Category Archives: Enzymology

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

More of Adenovirus’s Epigenetic Tricks

Posted on June 20, 2012 by Chris Womack

Adenovirus’s epigenetic power to reprogram cells goes beyond its ability to cause tumorous replication — G.J. Fonseca and colleagues at the Western University of Ontario report in the new Cell Host & Microbe that it’s also able to sabotage the interferon response, which usually functions as a first line of defense in infected cells. In an April post, I interviewed Roberto Ferrari about adenovirus research and its ability to push cells back into active tumor-like replication, so I thought this bit of news was an interesting incremental step in overall knowledge of how invaders — particularly adenovirus — use epigenetics against us. What a bunch of jerks! In particular, Fonseca and colleagues used a yeast two-hybrid screen to find out … Continue reading →

Posted in Chromatin Structure, Gene Regulation, Histone Modifications, Histones, Microbial Epigenetics, Ubiquitination, Virology | Tagged , , , , | Leave a comment

O-GlcNAcylation Epigenetic Mark is Palatable Research

Posted on June 14, 2012 by Nicole Kelesoglu

It’s well known that modern high calorie, sugary diets correlate with increasing rates of diabetes, obesity, neurodegenerative diseases (Alzheimer’s in particular), and cancers. Metabolic dis-regulation is associated and SUSPECT in all of these health problems. There are already over 14,000 records in the E3 Epigenetics publication database containing the word ‘Metabolism’. Researchers hope to show direct epigenetic events, leading to these disease outcomes. One such link, is the post-translational modification (PTM), O-GlcNAcylation. With the recent development of O-GlcNAc antibodies (thanks partially to grant initiatives by NCI in 2010), and improved mass spec techniques, the study of this unique type of sugar based PTM has become palatable. NIH scientists John A. Hanover, Michael W. Krause and Dona C. Love have just … Continue reading →

Posted in Cellular Biology, Enzymology, Gene Regulation, Genetics, Histone Modifications, History & Trends, Mass Spec, Metabolism, Nutrigenomics, O-GlcNAcylation | Tagged , , , , | 3 Comments

Parasitic Use of Our Epigenome

Posted on January 24, 2012 by Nicole Kelesoglu

One of the “perks” of pregnancy is hearing from your doctor that you should not be cleaning the kitty litter tray. Wait a second! What did you just say? Can you write that one down in an authoritative doctor’s note, please? Reason being – that if you have never been infected before, a primary infection from Toxoplasma cysts in cat feces can (rarely) be transmitted through the placenta to your baby. Apparently about a 1/3 of adults have antibodies against the parasite, Toxoplasma gondi. The infection is usually fairly insignificant. However, this infection becomes life threatening for those with poor immune systems. Think about those in the womb, post-chemotherapy or AIDS patients. Let’s face it, you cannot prevent “Fluffy” from … Continue reading →

Posted in Acetylation, Applications, Flow Cytometry, Histone Modifications, Histones, Immunology, Mass Spec, Microarray, Transcriptome, chIP | Tagged , , , | Leave a comment

Viral Etiquette Tips : The Epigenetic Effects of Life Long Guests

Posted on November 25, 2011 by Nicole Kelesoglu

Hello E3 scientists! Here are three etiquette tips for the modern virus. This week’s post is a bit of “tongue in cheek”, while pointing out some neat virology & epigenetics research!!!

Posted in Acetylation, Bioinformatics, Cellular Biology, Chromatin Structure, DNA Methylation, Genomewide Methylation Profiling, Immunology, Methylation, Oncogenes, Virology, chIP | Tagged , , , | 4 Comments

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 , , , , | 3 Comments

Histones Signal Other Proteins Too

Posted on September 9, 2011 by Chris Womack

Here’s an epigenetics first. It turns out that intermolecular signaling in epigenetics — all that ubiquination, methylation, and so forth — doesn’t always end at DNA or histones, where those two components go on just to regulate genes (or to encourage more modification of themselves and each other). Nope, John Latham and colleagues at the University of Texas M.D. Anderson Cancer Center reported in Cell last week that there’s at least one case — in yeast — in which a modified histone allows a non-histone protein to methylate another non-histone protein. That is, the signal travels from the Paf1 complex, to histone H2BK123 by ubiquination, to the COMPASS complex — which needs that ubiquination to di-methylate Dam1. (It’s far more … Continue reading →

Posted in Applications, Chromatin Structure, DNA Methylation, Gene Regulation, Histone Modifications, Methylation, Methyltransferases, Phosphorylation, Ubiquitination | Tagged , , | Leave a comment

Acetylation of Histone Variant H2A.Z Gone Haywire!

Posted on August 4, 2011 by Nicole Kelesoglu

The practice of making poor repairs with hay wire – wire used to bale staw – originated the slang phrase. It means non functioning or acting just plain crazy. We can now view H2A.Z as the histone variant that can go haywire. Dr. H Valdés-Mora and colleagues at the Garvin Institute of Medical Research in Sydney, an Epigenetics team headed by Susan Clark, have untangled the meaning behind seemingly conflicting published results. Pattern changes in the acetylation states of promoter-associated H2A.Z, are demonstrated as a mark of cancer-specific gene deregulation. Acetylated H2A.Z is exclusive to the epigenetic silencing marks of Trimethylate histone H3 on lysine 27 (H3K27me3) and/or DNA methylation. In prostate cancer, acetylated H2A.Z “was associated with oncogene activation … Continue reading →

Posted in Acetylation, Biomarkers, DNA Methylation, Histone Modifications, Histones, Oncology | Leave a comment

Cytosine-Mod Mysteries Sort-of Solved? Disappearing Methyls and Regulatory 5-hmCs

Posted on July 29, 2011 by Chris Womack

Last week’s excitement about the discovery of “seventh” and “eighth” DNA bases might’ve obscured parts of that work that shed a little more light on a very murky corner of epigenetics’ cytosine modifications — “Where do the methyls go?” And related research also published last week gets a bit closer to answering, “What does 5-hydroxymethyl-C really do, anyway?” The first, a Science paper by Yi Zhang and his group at the University of North Carolina, does introduce two new cytosine modifications, 5-formylcytosine and 5-carboxylcytosine. But more interesting, I think, is that the group gets halfway through proving a plausible mechanism for cytosine demethylation, which no one’s demonstrated yet. And during the same week, researchers at UCLA and New England Biolabs … Continue reading →

Posted in Applications, DNA Methylation, Developmental Biology, Gene Regulation, Genomewide Methylation Profiling, Methyl-specific Antibodies, Methyltransferases, Methyltransferases | Tagged , , , , | Leave a comment