Category Archives: Next Gen Sequencing

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

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

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 , , , , | 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

“Divergent Epigenetic Landscapes” of AML viewed through RRBS

Posted on June 29, 2012 by Nicole Kelesoglu

Acute myeloid leukemia (AML) is most common in older adults. However, it is rarely cured by standard chemotherapy alone in older patients. According to NCI, it is critical that complete remission occurs, or there is no survival benefit. There are many clinically active therapies, including epigenetic drugs. A big translational research goal is to develop effective therapeutic strategies to demonstrate how and when oncologists should use these therapies.  A clinical combinational treatment regime could be guided in part by genome-wide methylation profiling. Genes in CpG islands and their promoters have established aberrant methylation patterns in cancers.  Perhaps also genome-wide methylation will help reveal new mechanistic details leading to new drug discoveries. Reduced representation bisulfite sequencing (RRBS) was introduced by scientists … Continue reading →

Posted in Biomarkers, Clinical Studies, DNA Methylation, Genomewide Methylation Profiling, Leukemia, Next Gen Sequencing, Oncology, Reduced representation bisulfite sequencing | Tagged , , , , , | Leave a 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 , , , , | 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 , , , , | Leave a comment

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 , , , | Leave a comment