Tag Archives: DNA methylation

Epigenetics and Fat — Not Just Girth

Posted on November 20, 2012 by Chris Womack

In honor of the U.S. national day of gustatory indulgence, I thought I’d write about girth and fat. EpiExperts Twitter friend Graham Burdge and colleagues at the University of Southampton in the United Kingdom just published an interesting paper exploring how the fat content of a mother rat’s diet affects the polyunsaturated fats in her offspring’s cells and plasma, as well as how that diet may accomplish that feat — apparently it involves promoter methylation of the gene Fads 2. But first, girth. My co-blogger Nicole recently tweeted a blog post from U.S. National Institutes of Health Director Francis Collins, who shared a map by the U.S. Centers for Disease Control showing how obesity has swept the country since 1985. It’s bracing, … Continue reading →

Posted in DNA Methylation, Metabolism | Tagged , , , | Leave a comment

Canada Joins the International Human Epigenome Consortium – Q&A with Tomi Pastinen of Génome Québec

Posted on October 31, 2012 by Chris Womack

In an ambitious project investigating the interplay of environment, disease, and epigenetics, Canada is funneling $41 million into epigenomics research. It’s a multi-pronged effort to scrutinize a variety of tissue samples, disease states, and responses to environmental insults, so I called up Tomi Pastinen, the Canada research chair in human genetics, to learn more about the project. Here’s a lightly edited transcript of our conversation. But first, more about the project itself. It’s Canada’s entrée into the International Human Epigenome Consortium, and its announcement last week follows closely on the heels of last year’s launch of a European IHEC effort, BLUEPRINT (see our interview with the project’s Henk Stunnenberg here). While BLUEPRINT focused on blood epigenomes, which is common in … Continue reading →

Posted in Animal Models, Applications, DNA Methylation, Epigenome, Gene Regulation, Genomewide Methylation Profiling, Histone Modifications, Metabolism, Neuroscience, Next Gen Sequencing, Sodium Bisulfite Sequencing, Transcriptome | Tagged , , , , , , , , , , , , , | Leave a comment

The Epigenetics of Real-Life Stress and Serotonin

Posted on October 10, 2012 by Chris Womack

Sure, M.D.s often suffer a lot of pressure. But as I learned in a brief hospital job, nurses really bear the brunt of all the biological clean-up, red tape, weird hours, patient complaints, and snippy doctors’ demands. So this new study in PLoS One on stress-related epigenetic changes in shift-working female nurses really caught my attention, and seemed like a good followup that post on situational stress and epigenetics. Nurses under high stress appear to have their gene expression epigenetically regulated in a way that may decrease serotonin in the brain’s synapses. It seems a bit like the reverse of Prozac, and it bears a passing resemblance to what might happen at the beginning of depression. By interfering with serotonin … Continue reading →

Posted in DNA Methylation, Gene Regulation, Sodium Bisulfite Sequencing | Tagged , , | Leave a comment

Situational Stress Makes Short-Term Epigenetic Changes

Posted on August 27, 2012 by Chris Womack

Or so it appears, based on research by Gunther Meinlschmidt and colleagues. When they exposed 76 people to a stressful simulated social situation, they found changes in the methylation of two genes within an hour. What’s more, those two genes—oxytocin receptor (OXTR) and brain-derived neurotrophic factor (BDNF)—are important to human behavior. The oxytocin receptor conveys the hormone oxytocin’s effect at several sites in the body, including the brain. BDNF supports existing neurons, encourages their growth, and functions in memory and learning. The case isn’t perfectly conclusive yet, of course—with 76 subjects between 61 and 67 years old, the study could be larger. And the team measured gene methylation in blood samples—and not brain samples, of course—so it’s not clear that … Continue reading →

Posted in Behavioral Epigenetics, DNA Methylation | Tagged , , , | 1 Comment

The Epigenetics of Smoking During Pregnancy

Posted on August 10, 2012 by Chris Womack

Looking at around 474,000 CpG sites in cord blood from 1,062 newborns, a multi-institutional group of researchers took the first broad look at what happens epigenetically when pregnant moms smoke. Typical of epigenome scans, this one doesn’t make any clear links between methylation states and any diseases, though the researchers make a couple plausible connections, for example, suggesting that demethylation affects the AHRR gene’s role in fibroblast apoptosis in lungs. In any case, the data will be very useful to epigeneticists in general. Researchers from the NIH National Institute of Environmental Health Sciences, the Norwegian Institute of Public Health, the Haukeland University Hospital in Bergen, Norway, Duke University, and several other institutions published the paper online at the NIEHS website … Continue reading →

Posted in Applications, DNA Methylation, Developmental Biology, Gene Regulation, Genomewide Methylation Profiling, In Utero | Tagged , , , , | Leave a comment

Just How Similar ARE Newborn Identical Twins, Epigenetically Speaking?

Posted on July 27, 2012 by Chris Womack

It depends on which tissues you’re talking about. And epigenetic modification — or at least methylation — in newborns is dictated by genetic, environmental, and tissue-specific factors, according to research published this month by Lavinia Gordon and colleagues at the Murdoch Children’s Research Institute and six other universities, research centers, and hospitals. First the tissue-based factor. Using statistical clustering, the mostly Australian multi-institutional group found that the methylation profiles of identical twins segregated into the same categories — the same general patterns of DNA modification — more often or less often, depending on the DNA’s tissue of origin. in  placental tissue, 71 percent of twin pairs’ methylation patterns “clustered” together statistically. In cord blood mononuclear cells (CBMC), identical twins shared … Continue reading →

Posted in Applications, DNA Methylation, Genomewide Methylation Profiling | Tagged , , , , , | 2 Comments

A Device that Sorts Single Molecules of Methylated DNA – Q&A with Cornell’s Harold Craighead

Posted on May 24, 2012 by Chris Womack

Sure, single-cell sorting devices are cool and useful and all, but Harold Craighead’s lab at the Cornell University Department of Biomedical Engineering is developing a microfluidic device that can separate individual methylated DNA fragments from a single cell’s total genetic content. In a lab test reported in their recent open-access paper (pdf) in Proceedings of the National Academy of Sciences, the team used the device to separate methylated plasmids from among 11 femtograms of mixed DNA, hitting a 5.6 percent false-positive rate and 3.5-fold enrichment. That level of enrichment is typical of immunoprecipitation methods that need about 1,000 times as much input DNA. I spoke to Craighead last week to ask him a little more about the device and its … Continue reading →

Posted in Applications, DNA Extraction / Purification, DNA Methylation | Tagged , , | Leave a comment

Farming with Epigenetics

Posted on April 11, 2012 by Chris Womack

Every once in a while, I stumble upon an enthusiastic mention of epigenetics on some agricultural site. This week, it was this one at the Cattle Site, which seems to be reposting this report (pdf) from the European Union’s Sustainable Animal Breeding (SABRE) project. Since epigenetics promises to offer people new ways to control gene expression — and therefore certain diseases, traits, developmental patterns, and so on — I’d assumed that it’d take root right away in agriculture (ta-dum dum). After all, engineered plants and animals became commonplace during the ’90s, when the technology was still pretty young. Heck, DNA sequencing was still a manual affair. But so far, it seems like agriculture hasn’t really embraced it yet. For this … Continue reading →

Posted in Applications, DNA Methylation, Plant Epigenetics | Tagged , , , | 6 Comments

Looking for Timebombs in the Genome — Retrotransposons & Epialleles

Posted on March 28, 2012 by Chris Womack

Buried in the mammal genome are more than a million virus-like stretches of DNA that epigenetic mechanisms work constantly to suppress — but once in a while, they slip up. If that happens nearby an important gene, it could mean physical changes, or even disease. And with bioinformatics and lab work, Muhammad Ekram and colleagues at Louisiana State University are trying to find out where these timebombs might be. They’ve found 143 candidates so far. They’re working with mice in Joomyeong Kim’s LSU lab, but the virus-like DNA sequences — retrotransposons — make up a large chunk of the genomes of most mammals. In mice, they’re about 40 percent of the genome, and in humans they account for more than … Continue reading →

Posted in Applications, DNA Methylation, Histone Modifications, Transcriptome | Tagged , , , , , | Leave a comment

Exercise & Rapid Muscle Methylation Changes – Q&A with Romain Barrès

Posted on March 14, 2012 by Chris Womack

Right after biking — and probably even rowing or slaloming — your muscle cells make quick epigenetic DNA alterations that epigeneticists previously considered long-lived and often long-to-form. And the amount of change depends on the intensity of exercise. To find out more about the upshot for this rapidly changing field, for epigeneticists themselves, for possible diabetic treatments, and even for good ol’ Lamarck himself, I spoke to lead author Romain Barrès, who conducted the research with colleagues at the Karolinska Institutet in Stockholm, the University of Copenhagen, and Dublin City University. Within 20 minutes of acute exercise, the DNA in muscle cells becomes demethylated at certain gene-promoter sites — there’s no full account of all the changes yet, but Barrès and colleagues … Continue reading →

Posted in DNA Methylation, Gene Regulation, Genomewide Methylation Profiling | Tagged , , , , , | Leave a comment