Author Archives: Nicole Kelesoglu

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

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 , , , | Leave a comment

New Years Resolution, Reflection on Cancer Research

Posted on January 14, 2013 by Nicole Kelesoglu

The beginning of a new year is a time for reflection. There have been two news items which have struck me in regard to epigenetics and cancer research, recently. Dr. James Watson, Nobel Prize winner, and co-discoverer of the double helix structure of DNA, has published a controversial, open access paper in the journal Open Biology. Cancer research has not produced cures, but merely temporary life extentions for those facing metastatic cancers. The sequencing of the human genome and identification of individual cancer cell mutation drivers of disease, have not produced cures. Dr. Watson points out that once cancer turns metastatic, resistance to gene-targeted drugs is rampant. In the metastatic process, DNA sequence mutations often don’t change. Rather their expression … Continue reading →

Posted in Epigenome, Genetics, History & Trends, Oncology | Tagged , , , , | Leave a comment

Sirtuin3 Reprograms Mitochondrial Epigenetic Pathways: How Diet Affects Age

Posted on December 11, 2012 by Nicole Kelesoglu

When it comes to acetylation and epigenetics your mind probably goes right to histones. Acetylated histones are associated with relaxed, transcriptionally active DNA. However, acetylation is an important post-translational modification of lysine in many cellular proteins. It is as widespread as phosphorylation. It is reversable. Functionally, acetylation is known to be involved in the effects of calorie restriction on metabolism and aging. Now the first direct evidence of a mechanism underlying this process has been reported. The journal Molecular Cell has recently published Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome, authored by scientists from the University of Wisconsin-Madison and the University of Tokyo. They used model mice with age-related hearing loss for this study. This … Continue reading →

Posted in Animal Models, Mass Spec, Regenerative Medicine | 1 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

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

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

Nanobodies: Tools for ChIP and Epigenetics targets?

Posted on September 17, 2012 by Nicole Kelesoglu

So I was exploring the wide world of epigenetics research on the internet as we often do at E3, when I came upon this paper. T. Nguyen Duc et al. Nanobody-Based Chromatin Immunoprecipitation Methods Mol Biol. 2012;911:491-505. Now this ChIP protocol isolates a transcription factor from the lysate of the hyperther- moacidophilic archaeon,  Sulfolobus solfataricus. Not as interesting for most of us as say, exploring the histone code in breast cancer cells. However what about this business of using of nanobodies rather than polyclonal antibodies for ChIP? What are nanbodies (Nab)? These are single heavy chain only antibodies, produced by llamas or camels immunized with the antigen target. Their Vhh domain is subcloned so that nanobodies can be produced cheaply, … Continue reading →

Posted in Applications, Clinical Studies, Imaging, chIP | Tagged , , | Leave a comment