Category Archives: Genomewide Methylation Profiling

Tet1 Enzyme Based Enrichment Method for Methylome Sequencing: TamC-Seq

Posted on March 12, 2013 by Nicole Kelesoglu

Here’s another great advance in methylome sequencing. You all know about bisulfite sequencing, the “gold standard” method. Unfortunately it’s expensive.  It also requires a lot of sample, due to DNA degradation. There are enrichment methods, like MeDIP-seq, that are relatively cheap. However, there is the drawback of CpG density bias. Excitingly, there is a new enzyme based enrichment method, called TamC-Seq that requires less sample, less money, and provides excellent coverage for genome-wide profiling. The devlopers are from the He group, University of Chicago. The paper is Liang Zhang et al. Tet-mediated covlent labelling of 5-methylctosine for its genome-wide detection and sequencing. (2013) Nature Communications, (4) 1517 So how does it work? Their protocol uses mouse Tet (Ten-eleven translocation)-1, (or … Continue reading →

Posted in Applications, DNA Methylation, Genomewide Methylation Profiling, Glycosylases, Hydroxymethylation, Methylation, New Lab Methods, Next Gen Sequencing | Tagged , , , , | Leave a comment

Introducing Aba-seq for Enzyme Based High-Res Mapping of Mammalian Hydroxymethylomes

Posted on February 22, 2013 by Nicole Kelesoglu

New England Biolabs is well known for its extensive in house research programs – churning out numerous publications every year. The role of hydroxymethylation as a possible cancer biomarker is a topic of keen interest for all Epigenetics researchers. So, NEB researchers are especially enthused about their recent publication in Cell, along with their collaborators from Emory University School of Medicine. Sun, Z. et al. High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells. (2013) Cell Reports 3, 567-576. describes the Aba-seq method, an AbaSI enzyme based high-resolution hydroxymethylome mapping. (Open access.) In nature, AbaSI is a weapon in the arms race between bacteria and bacteriophages. Wildtype bacteriophages such as T4, are resistant to most restriction enzymes due … Continue reading →

Posted in Applications, Biomarkers, DNA Methylation, Enzymology, Genomewide Methylation Profiling, Hydroxymethylation, Methylation Sensitive Restriction Enzymes, New Lab Methods, Oncology, Stem Cells | Tagged , , , , , | Leave a comment

SMRT Sequencing Studies Methyltransferease Driven Virulence in E.coli (0104:H4)

Posted on November 26, 2012 by Nicole Kelesoglu

Microbiologists rushed to respond to the 2011 pathogenic E.coli (0104:H4) outbreak in Europe. The new strain’s DNA was sequenced within 3 days time. The trace back investigation identified an organic bean sprouts field as the source. Now, Pacific Biosciences with collaboration from New England Biolabs, reports Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing in the journal, Nature Biotechnology (open access paper). Epigenetic analysis reveals the potential for restriction modification methyltransferase enzymes (RM MTases) to have important roles in this pathogenic phenotype. 0104:H4 phenotype virulence has been defined by its production of high levels of Shiga toxin. AND it turns out that this strain has specific MTases that can promote that production. SMRT sequencing … Continue reading →

Posted in DNA Methylation, Genomewide Methylation Profiling, Methyltransferases, Microbial Epigenetics, New Lab Methods, Next Gen Sequencing | Tagged , , , , | Leave a comment

The Easy Way to Study Microbe Methylomes… use SMRT sequencing!

Posted on November 5, 2012 by Nicole Kelesoglu

The most recent pub from the stream of research put forth by New England Biolabs scientists, is a collaboration with scientists from Pacific Biosciences™ . See this open access paper Iain A. Murray et al. The methylomes of six bacteria. (2012) Nucleic Acids Research. It demonstrates how the 3rd generation SMRT DNA sequencing system is used to explore bacterial methylomes. Many exciting discoveries about microbe epigenetic systems are sure to follow this technological advance! So why is DNA methylated in bacteria? Mainly it functions as part of restriction modification systems. But bacterial methyltransferases also take part in gene expression, host-pathogen interactions, DNA damage, and DNA repair. Microbe methylation modifications include N6-methyladenine (6-mA), N4-methylcytosine (4-mC) & 5-methylcytosine (5-mC). Single-molecule, real-time sequencing, … Continue reading →

Posted in Applications, Bioinformatics, DNA Methylation, Genomewide Methylation Profiling, Microbial Epigenetics, New Lab Methods, Next Gen Sequencing, Software | 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

A Better Way to Discriminate iPSCs vs ESCs

Posted on October 17, 2012 by Nicole Kelesoglu

First of all, a hearty congratulations to Dr. Shinya Yamanaka and Dr. John Gurdon for winning this year’s Nobel prize for Medicine, for their discoveries that adult cells could be transformed back to embryonic-like states. Recently, Dr. Yamanaka has publicly warned of dangerous “stem cell therapies” currently offered in various countries, without any pre-clinical testing in animals. This was an important message considering possible tragedies, both for any patients desperate for a cure, who end up sick or dead…and for the public, who might lose their trust in potential future stem cell therapies developed safely under strict scientific methods. Induced pluripotent stem cells (iPSCs) can be transformed from somatic cells, through the expression of only four transcription factors, using Kyoto … Continue reading →

Posted in Cellular Biology, DNA Methylation, Reduced representation bisulfite sequencing, Regenerative Medicine, Stem Cells | Tagged , , , | Leave a comment

5hmC Regulates Cellular Differentiation

Posted on August 17, 2012 by Nicole Kelesoglu

What was once surprising is now established. DNA methylation is not static after imprinting. All genes are not silenced “forever” through DNA methylation.  But how does this dynamic and reversible mechanism work? As the hypothesis goes, 5hmC is a step in the de-methylation process initiated by Tet dioxygenases.  The news today is that 5hmC is more than just a quick step, it has function. In Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. (2012) Nucleic Acids Research, 1-11. A.A. Serandour & S. Avner et al. show that conversion of 5mC to 5hmC activates enhancers – even pointing to it as an early step in the enhancer activation process. Can we all say functional signalling mark? Some of you might be saying … Continue reading →

Posted in Cellular Biology, Conformation Capture, DNA Methylation, Genomewide Methylation Profiling, Histone Modifications, Hydroxymethylation, Methyl-specific Antibodies, Methylated DNA Capture, Next Gen Sequencing, Transcriptome microarray, chIP | Tagged , , , , , | 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 , , , , | 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

Will the Long History of Breast Cancer Research Culminate with Epigenetics Based Personalized Medicine?

Posted on July 13, 2012 by Nicole Kelesoglu

In the first century A.D, Roman family Greek slaves were surgeons. Celsus wrote an encyclopedic describing their methods in latin, laying a foundation for scientific literature on medical practice and surgery. The idea of diagnosis became paramount at this time, requiring close study and record keeping of injury and disease symptoms. It was understood that some breast cancers could be extirpated with breast removal. In the 19th century, after anesthesia and antisepsis had been established, (thank heavens!) a Johns Hopkins Hospital surgeon named William Stewart Halsted introduced, perhaps, the greatest advance to breast cancer treatment. The radical mastectomy. Throughout beast cancer history, the best prognosis post treatment, seemed to be based on early stage diagnosis. (1.) Today we have exceptional … Continue reading →

Posted in Biomarkers, Breast cancer, Clinical Studies, DNA Methylation, Genomewide Methylation Profiling, History & Trends, Microarray, Personalized Medicine, Transcriptome | Tagged , , , | 1 Comment