchers have tied a particular gene to the development of cortical convolutions — the prominent but enigmatic folds covering the surface of the human brain. Their discovery should shed some light on these characteristic contours, which have been the subject of wild speculation for ages, and perhaps also provide a better understanding of how such brain ridges form, how they evolved from our pre-human ancestors and, ultimately, how they influence brain function.The exact role of cortical convolutions remains unknown, but theories have abounded. (Some, for example, have suggested that the folds act as the body’s cooling system and others have even proposed that Albert Einstein’s genius could have been traced to a single cortical fold on his brain.)Now, leveraging advances that permit a closer look at how these folds develop, research published in the 14 February issue of Science shows that a mutation affecting GPR56 causes cortical convolutions around the brain’s Sylvian fissure — a particularly deep indentation — to develop thinner and more convoluted than usual. The finding, which suggests that genes may assert control over the brain’s physical folding on a section-by-section basis, provides insight into the mysterious cortical development process.”There is already a list of genetic mutations that cause abnormal neocortical folding, which can be used for prenatal testing,” explained Byoung-il Bae from the Division of Genetics and Genomics at Boston Children’s Hospital and Harvard Medical School in Boston, Massachusetts, one of the lead authors of the Science report. “We intend to add this mutation to some of the panels.”Bae and colleagues from around the world investigated the genomes of five individuals with abnormalities on Broca’s area, or the language center of the brain. These study participants were from three different families — one Turkish and two Irish-American — and they suffered from refractory seizures as well as intellectual and language difficulties.The researchers found that all five patients harbored a mutation on a particular regulatory element that influences the GPR56 gene. Such regulatory DNA doesn’t code for any proteins itself but promotes the expression of genes elsewhere on the genome. Geneticists have long-suspected that such non-coding regions of the genome could play important roles in evolution. To observe the specific effects of the GPR56 “promoter” DNA sequence, Bae and his team used genetically modified mice.They discovered that low expression of GPR56 (gauged by low levels of mRNA) decreases the production of neuroprogenitor cells — those that will eventually give rise to neurons — around Broca’s area and the Sylvian fissure. By contrast, overexpression of the gene boosts the production of such progenitor cells in that region. …

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RNA sequencing of 750-year-old barley virus sheds new light on the Crusades

Scientists have for the first time sequenced an ancient RNA genome — of a barley virus once believed to be only 150 years old — pushing its origin back at least 2,000 years and revealing how intense farming at the time of the Crusades contributed to its spread.Researchers at the University of Warwick have detected and sequenced the RNA genome of Barley Stripe Mosaic Virus (BSMV) in a 750-year-old barley grain found at a site near the River Nile in modern-day Egypt. Their study is published in the journal Scientific Reports.This new find challenges current beliefs about the age of the BSMV virus, which was first discovered in 1950 with the earliest record of symptoms just 100 years ago.Although ancient DNA genomes have been sequenced before, ancient RNA genomes have not been as RNA breaks down more rapidly than DNA — generally around 50 times as fast.However in extremely dry conditions, such as those at the site in Qasr Ibrim in Lower Nubia where the barley was found, RNA can be better preserved and this has allowed the scientists to successfully sequence its genome.Using the new medieval RNA to calibrate estimates of the rate of mutations, the researchers were able to trace the evolution of the Barley Stripe Mosaic Virus to a probable origin of around 2,000 years ago, but potentially much further back to the domestication of barley in the Near East around 11,000 years ago.BSMV is transmitted through seed-to-seed contact so it is likely to originally have been transferred from the wild grass population to an early cultivated form of barley while the seeds were stored.Dr Robin Allaby of the School of Life Sciences at the University of Warwick, who led the study, said: “It is important to know as much as we can about virus evolution as emerging infectious plant diseases are a growing threat to global food security, and of those viruses account for almost half.”History tells us about the devastation caused by the emergence of disease from wild hosts in disparate countries, such as the Central American origin of the oomycete that led to the Irish potato famine.”We need to build up an accurate picture of the evolution of different types of virus so we can make better decisions about policies on plant movement.”The medieval RNA from Qasr Ibrim gives us a vital clue to unlock the real age of the Barley Stripe Mosaic Virus.”It is very difficult to understand how a plant disease evolved by solely relying on recent samples, however this 750-year-old example of the virus allows us to more accurately estimate its evolution rates and date of origin.”Without the Medieval RNA evidence, the virus appears to be much younger than it actually is, when in fact its origins go back thousands of years.”It’s possible that other viruses that similarly appear to be very recent may in fact have a more ancient origin.”The researchers believe that the Medieval BSMV genome came from a time of rapid expansion of the plant disease in the Near East and Europe.This coincided with the tumult of the Crusades which saw the Christian lands of Europe take arms against the Muslim territories of the Near East with their sights set on the city of Jerusalem. The seventh Crusade of Louis IX in 1234 is the most closely aligned in date to the origin of the virus expansion.The researchers believe the massive war effort could have caused the virus to spread, fuelled by an intensification of farming in order to feed the armies engaged in the campaign.This made contact with cultivated barley and wild grass more likely, providing opportunities for the virus to ‘jump’ into the crop.Genetic evidence also points to a split into an east and west BSMV lineage around the end of the 15th century, around 100 years after the Mongol Empire stabilised the Silk Road. It is likely that BSMV was transported to the east via trade routes such as the Silk Road in the late Medieval period.In more recent history, the virus appears to have spread to the US from Europe around 120-150 years ago.The research was supported by the research funding body BBSRC.Story Source:The above story is based on materials provided by University of Warwick. Note: Materials may be edited for content and length.

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Puzzling question in bacterial immune system answered

A central question has been answered regarding a protein that plays an essential role in the bacterial immune system and is fast becoming a valuable tool for genetic engineering. A team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have determined how the bacterial enzyme known as Cas9, guided by RNA, is able to identify and degrade foreign DNA during viral infections, as well as induce site-specific genetic changes in animal and plant cells. Through a combination of single-molecule imaging and bulk biochemical experiments, the research team has shown that the genome-editing ability of Cas9 is made possible by the presence of short DNA sequences known as “PAM,” for protospacer adjacent motif.”Our results reveal two major functions of the PAM that explain why it is so critical to the ability of Cas9 to target and cleave DNA sequences matching the guide RNA,” says Jennifer Doudna, the biochemist who led this study. “The presence of the PAM adjacent to target sites in foreign DNA and its absence from those targets in the host genome enables Cas9 to precisely discriminate between non-self DNA that must be degraded and self DNA that may be almost identical. The presence of the PAM is also required to activate the Cas9 enzyme.”With genetically engineered microorganisms, such as bacteria and fungi, playing an increasing role in the green chemistry production of valuable chemical products including therapeutic drugs, advanced biofuels and biodegradable plastics from renewables, Cas9 is emerging as an important genome-editing tool for practitioners of synthetic biology.”Understanding how Cas9 is able to locate specific 20-base-pair target sequences within genomes that are millions to billions of base pairs long may enable improvements to gene targeting and genome editing efforts in bacteria and other types of cells,” says Doudna who holds joint appointments with Berkeley Lab’s Physical Biosciences Division and UC Berkeley’s Department of Molecular and Cell Biology and Department of Chemistry, and is also an investigator with the Howard Hughes Medical Institute (HHMI).Doudna is one of two corresponding authors of a paper describing this research in the journal Nature. The paper is titled “DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.” The other corresponding author is Eric Greene of Columbia University. Co-authoring this paper were Samuel Sternberg, Sy Redding and Martin Jinek.Bacterial microbes face a never-ending onslaught from viruses and invasive snippets of nucleic acid known as plasmids. To survive, the microbes deploy an adaptive nucleic acid-based immune system that revolves around a genetic element known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. Through the combination of CRISPRs and RNA-guided endonucleases, such as Cas9, (“Cas” stands for CRISPR-associated), bacteria are able to utilize small customized crRNA molecules (for CRISPR RNA) to guide the targeting and degradation of matching DNA sequences in invading viruses and plasmids to prevent them from replicating. There are three distinct types of CRISPR-Cas immunity systems. …

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Bird study finds key info about human speech-language development

Oct. 17, 2013 — A study led by Xiaoching Li, PhD, at the LSU Health Sciences Center New Orleans Neuroscience Center of Excellence, has shown for the first time how two tiny molecules regulate a gene implicated in speech and language impairments as well as autism disorders, and that social context of vocal behavior governs their function. The findings are published in the October 16, 2013 issue of The Journal of Neuroscience.Share This:Speech and language impairments affect the lives of millions of people, but the underlying neural mechanisms are largely unknown and difficult to study in humans. Zebra finches learn to sing and use songs for social communications. Because the vocal learning process in birds has many similarities with speech and language development in humans, the zebra finch provides a useful model to study the neural mechanisms underlying speech and language in humans.Mutations in the FOXP2 gene have been linked to speech and language deficits and in autism disorders. A current theory is that a precise amount of FOXP2 is required for the proper development of the neural circuits processing speech and language, so it is important to understand how the FOXP2 gene is regulated. In this study, the research team identified two microRNAs, or miRNAs, — miR-9 and miR-140-5p — that regulate the levels of FOXP2. (MicroRNAs are a new class of small RNA molecules that play an important regulatory role in cell biology. They prevent the production of a particular protein by binding to and destroying the messenger RNA that would have produced the protein.) The researchers showed that in the zebra finch brain, these miRNAs are expressed in a basal ganglia nucleus that is required for vocal learning, and their function is regulated during vocal learning. More intriguingly, the expression of these two miRNAs is also regulated by the social context of song behavior — in males singing undirected songs.”Because the FOXP2 gene and these two miRNAs are evolutionarily conserved, the insights we obtained from studying birds are highly relevant to speech and language in humans and related neural developmental disorders such as autism,” notes Xiaoching Li, PhD,LSUHSC Assistant Professor of Cell Biology and Anatomy as well as Neuroscience. …

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Cell growth discovery has implications for targeting cancer

Oct. 11, 2013 — The way cells divide to form new cells — to support growth, to repair damaged tissues, or simply to maintain our healthy adult functioning — is controlled in previously unsuspected ways UC San Francisco researchers have discovered. The findings, they said, may lead to new ways to fight cancer.The steps leading a quiet cell to make and divvy up new parts to form daughter cells rely on some of the cell’s most complex molecular machines. Different machines play key roles at different stages of this cell cycle. Each of these cellular machines consists of many proteins assembled into a functioning whole. They carry out such tasks as repairing DNA in the newly replicated gene-bearing chromosomes, for instance, or helping pull the chromosomes apart so that they can be allocated to daughter cells.In a study published online on October 10, 2013 in the journal Molecular Cell, UCSF researchers led by molecular biologist Davide Ruggero, PhD, associate professor of urology, and computational biologist Barry Taylor, PhD, assistant professor of epidemiology and biostatistics, found that the production of entire sets of proteins that work together to perform such crucial tasks is ramped up together, all at once — not due to the transcription of genes into messenger RNA, a phenomenon scientists often study to sort out cellular controls — but at a later stage of gene expression that occurs within the cell’s protein-making factories, called ribosomes.”We have found that these proteins are regulated specifically and exquisitely during the cell cycle,” Ruggero said. When this regulation falters, it wreaks havoc in the cell, he added. “Cell-cycle control is a process that is most often misregulated in human disease,” he said.More specifically, the researchers found that this coordinated timing of protein production during the cell cycle is largely governed at the tail end of gene expression, within the ribosome, where cellular machinery acts on messenger RNA to churn out the chains of amino acids that eventually fold into functional form as proteins.In 2010 Ruggero reported key evidence suggesting that this stage of protein production, called “translation,” might be an often-neglected process in many tumors, ranging from lymphomas, multiple myeloma and prostate cancer.In the new study, the researchers examined translation of messenger RNA into protein at the classic phases of the cell cycle, before the cell actually divides. These are the G1 phase, when cells grow and make lots of proteins before replicating their DNA; the S phase, when cells replicate their DNA; and the G2 phase, when cells make internal components known as organelles, which they divvy up along with the chromosomes when the cell actually divides during mitosis.The scientists used a technique know as ribosome profiling, originally developed for yeast cells in the lab of Jonathan Weismann, PhD, Howard Hughes Investigator at UCSF and professor of cellular and molecular pharmacology, to figure out which messenger RNA was being translated into protein by the ribosome during human cell division. They then used computational techniques developed by Taylor’s lab team along with the lab team of Adam Olshen, PhD, professor of epidemiology and biostatistics, to better quantify which genes had been translated into proteins.By conducting a genome-wide investigation of translation and interrogating the data with sophisticated computer algorithms, the researchers discovered that different groups of protein were made in abundance at a particular phase, only to be quieted during another phase of the cell cycle. …

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Innate virus-killing power discovered in mammals

Oct. 10, 2013 — Scientists have a promising new approach to combating deadly human viruses thanks to an educated hunch by University of California, Riverside microbiology professor Shou-Wei Ding, and his 20 years of research on plants, fruit flies, nematodes and mice to show the truth in his theory.Researchers led by Ding, who heads a lab in UC Riverside’s Institute for Integrative Genome Biology, have discovered that, like plants and invertebrate animals, mammals use the RNA interference (RNAi) process to destroy viruses within their own cells.Their findings will be published in the Oct. 11 issue of the journal Science.Until now, scientists were unable to prove that mammals use RNAi for killing viruses, but ironically, it was Ding’s earlier research into plants, nematodes and fruit flies that helped him find the key: viruses have been outwitting that innate protection in our cells by using proteins to suppress our virus-killing mechanism.Remove the suppressor protein from the virus, Ding’s research discovered, and the subject’s body will quickly eliminate the virus using the RNAi process, which sends out small interfering RNAs (siRNAs) to kill the disease.In their research on young mice, for instance, all the subjects died when they were infected with the Nodamura virus, but when Ding’s researchers removed the suppressor protein called B2 from the virus, the infected mice began producing huge armies of the virus-attacking siRNAs and lived, unaffected by the otherwise lethal infection.”Many have tried to do this, that is, find the viral siRNAs in mammals, but they could not find the key,” said Ding. “The key was our prior knowledge of the B2 protein in the Nodamura virus, a virus few people know about. Other scientists asked me, ‘What is the Nodamura virus?’ They have been studying the more well-known human viruses, but Nodamura virus infection of mice proves to be the best model.”How did Ding know where to look? The China native was partly acting on a hunch that started when he was a graduate student at the Australia National University in the late 1980s. There, during a lecture, he learned that the genomes of viruses infecting plants and animals are actually very similar, even though plants and animals are very different.That, and further discussions with his mentor Adrian Gibbs, an expert on molecular evolution of viruses and a fellow of the Australian Academy of Sciences, “made me think there must be a common anti-viral mechanism in plants and animals to keep their viruses similar,” he said.Ding produced the first evidence for that hypothesis while working with Bob Symons in the Waite Institute in South Australia, studying cucumber mosaic virus, a devastating, aphid-carried disease that infects more than 1,000 plant species, including many important crops.Using computational analytical skills learned from Gibbs, Ding discovered a small gene in the virus other scientists had overlooked. He named the gene 2b and showed that it plays an essential role in helping the virus spread within the host plant. Based on his results, and published studies on the B2 protein of Flock house virus, an insect pathogen, Ding proposed in a 1995 paper that 2b and B2 proteins act by suppressing the host’s antiviral defense.Fueled by that idea, Ding moved to Singapore in 1996 to set up his own laboratory in the Institute of Molecular Agrobiology. There, in collaboration with a British group led by RNAi-expert David Baulcombe, Ding’s group discovered that the 2b protein did indeed suppress the RNAi virus-fighting properties in plants. …

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New antiviral response discovered in mammals

Oct. 10, 2013 — Many viral infections are nipped in the bud by the innate immune response. This involves specific proteins within the infected cell that recognize the virus and trigger a signalling cascade — the so-called interferon response. This activates a protective mechanism in neighbouring cells and often results in the death of the primarily infected cell.In plants and invertebrates another mechanism is known to function in antiviral immune response: the so-called RNA interference (RNAi) pathway. RNAi uses an intermediate of the viral proliferation process to build a weapon against the virus. Although RNAi also exists in mammals, researchers have until now thought it to be involved in other cellular processes required for gene regulation but not in antiviral immunity. Evidence that RNAi does indeed contribute to mammalian antiviral defence is now published in Science by Olivier Voinnet, professor for RNA biology at ETH Zurich, and his colleagues.Small interfering RNAs as specific antiviral weaponsThe researchers infected mouse embryonic stem cells with two viruses, the encephalomyocarditis virus (EMCV) and the Nodamura virus (NoV). Subsequently, they were able to detect short RNA molecules of about 22 nucleotides in length within the cells. The sequence of these RNA clearly corresponded to the viral genome and they displayed all the characteristics of the main effector molecules of RNAi called the small interfering or siRNAs. This provided evidence that the virus infection had activated the RNAi machinery of mammalian cells.The trigger for RNAi is an unusual RNA molecule that arises when the viral genome is copied: a long, double-stranded RNA molecule. …

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How chromosome ends influence cellular aging

Sep. 11, 2013 — By studying processes that occur at the ends of chromosomes, a team of Heidelberg researchers has unravelled an important mechanism towards a better understanding of cellular aging. The scientists focused on the length of the chromosome ends, the so-called telomeres, which can be experimentally manipulated. Their research, which was conducted at the Center for Molecular Biology of Heidelberg University (ZMBH), allows for new approaches in the development of therapies for tissue loss and organ failure associated with senescence (cellular aging). The research results may also be significant for cancer treatment. They were recently published in the journal Nature Structural & Molecular Biology.Share This:Each cell contains a set of chromosomes in which the vast majority of our genetic information is stored in the form of DNA. This information must be protected to ensure the proper functioning of the cell. To achieve this, the very ends of the chromosomes, the telomeres, play an important role in protecting the chromosomal DNA from being degraded. “We can imagine that telomeres are analogous to the plastic caps at the ends of our shoelaces. Without them, the ends of the laces get frayed and eventually the entire shoelace does not function properly,” explains Dr. …

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Versatile microRNAs choke off cancer blood supply, suppress metastasis

Sep. 11, 2013 — A family of microRNAs (miR-200) blocks cancer progression and metastasis by stifling a tumor’s ability to weave new blood vessels to support itself, researchers at The University of Texas MD Anderson Cancer Center report today in Nature Communications.Patients with lung, ovarian, kidney or triple-negative breast cancers live longer if they have high levels of miR-200 expression, the researchers found.Subsequent experiments showed for the first time that miR-200 hinders new blood vessel development, or angiogenesis, and does so by targeting cytokines interleukin-8 (IL-8) and CXCL1.”Nanoparticle delivery of miR-200 blocked new blood vessel development, reduced cancer burden and inhibited metastasis in mouse models of all four cancers,” said Anil Sood, M.D., professor of Gynecologic Oncology, senior author of the study.The team’s findings highlight the therapeutic potential of nanoparticle-delivered miR-200 and of IL-8 as a possible biomarker for identifying patients who might benefit from treatment. Sood said safety studies will need to be completed before clinical development can begin.Micro RNAs do not code for genes like their cousins, the messenger RNAs. They regulate gene activation and expression.”We initially looked at miR-200 because we have an approach for targeting and delivering these molecules with nanoparticles and miR-200 is known to inhibit EMT, a cellular transition associated with cancer progression and metastasis,” said Sood, who also holds the Bettyann Asche Murray Distinguished Professorship in Ovarian Cancer Research.First author Chad Pecot, M.D., a fellow in Cancer Medicine, said initial research provided a new perspective. “Cautionary tales emerged from the literature about poor outcomes in hormone-positive breast cancer, so we decided to delve more deeply into understanding the mechanisms involved.”miR-200 effect differs by breast cancer typeSood and colleagues analyzed hundreds of annotated ovarian, renal, breast and non-small cell lung cancer samples from The Cancer Genome Atlas for expression of all five miR-200 family members. Low expression of miR-200 was associated with poor survival in lung, ovarian and renal cancers, but improved survival for breast cancer.However, they found a striking difference when they analyzed breast cancers by those that are hormone-receptor positive (luminal) and those that lack hormone receptors or the HER2 protein, called triple-negative breast cancer. High expression for miR-200 was associated with improved survival for triple-negative disease, which is more difficult to treat due to its lack of therapeutic targets.Gene expression analysis of ovarian and lung cancer cell lines pointed to an angiogenesis network involving both IL-8 and CXCL1. By mining public miRNA and messenger RNA databases, the researchers found:• An inverse relationship between expression of four of the five members of the miR-200 family and IL-8. • Lung, ovarian, kidney and triple-negative breast cancer all have elevated IL-8 and CXCL1 expression compared to hormone-positive breast cancers. • Elevated IL-8 associated with poor overall survival in lung, ovarian, renal and triple-negative breast cancer cases.Treating cancer cell lines with miR-200 decreased levels of IL-8 and CXCL1, and the team also identified binding sites for these genes, meaning they are direct miR-200 targets.Mice treated with miR-200 family members delivered in a fatty nanoparticle developed by Sood and Gabriel Lopez, M.D., professor of Experimental Therapeutics, had steep reductions in lung cancer tumor volume, tumor size and the density of small blood vessels compared to controls. …

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Genome of elastomeric materials creates novel materials

Sep. 9, 2013 — A wide range of biologically inspired materials may now be possible by combining protein studies, materials science and RNA sequencing, according to an international team of researchers.”Biological methods of synthesizing materials are not new,” said Melik C. Demirel, professor of engineering science and mechanics, Penn State. “What is new is the application of these principles to produce unique materials.”The researchers looked at proteins because they are the building blocks of biological materials and also often control sequencing, growth and self-assembly. RNA produced from the DNA in the cells is the template for biological proteins. Materials science practices allow researchers to characterize all aspects of how a material functions. Combining these three approaches allows rapid characterization of natural materials and the translation of their molecular designs into useable, unique materials.”One problem with finding suitable biomimetic materials is that most of the genomes of model organisms have not yet been sequenced,” said Demirel who is also a member of the Materials Research Institute and Huck Institutes of Life Sciences, Penn State. “Also, the proteins that characterize these materials are notoriously difficult to solubilize and characterize.”The team, lead by Ali Miserez, assistant professor, School of Materials Science and Engineering, Nanyang Technological University, Singapore, looked at mollusk-derived tissues that had a wide range of high-performance properties including self-healing elastomeric membranes and protein-based polymers. They combined a variety of approaches including protein sequencing, amino acid composition and a complete RNA reference database for mass spectrometry analysis. They present their results in a recent issue of Nature Biotechnology.The researchers looked at three model systems. …

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Protein that protects nucleus also regulates stem cell differentiation

Aug. 29, 2013 — The human body has hundreds of different cell types, all with the same basic DNA, and all of which can ultimately be traced back to identical stem cells. Despite this fundamental similarity, a bone cell has little in common with a brain cell when it comes to appearance or function. The fact that bone is rigid and mechanically distinct from soft fat or brain had been speculated to play some role in differentiation to new cells in those parts of the body, but mechanisms have been unclear.Now, a study by researchers at the University of Pennsylvania have shown that a protein found in the nuclei of all cells — lamin-A — plays a key role in the differentiation process.The study was led by professor Dennis Discher and postdoctoral researchers Joe Swift and Irena Ivanovska of the Department of Chemical and Biomolecular Engineering in Penn’s School of Engineering and Applied Science.It was published in the journal Science.Lamin-A is a protein found in the nucleus of all adult cells. This rope-like protein forms a protective netting around the DNA contained at the core of the nucleus.The first hint that lamin-A might be involved in regulating the stiffness of nuclei came from diseases that lead to abnormal protein. One such disease, progeria, has symptoms akin to premature aging, including brittle bones and muscle wasting. But while these stiff tissues are affected, soft tissues such as brain and blood remain normal.As a self-assembling filament, lamin-A is like a rope in that, when it is pulled, it becomes taut. As this stiffness would be better suited to resisting the pull of neighboring cells, the researchers speculated that such a protein would be more abundant in tissues, like bone, cartilage and muscle, that need to be stiff to resist the stresses and strains of everyday activity.”We hypothesized that higher levels of lamin-A in the nuclei of stiffer tissues would be appropriate to a greater need to prevent breakage of the precious DNA surrounded by the lamin-A net,” Discher said.To determine how levels of lamin-A varied between cell types, the researchers took tissue cells from both mice and humans, broke the cells apart and fed them to a mass spectrometer to quantify the many protein components.The researchers then looked for any correlation between the amounts of the numerous proteins detected and the elasticity of the source tissue. Since the material outside cells called extracellular matrix is known to be particularly abundant in stiff tissues like bone and cartilage, they expected to see correlations with matrix proteins like collagen. However, they also found evidence supporting their hypothesis that nuclear lamin-A levels also increase dramatically from softer to more rigid tissues.”The mass spectrometry lets us look at and quantify hundreds of proteins at the same time,” Swift said. …

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Protein predicts breast cancer prognosis

Aug. 29, 2013 — Researchers have identified a protein that they believe may help predict breast cancer prognosis, potentially relieving thousands of women at low risk from having to undergo painful, oft-debilitating therapies, while insuring the most successful treatments for those at high risk.The research was published ahead of print in the journal Molecular and Cellular Biology.Using bioinformatics techniques, the authors showed that the levels of expression of some 1,200 genes that are directly controlled by the enzyme, EZH2, correlates with the aggressiveness of breast cancer cases.”The analysis pipeline that we developed will be useful for stratification of breast cancer patients,” says Elizaveta V. Benevolenskaya of the University of Illinois at Chicago, a researcher on the study. “That stratification will enable clinicians to accurately predict breast cancer progression. The level of expression of a subgroup of EZH2-bound genes could have further predictive value, indicating, for example, that a specific treatment regime is needed.”In the study, she and her collaborators generated breast cancer cells in which they could dampen expression of EZH2 using a technique called RNA inhibition. Inhibiting EZH2 expression reactivated the genes this enzyme controls, which resulted in less aggressive cancer phenotypes.In addition to predicting aggressiveness, Benevolenskaya says small molecule inhibitors of EZH2, which have recently become available, could be developed as therapeutic drugs for breast cancer. The advantage of small molecules is that they are cheaper to manufacture, and generally can be taken by mouth, unlike larger molecules, which must be given by injection.Besides breast cancer, EZH2 overexpression appears to be associated with a worse prognosis in prostate, endometrial, and melanoma tumors. The computational analysis used in their research could also be helpful for predicting the aggressiveness of these and other cancers, says Benevolenskaya.

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How quickly can a bacterium grow? E. coli can replicate close to thermodynamic limits of efficiency

Aug. 27, 2013 — All living things must obey the laws of physics — including the second law of thermodynamics, which states that the universe’s disorder, or entropy, can only grow. Highly ordered cells and organisms appear to contradict this principle, but they actually do conform because they generate heat that increases the universe’s overall entropy.Still, questions remain: What is the theoretical threshold for how much heat a living cell must generate to fulfill its thermodynamic constraints? And how closely do cells approach that limit?In a recent paper in the Journal of Chemical Physics, MIT physicist Jeremy England mathematically modeled the replication of E. coli bacteria and found that the process is nearly as efficient as possible: E. coli produce at most only about six times more heat than they need to meet the constraints of the second law of thermodynamics.”Given what the bacterium is made of, and given how rapidly it grows, what would be the minimum amount of heat that it would have to exhaust into its surroundings? When you compare that with the amount of heat it’s actually exhausting, they’re roughly on the same scale,” says England, an assistant professor of physics. “It’s relatively close to the maximum efficiency.”England’s approach to modeling biological systems involves statistical mechanics, which calculates the probabilities of different arrangements of atoms or molecules. He focused on the biological process of cell division, through which one cell becomes two. During the 20-minute replication process, a bacterium consumes a great deal of food, rearranges many of its molecules — including DNA and proteins — and then splits into two cells.To calculate the minimum amount of heat a bacterium needs to generate during this process, England decided to investigate the thermodynamics of the reverse process — that is, two cells becoming one. …

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Molecular explanation for degenerative disease proposed

Aug. 16, 2013 — An international collaboration jointly led by scientists from Trinity College Dublin has shed new light on the origins and molecular causes of age related degenerative conditions including Motor Neuron Disease (MND). The new perspective provided by this work may lead the way to new treatments and early diagnoses.The article which has just been published in the leading peer reviewed, international journal Cell, offers new opportunities for early diagnosis of age related degenerative diseases before symptoms appear, including through the identification of disease causing genes. It also suggests specific strategies for developing therapies which might have both preventative and therapeutic benefits for this class of degenerative disease.Commenting on the significance of the findings co-lead author Professor Mani Ramaswami, Professor of Neurogenetics at the School of Genetics and Microbiology, Trinity College Dublin said: “Degenerative diseases, such as MND, are a poorly understood and largely untreatable set of life limiting diseases which can leave people unable to do the everyday things that the rest of us, particularly the young, take for granted. These age-associated diseases have far-reaching socioeconomic impacts. If you can predict the disease you may be in a position to slow down its onset and progression through therapeutic interventions. With these types of diseases this is significantly more effective than trying to treat the condition once symptoms have appeared. The potential for early diagnosis and delaying the onset of motor or cognitive decline by perhaps ten years is of potentially profound importance in an aging society.”There are nearly 120,000 cases of MND diagnosed worldwide each year with about 300 people in Ireland living with the disease at any one time.The research just published proposes that the normal biology of mRNA regulation in neurons, in which RNA is generally silenced and only activated in the correct place and time, makes it susceptible to both age-related decline and disturbance by genetic mutation. Altered RNA regulation (ribostasis), therefore, may be a frequent causative factor in degenerative disease. While normal RNA regulation involves regulated and reversible assembly of RNA-protein particles, both increased cellular age and mutation push the process towards hyperassembly, which leads to altered pools of RNA or RNA regulatory proteins in neurons that contribute to their eventual death. …

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Enhancer RNAs may open new avenues for gene therapy

Aug. 13, 2013 — A study investigating the function of the recently discovered enhancer RNA molecules may open new avenues for gene therapy. According to the study researchers, altering the production and function of these molecules could affect the expression of genes and, in consequence, possibly also the progression of various diseases.Published in Molecular Cell on 8 August, the study was carried out in collaboration between the University of California, San Diego and the University of Eastern Finland.Besides promoters located in the beginning of genes, gene expression is also regulated by enhancers which may be located as far as thousands of base pairs away from the gene they regulate. Enhancers have been shown to be responsible for cell-specific gene regulation. Previously, it was thought that the number of enhancer sequences in a differentiated cell is static; however, recent findings are starting to disprove the idea. In 2010, it was discovered that non-coding RNA molecules were being produced from the enhancer regions. The first observations relating to the biological function of these enhancer RNAs, or eRNAs, were published earlier this year. However, no study to date has addressed the question of whether enhancer transcription is of functional importance.In the study researchers used genome-wide approaches to demonstrate that inflammation response causes the emergence of novel enhancers in primary macrophage cells. For the first time ever, the study used this formation of novel enhancer regions to describe the selection of enhancers and the progression of the activation from transcription factor binding to histone acetylation and eRNA transcription, finally leading to the mono- and dimethylation of histone H3 lysine 4 (H3K4me1/2). The H3K4me1 and H3K4me2 histone modifications are the very markers generally used to identify the location of enhancer regions on DNA. …

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