In the last few years, coverage of epigenetics research and findings has spilled into a variety of mainstream news media, making agouti mice the official image of the field. Stay in the know by checking out the Epi Buzz often and impress your fellow epigenetics enthusiasts by sharing breaking news during lab meetings and conferences.
December 16th, 2008. What’s good for the goose is good for the gander, so why shouldn’t bisulfite sequencing be used to study RNA cytosine methylation? Until recently, the harsh reaction conditions required for bisulfite deamination were considered detrimental to RNA stability. However, Matthias Schaefer and colleagues developed an RNA bisulfite sequencing procedure that reproducibly and quantitatively detected cytosine methylation of tRNAs and rRNAs. Read more... December 10th, 2008. In the past few years, ncRNAs have progressed from interesting anomalies to what some researchers think constitute the majority of the mammalian transcriptome. However, as reviewed by John Mattick and coworkers at the University of Queensland and the Ludwig Institute for Cancer Research (both in Australia), it’s increasingly difficult to distinguish coding from noncoding RNAs on the basis of sequence alone. Read more... December 6th, 2008. Single male fruit flies take note: stay away from those lovely lab-raised ladies. The progeny of wild-caught male and laboratory-strain female Drosophila are sterile, whereas the offspring of wild females and lab-strain males are fertile. Read more... December 2nd, 2008. It’s December, the time of year when much of the States is blanketed in a frosty mantle of the white stuff. But as recently reported in Molecular Cell, the ACA45 RNA appears to have pulled the ultimate snow job. Nikolaus Rajewsky, Gunter Meister, and colleagues revealed that ACA45, which was previously thought to function exclusively as a small nucleolar RNA (snoRNA), is also processed to a shorter sequence with miRNA-like functions. Read more... November 23rd, 2008. What makes some tumors as gentle as purring kittens and others of the same cancer type as ferocious as saber-toothed tigers? A miRNA (miR-101) was recently shown to take a bite out of cancer by inhibiting the EZH2 histone methyltransferase. The study by Arul Chinnaiyan and co-workers at the University of Michigan Medical School, the National Cancer Centre (Singapore), and the Genome Institute of Singapore appeared in a recent issue of Science. Read more... November 17th, 2008. Do you remember the name of your fourth-grade teacher? How about what you had for lunch last Thursday? Highschool Prom date? Yeah, we went stag too, but if you're having a hard time remebering key events, ncRNAs may be to blame! The human brain expresses high numbers of ncRNAs, and mounting evidence indicates important contributions of ncRNAs to memory formation and maintenance. Read more... November 12th, 2008. Everywhere you look, be it Science or Nature, US Weekly (OK, not quite), silencing by ncRNAs is making headlines. But the targets and mechanisms of this silencing are not always clear. A recent report by Peter Fraser and co-workers at The Babraham Institute (UK) and several other universities and centers in Japan and Europe has revealed that a long (>200-nt) ncRNA called Air silences a target gene by...Read more November 12, 2008. Unfortunately, the KISS principle (‘keep it simple, stupid’) doesn’t apply to chromatin. Although we’d like to think that certain histone modifications are always “good” for gene transcription and others are invariably “bad,” Barbara Panning and co-workers at the University of California San Francisco have found that in embryonic stem cells (ESCs), the transcriptional outcome of some genes depends on...Read more November 5th, 2008. DNA, it has turned out, isn't all it was wound up to be. Forced to look elsewhere, scientists like Rob Darnell and his crew at Rockefeller University have developed a genome-wide platform to study how specialized proteins regulate RNA in living cells. Read more... November 1st, 2008. Doctors of the future might say, “Take two viruses and call me in the morning.” Although viruses are conventionally viewed as harmful infectious agents, scientists are now harnessing the power of viruses to try to combat diseases such as cancer. Concerns over the safety of cancer-destroying, or oncolytic, viruses stem from their potential to damage healthy tissues. Now a team of Mayo Clinic researchers led by Stephen Russell has discovered a way to control potential therapeutic viruses with miRNAs. Read more... November 5, 2008. A very difficult-to-treat child leukemia may benefit from the discovery of a small but potent epigenetic change that launches the cancer⎯but could potentially be reversed relatively easily, preventing cancer-promoting genes from being turned on. Read more... October 24th, 2008. Proving that great minds think alike, two independent research groups have used similar methods to examine the impact of individual miRNAs on the proteome. Read more... October 22nd, 2008. Like a conscientious librarian, miRNA can’t seem to resist saying “Shhhh!” whenever the opportunity arises, whether in post-transcriptional or, as a new study suggests, in transcriptional silencing of genes. Although miRNAs were initially thought to suppress gene expression primarily through translational inhibition, recent evidence suggests additional roles for miRNAs in regulating gene expression in the nucleus. Read more... October 15th, 2008. Every great star has a sidekick who sometimes threatens to steal the show: Batman had Robin, Sherlock Holmes had Dr. Watson, and Hillary had Bill. Likewise, some proteins appear to have an intron-encoded miRNA sidekick that neutralizes the “bad guys” so that the protein can effectively perform its cellular function, as demonstrated in a recent NAR paper by Sailen Barik at the University of South Alabama. Read more... September 24th, 2008. The methylation of histones at specific sites has been linked to both transcriptionally active and repressive chromatin. However, the structural basis for these effects has been difficult to study because homogeneous populations of methylated histones were not available for x-ray crystallography. Read more... September 26th, 2008. It turns out that the small but mighty inhibitors of gene expression have an achilles heel and can be served up a taste of their own effect. Qihong Huang, Alexander Deiters, and colleagues at The Wistar Institute, North Carolina State University, and the University of Pennsylvania School of Medicine discovered the first small molecule inhibitor of miRNA. Read more October 13th, 2008. The Evil Twin is a staple of countless soap operas, movie plots AND epigenetics studies. But in real life, how can identical twins with the same genes sometimes exhibit drastic differences in personality or behavior? Check out one of the lastest studies implicating epigenetic mechanisms in the observed large scale gene expression differences in gentically identical mice. Read more... September 16th, 2008. Some might recall playing with Mr. Potato Head as a child (or maybe earlier this morning). By sticking different noses, mouths, eyes, shoes, or other accessories on the basic potato head module, you could generate a variety of silly-looking spuds. Similarly, the interaction of different accessory proteins with the miRNA-argonaute complex might determine the fate of the targeted mRNA...Read more Sept 1st, 2008. The tumultuous relationship between some epigenetic elements resembles many Hollywood romances: on again, off again, brief stint in rehab (only kidding), on again. The association between the family of Polycomb repressive complexes (PRCs) and DNA methylation is no exception. A team of researchers from USC’s Norris Cancer Center, Nimblegen, and the Weizmann Institute took a closer look at this interplay, aiming to shed a little light on the situation. Read more... September 30th, 2008. Recent evidence has shown that the let-7 miRNA bites the hand that feeds it . . . and in an unconventional way. By searching for short sequences conserved at the nucleotide level in the coding regions of 17 species, Hilary Coller and co-workers at Princeton University identified three let-7 target sites within the coding sequence of the miRNA-processing enzyme Dicer. Read more... October 15th, 2008. Over the years mutants like E.T., the Hulk, Yoda, and the X-Men to name a few, have all left a lasting impression in our lives. That's why when a group of John's Hopkins researchers, led by jef Boeke, produced a library of synthetic histone H3 and H4 mutants to probe the function of each residue systematically, we couldn't help but get excited. Read more... October 6th, 2008. Researchers have been puzzled by the discovery of several-kilobase-long, polyadenylated transcripts that overlap functional coding regions but do not themselves encode proteins.Some of these ncRNAs are transcriptional trailblazers that pave the way for gene expression by remodeling promoter chromatin. Read more... October 1st, 2008. Let’s face it: it’s an RNA world. In addition to RNA’s many genetic, catalytic, and structural roles, the discovery of small non-coding RNAs has unveiled an entire continent of epigenetic functions. Small RNAs act in processes such as mRNA destruction, translational inhibition, and DNA methylation. Now it appears that, at least in plants, small RNAs are also involved in DNA demethylation. Read more September 8th, 2008. To divide uncontrollably, cancer cells must acquire a mechanism that prevents the progressive shortening of chromosome ends (telomeres) with each cell division. Telomerase, the most famous stabilizer of telomere length in cancer and other rapidly dividing cells, is a reverse transcriptase that adds DNA repeats to chromosome ends. However, Maria Blasco and co-workers at the Spanish National Cancer Center showed recently that an epigenetic mechanism also regulates the length of telomeres in human cancer cells. Read more... September 6th, 2008. In this contentious election year, political candidates have accused their opponents of being “too liberal” or “ultraconservative.” In the interest of bipartisanship, EpiGenie would like to point out that even the most flaming liberal has a few “ultraconservative” elements within them, ultraconserved elements (UCEs) of the genome, that is. These >200-bp genomic sequences are 100% identical among human, mouse, and rat genomes. Read more... September 16th, 2008. Human blood serum is cellular buffet of different biological molecules sampled continuously from every tissue of the body. So it’s not surprising that many researchers have attempted to identify biomarkers in serum that reflect a particular physiological or disease state. Most of these potential biomarkers are proteins (important-yes, exciting-not really)...Read more September 24th, 2008. A sensitive new nanotechnology assay might represent a “quantum leap” in DNA methylation detection. The technique, which was developed by Vasudev Bailey and co-workers at The Johns Hopkins University School of Medicine, uses quantum dots⎯fluorescent nanocrystals of a semiconductor material⎯to sensitively detect and quantify minute amounts of methylated DNA. Read more August 17, 2008. Gone are the days when microRNAs (miRNAs) were relegated to the unimportant “junk heap” of sequences cluttering up the genome. Another recent paper by Irene Bozzoni and colleagues at the University of Rome posits an important evolutionary role for miRNAs in determining species identity. Read more... August 17th, 2008. In our opinion, it’s time for change. No longer can the genetic and epigenetic causes of cancer and the resulting changes in gene expression be analyzed separately, with little regard for their interdependency.
In this spirit, Jeremy Squire and coworkers at the Hospital for Sick Children, the Ontario Cancer Institute, and Queen’s University (all in Canada) conducted the first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression. Read more... September 24th, 2008. It was the best of times, it was the worst of times⎯one parental allele was transcribing like gangbusters, and the other was permanently stalled. Each of us carries a set of genetically distinct chromosomes from mom and dad, and increasing evidence indicates that the two parental genomes also have widespread epigenetic differences. Read more August 8th, 2008. There’s a new addition to the original set of grants rolled out with the NIH’s Epigenetics Roadmap. OK, well it’s not brand new. A few weeks back the NIH announced another grant...Read more July 28th, 2008. With all the hype around Batman-The Dark Knight, we missed one of the most recent heroic efforts to facilitate global methylation studies. The unveiling of a Bayesian tool for methylation analysis (Batman) enables researchers to estimate absolute methylation levels across a range of CpG dense regions using methylated DNA immunoprecipitation (MeDIP) approaches combined with either microarrays (MeDIP-Chip) or deep sequencing (MeDIP-Seq). Read more
July 21st, 2008. Epigenetics and imprinting have been cohabiting the same sentence for years now, but Imprinting and EpiPanels are a more recent duo. Sequenom recently launched a third EpiPanel. The Imprinting EpiPanel is a pre-validated set of primers targeting CpG regions in commonly-studied genes from which the methylation pattern is either paternally or maternally derived. Read more... July 15th, 2008. Let the blame game begin. In addition to our lifestyle habits, our mothers could have something to do with those stubborn pounds that don’t seem to shed. An interesting obesity studying involving DNA methylation has provided new evidence suggesting that obese moms give birth to kids who have a propensity to become even more obese...Read more
August 7th, 2008. Last week PLoS Genetics ran a great paper from Anders Lindroth and colleagues illustrating a mutually exclusive relationship between DNA Methylation and methylation of H3K27 in the a differentially methylation domain (DMD) of an imprinting control region (ICR). Read more August 21st, 2008. Most techniques focused on analyzing DNA methylation status in focused territories in the methylome involve bisulfite conversion of DNA followed by PCR amplification of the target region. Read more... July 1st, 2008. Although the German football club fell just short of taking the Euro 2008, the country’s biotech mogul is setting the pace this year with a series of epigenetics product releases. In the last few weeks the company announced several significant additions to it’s EpiTect line of products for DNA Methylation analysis and to its miScript miRNA Analysis product line. Read more... July 14th, 2008. Not even a month after announcing a reagent supply agreement with OncoMethylome Sciences, LabCorp has announced the commercial availability of the Methylation-Specific PCR Assay for monitoring the methylation status of Vimentin DNA... Read more
August 1st, 2008. In case you haven’t noticed, we’re big fans of graphics. The old saying about the picture being worth a thousand words is true and it’s way cheaper than paying our tech writers so we’re sending a big EpiGenie salute to the team of UK researchers that pulled together a nice review on the dietary factors affecting DNA methylation. Read more May 14, 2008. As Next Generation Sequencing transitions into the Now, additional advances on the chemistry and sample preparation side of the equation are soon to make these machines as flexible as a Cirque du Soleil performer. We’ve seen how these platforms can transform chromatin and transcription factor location analysis, but methods for investigating DNA methylation in complex genomes, like human, have been more limited. Recent adaptations to previous methylation analysis sample preparation methods aim to tackle the elusive “5th base.” Read July 21st, 2008. Last week, researchers from the Karolinska Institute and the University of London released data on an innovative approach for studying RNA-RNA interactions. Data supporting the multitude of RNA functions in our cells continues to pour in, but challenges in analyzing the effecting complexes in cellular processes persist, so we tip our hats to this team for developing a method that facilitates the study of RNA-RNA interactions. Read more May 21st, 2008. A group of researchers up at the British Columbia Cancer Agency stepped up and created MD-SeeGH (Multi-Dimensional SeeGH). Previously SeeGH was released primarily for analyzing array-based CGH data, but the team made some significant upgrades. Read more... July 21st, 2008. A recent paper by Jan Pawlicki and Joan Steitz at Yale revealed that Drosha processes pri-miRNAs co-transcriptionally. Pri-miRNA transcripts that were engineered to be retained at transcription sites or that had flanking exons were processed more efficiently...Read more August 1st, 2008. The BK channel (Slowpoke, MaxiK), a large conductance calcium- and voltage-activated potassium channel, is one of the best established alcohol targets in the nervous system and has been previously shown to play an important role in behavioral and molecular tolerance to alcohol in both invertebrates and vertebrates [1−4]. Dr Andrzej Pietrzykowski, Ryan Friesen, and colleagues in the laboratory of Dr Steven Treistman
(Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA), investigated how alcohol can alter the form and function of the BK channel through microRNA (miRNA) regulation of specific...Read more May 31st, 2008. The Park Plaza Hotel in Boston held the Oscars for Epigenetics researchers this week with 50+ great talks from big names like Peter Laird, Susan Clark Peter Jones, Jean-Pierre Issa, Stephen Baylin and more. The vast majority of the presentations were focused on DNA Methylation ....Read More July 13th, 2008. Finally a WAR with no conflict. We have to give a big electronic high five to the group from the University of Copenhagen who just introduced a very helpful web utility. WAR-Webserver for aligning structural RNAs is a very handy site that allows you to use the best algorithms for aligning and predicting the consensus secondary structure for a set of non-coding RNA sequences...Read more May 11, 2008. When Columbia University researchers looked at transcriptomes of schizophrenic mouse brains, they found most of the dys-regulated RNAs in both the pre-frontal cortex and the hippocampus had something in common..... Read April 5th, 2008. Whether you had a few too many at a wedding, or had a night on the town that led to streaking, we’ve all said it. “I’m never drinking again!” But for some individuals it’s not that easy. Alcohol withdrawal, similar to that of many substances, can lead to serious anxiety.
Researchers at the University of Illinois at Chicago and Jesse Brown VA Medical Center in Chicago recently found that increased histone deacetylase (HDAC) activity in an area of the brain called the amygdala was associated with the often severe anxiety......Read September 9th, 2008. OK this one is a week old, but we love a paper that addresses epigenetic regulation of epigenetic regulators, so we couldn’t resist a recent PNAS report that identified a miRNA DNA methylation signature for human cancer metastasis. Like proteins, miRNAs act as oncogenes, tumor suppressors, and metastatic mediators, and their expression can be influenced by promoter methylation status. So Manel Esteller at the Spanish National Cancer Research Center and colleagues at several universities, hospitals, and institutes in the U.S. and Europe characterized miRNAs that were upregulated upon treatment of metastatic cancer cells with a demethylating agent. Read more... April 24th, 2008. The ex-Ambion miRNA gurus, who recently spun out Mirna Therapeutics to dedicate more resources to the growing miRNA therapeutics field, will launch the first validated miRNA diagnostic assay for pancreatic cancer in early May....Read |
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