Monthly Archives: March 2012

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

Further Evidence of the Importance of 5-hydroxymethylation in Cancer

Posted on March 20, 2012 by Nicole Kelesoglu

The discovery of the “6th base”, 5-hydroxymethylated cytosine, has resulted in rapid fire publication activity.  Researchers are exploring it’s part in demethylation dynamics, and its epigenetic function. Today I wanted to highlight the paper, H. Yang, et al. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation (March 2012) Oncogene 1-7. It provides further detailed analysis that is complementary to the work described by Hafner et al., please see my Q&A with Dr. Yegnasubramanian. The Oncogene paper research group, mainly out of Fudan University, looked at additional tissue types using an anti-5-hmC antibody for immunolocalization in paraffin embedded samples. They sampled human breast, prostate, liver, lung and pancreas, comparing them with corresponding matched normal surrounding tissues. … Continue reading →

Posted in Biomarkers, DNA Methylation, Diagnostics, History & Trends, Imaging, Immunohistochemistry, Oncology | 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

It’s not over until the RNA sings…

Posted on March 6, 2012 by Nicole Kelesoglu

Epigenetic regulation is accomplished by a series of interdependent systems. It’s overall effect on gene expression is often compared to a musical composition. Today I’m thinking of opera in particular…since I’m proud to say that my uncle Robert Aldridge just won a Grammy for best contemporary classical composition. Bravo Uncle Bob! So you probably know the silly old saying, “It’s not over till the fat lady sings”, right? There are numerous well studied roles in the epigenetic opera….modifications of DNA, chromatin and histones, enzymes activities like DNA and protein methyltransferase, etc….but today let’s think of RNA expression as the grand finale. Once a gene has been physically exposed through modifications to chromatin and histone structural proteins, and expression takes place…those … Continue reading →

Posted in Bioinformatics, Cell Culture Models, Cellular Biology, Gene Regulation, Gene Silencing, Histone Modification Assay, Non-coding RNA, chIP, siRNA | Tagged , , , , | Leave a comment