Tag Archives: methylation

Methylome Data in Lethal Prostate Cancer Supports Personalized Medicine

Posted on January 30, 2013 by Nicole Kelesoglu

Recent surprising evidence has shown that metastatic tumors usually do not vary in their genomes within an individual. Yet, these tumors behave differently at different sites around the body. Does that mean that epigenetic profiling will be too variable to target for cancer treatment? In a word, no. Martin J. Aryee et al., from Johns Hopkins, have published their work in DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases in Science Translational Medicine. They looked at methylation signatures, including total methylation and allele-specific methylation (ASM) in lethal metastatic prostate cancer, among tumors from 24 donors. Methylated DNA was enriched from the genomic DNA using a Methyl-CpG Binding Domain (MBD) -based capture. Their MBD-SNP assay provided … Continue reading →

Posted in Biomarkers, Epigenome, Methylated DNA Capture, Microarray, Oncology | Tagged Epigenetics, MBD, methylation, Prostate cancer | 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 Cancer, chronic disease, diagnostics, diet, DNA methylation, environmental factors, epigenome, histone acetylation, histone ubiquination, In Utero, International Human Epigenome Consortium, methylation, transcription regulation, Translational research | Leave a comment

What could epigenetics reveal to us about human evolution?

Posted on September 3, 2012 by Nicole Kelesoglu

Sometimes you don’t need Indiana Jones to solve an archaeological mystery, sometimes you need a geneticist. The research article Matthias Meyer et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. (2012) Science, proves that point. In the article the whole genome of a little girl who lived ~80,000 years ago, and belonged to an ancient human species called the Denosivans, is sequenced from a (big) tooth and a (tiny) knuckle. Listen here to an NPR interview on the subject. These results are why archaeologists have become as fired up as geneticists are, over next generation sequencing. NGS has recently had a tremendous impact on their field, by producing valid ancient DNA results from some incredibly rare and precious … Continue reading →

Posted in DNA Methylation, Evolutionary Epigenetics, Next Gen Sequencing | Tagged Ancient DNA, Denisovans, Epigenetics, Evolution, methylation | Leave a 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 DNA methylation, environmental factors, Epigenetics, In Utero, methylation | Leave a comment

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 5hmC, DNA, Epigenetics, methylation, oxBS-Seq | 1 Comment

Will Epigenetics Help Overcome Cisplatin Resistance in Ovarian Cancers?

Posted on January 10, 2012 by Nicole Kelesoglu

Hello Epiexperts! There are a couple recent open access papers to point out to you this week. Both relate to ovarian cancer progression and desensitization to the chemotherapy, Cisplatin. Cisplatin resistance is the primary obstacle to surviving ovarian cancer. These cancers are rare thankfully, but the 5 year survival rate is only 15-20%. Epigentics researchers are actively engaged in confronting this challenging disease. There are several Phase II clinical trials in progress for individual and combinational therapies using DNA methylation inhibitors and histone deacetlase (HDAC) inhibitors. Until those epigenetics based therapy trial results are available, as things stand, the current outlook is bleak. Please see this piece by Donna Trussell, in the Washington Post. She writes from her personal perspective … Continue reading →

Posted in Bioinformatics, Biomarkers, Clinical Studies, DNA Methylation, Databases, Genetics, Genomewide Methylation Profiling, History & Trends, Methylated DNA Capture, Next Gen Sequencing, Oncology, Real-time PCR, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged Bioinformatics, Cisplatin, Epigenetics, methylation, Ovarian Cancer | Leave a comment

New & Simplified DNA Methylation Profiling Method: Bio CAP (Biotinylated CxxC Affinity Purification)

Posted on December 26, 2011 by Nicole Kelesoglu

When a portrait artist is drawing a subject, it is often helpful to view the work in progress, as a reflection in a mirror. Somehow it re-attunes the mind’s eye to better assess the quality of the image. In a similar way, recently developed methods allow scientists to reflect on disease, or developmental states, by isolating NON-methylated DNA for profiling. Illinngworth et al., cleverly developed the CAP method in 2008. It produces profiles of non-methylated DNA using a zinc finger CxxxC domain which specifically recognizes non-methylated CpGs. The downsides to this method are that it requires a high-resolution chromatographic system, a large amount of the recombinant CxxC module, large amounts of input DNA (to account for elution and handling steps), … Continue reading →

Posted in Applications, Bioinformatics, DNA Methylation, Genomewide Methylation Profiling, New Lab Methods, Next Gen Sequencing, Real-time PCR | Tagged Bio-CAP, CAP, DNA methylation, Epigenetics, methylation | Leave a comment

Bee-lieve it! Epigenetics Differentiates the Hive : Guest Post by NEB Scientist Rick Feehery

Posted on November 11, 2011 by New England Biolabs

Keeping honeybees runs in our family. My wife’s father keeps many hives, his father kept hives, his father and so on. Our one hive this year produced over 30 pound of honey. Fresh honey is a real treat as the flavor stems from the local fauna: purple loosestrife and apple blossoms. Very different from what you get from the local food mart. Aside from the obvious agricultural benefit that honeybee provides, pollination of plants in the food chain, they are really fascinating insects to observe. Every other year on average in the spring time when the weather is warm and the sky is clear, we can hear a district loud buzzing sound from the hive. A mass exodus of bees … Continue reading →

Posted in Animal Models, DNA Methylation, Methyltransferases, Nutrigenomics | Tagged Bees, Epigenetics, methylation, NEB, Royalactin | 3 Comments

Identical Twins are Not Identically Imprinted : Epigenome in Context of the Genome

Posted on October 28, 2011 by Nicole Kelesoglu

As is the case with their fingerprints, imprinted genes are NOT identical in identical twins. In fact, methylation levels vary notably, yet randomly, in localized imprinted regulatory regions, between MZ twins. Even cooler, a new epigenetics clue came out of demonstrating this imprinting variability. This month in PloS one, the collaborators from the Garvin Institute, the University of Nijmegen Medical Centre, the Queensland Institute of Medical Research and St. Vincent’s Clinical School, University of NSW, produced the paper Impact of the Genome on the Epigenome Is Manifested in DNA Methylation Patterns of Imprinted Regions in Monozygotic and Dizygotic Twins. by Marcel W. Coolen et al. Blood samples from 128 pairs of identical, and 128 pairs of fraternal teen aged twins, … Continue reading →

Posted in Autism, Bioinformatics, DNA Methylation, Developmental Biology, Divergent Transcription, Gene Regulation, Gene Silencing, Genomewide Methylation Profiling, In Utero, Mass Spec, Methylation Specific PCR, Next Gen Sequencing, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged epigenome, Garvin, methylation, twins | Leave a comment