Monthly Archives: May 2012

Trangenerational Epigenetic Inheritance: An Environmental Toxin Exposure & Stress Combinational Phenotype

Posted on May 31, 2012 by Nicole Kelesoglu

How much of an expert are you on environmental toxins and epigenetic inheritance? Practically everyone is aware of DTT. Many of us are aware of the plasticizer BPA. But how many of us are aware of vinclozolin? If you work in the field of epigenetics, you should be. The lab of Michael Skinner, at Washington State University, has been able to use this fungicide to study transgenerational epigenetic inheritance in male rat germ lines. What is it, though? In this case, after initial exposure to the environmental toxin in utero, a transgenerational epigenetic inheritance phenotype exists at least through the third generation in a lineage, in absence of that toxin. The vinclozolin rat model was applied recently in the Skinner … Continue reading →

Posted in Animal Models, Behavioral Epigenetics, Bioinformatics, Evolutionary Epigenetics, Microarray, Transcriptome | Tagged , , | Leave a comment

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

Viral MicroRNA Mimicing Cellular MicroRNA? and a New Dual-Fluuorescent Reporter System

Posted on May 17, 2012 by Nicole Kelesoglu

A team out of the Chinese Academy of Sciences has reported both a new dual-fluorescent reporter system, and an insight on a suspected general phenomenon of functionally matched viral and cellular microRNA in viral-host interactions. You X, Zhang Z, Fan J, Cui Z, Zhang X-E (2012) Functionally Orthologous Viral and Cellular MicroRNAs Studied by a Novel Dual-Fluorescent Reporter System. PLoS ONE 7(4): e36157. Now for context, the gist of what’s known about microRNAs (miRNA) is that they can be thought of as epigenetic post-transcriptional volume control. Modulating…fine tuning…dialling gene expression up or down.   MicroRNAs are ~18-24 nucleotide molecules that are processed from long, highly evolutionarily conserved sequences in organisms and viruses. Such pre-miRNA sequences are located at protein gene introns, … Continue reading →

Posted in Biomarkers, Cellular Biology, Imaging, Immunology, Leukemia, Microbial Epigenetics, New Lab Methods, Non-coding RNA, Oncogenes, Virology, microRNA | Tagged , , , , , | Leave a comment

‘Intelligent Design’ Crowd Projecting onto Epigenetics Too?

Posted on May 9, 2012 by Chris Womack

Seems like “Intelligent Design” proponents are adopting epigenetics in their newest argument that Darwin had it all wrong. Published in February, The Mysterious Epigenome: What Lies Beyond DNA, by theology professor Thomas Woodward and cataract surgeon James Gills, takes readers on a tour of biological molecules and processes, describing flagella, DNA, RNA, and so forth, to eventually conclude that it’s all far too complex to have evolved at all. Here’s a quote from the book posted by an admirer: [T]he epigenome adds tremendous pressure to the already-weak Darwinian explanatory apparatus. Random changes, inherited over generations, must not just explain the explosion of DNA as one moves up the purported tree of life; one must also now explain by these mindless … Continue reading →

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Oxidative Bisulfite Sequencing (oxBS-Seq) A Brilliant Advance for Epigenetics

Posted on May 2, 2012 by Nicole Kelesoglu

There is exciting news regarding a new method to detect 5-hmC quantitatively at high resolution – using any sequencing platform. The new method, termed oxidative bisulfite sequencing (oxBS-Seq) , was applied to explore the 5-hmC mark’s potential functional role in epigenetic plasticity. First author Michael J. Booth, along with collaborators from the Wolf Reik lab at the Babraham Institute, and Shankar Balasubramanian lab at Cambridge University, have reported their work in Science Magazine. In brief, this method uses potassium perruthenate (KRuO4) oxidation to convert 5hmC to 5fC (formylcytosine), and is followed up by conventional bisulfite conversion. Through this process C and 5-hmC sites convert to Uracil, whereas 5-mC does not. OxBS-Seq data is then subtracted from BS-Seq data. The group … Continue reading →

Posted in Applications, Divergent Transcription, Genomewide Methylation Profiling, History & Trends, Hydroxymethylation, New Lab Methods | Tagged , , , , | 1 Comment