Tag Archives: epigenome

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

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

Essence of Breast Cancer Profiling using Integrative Functional Genomics

Posted on October 5, 2012 by Nicole Kelesoglu

Yu Bo is a highly respected, world famous chef who prepares modern versions of Chinese cuisine. His dishes are terrifically creative in their presentation of traditional Cheng Du providence flavors. Yu Bo’s process reveals the ‘essence’ of a dish, displaying it through modern culinary procedures and techniques. This inventive process is similar to how biological information can be processed to reveal an essential disease profile. Breast cancer has many known associated single-nucleotide polymorphisms(SNPs). Most do not disrupt coding gene sequences. How can we discover which are causing disease? Because exhaustive functional analysis of all GWAS results just doesn’t make sense, Richard Cowper-Sal-lari et al Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression (2012) … Continue reading →

Posted in Bioinformatics, Biomarkers, Breast cancer, Chromatin Structure, Cistrome, Epigenome | 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