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Features

EpiGenie Features call out new Methods, provide Insights into emerging trends, or sometimes just share technical tips from the experts in our community.

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SCAN-ing For Chromatin Gold

March 2, 2010

If you run enough tedious ChIP experiments, it feels like you might as well be panning for gold back in the 1800s; doing a lot of work for a few nuggets of data. Luckily some technological wizards at Cornell University have your back and are working on a new system called SCAN (Single Chromatin Analysis […]

CpG Methyltransferases Caught in the Act-and in Real Time

February 17, 2010

Being “caught in the act” isn’t usually a good thing, but catching DNA methyltransferases in the act is a very good thing for epigeneticists. A team at the University of Southampton (U.K.) now reports that they have developed a reproducible, real-time fluorescent assay that will help scientists understand how these enzymes regulate themselves, interact with […]

State of Methylome Analysis: Genome-Wide Methylation Techniques Review

February 11, 2010

The State of the Union Address and the drama/commentaries that accompany it have come come and gone, but a fresh Nature Review produced by USC’s Peter Laird now provides the epigenetics community with a State of Methylome Analysis. For the epigenetics researcher, it is every bit as insightful but won’t take as much time to […]

Bisulfite Sequencing in Plants: Tips for “Going Green”

January 21, 2010

Figuring out human DNA methylation patterns with bisulfite sequencing can be tough, but the complexities of plant DNA methylation can turn your lab into a Little Shop of Horrors. That’s because plants methylate cytosine residues not only in the CG sequence context, but also in CHG and CHH (where H is any nucleotide but guanine). […]

Getting Amped on Bisulfite Conversion

January 21, 2010

Some of the biggest issues associated with bisulfite conversion aren’t really related to the bisulfite conversion process itself, but rather the downstream assays interpret the base conversion. After all, if a C is converted to a U in a test tube and nothing can assay it effectively, was in really converted? OK, enough bisulfite philosophy. […]

More DNAm Data, Less Sample: Reduced Representation is No BS

January 13, 2010

When someone tells you that they can save you time, money and sample, the magic trifecta for most scientists, your first thought is probably: “Bull&@%!”…your second thought might be: “Where do I sign up?” A new Nature Methods article from researchers at Broad, MIT, Harvard, and the Max Planck Institute promises to do just that […]

RIP-Chip Tears Into miRNP Complex Analysis

January 6, 2010

Solving the mysteries of miRNA:mRNA interactions has been a tough case to crack. Correlation studies, and miRNA target prediction algorithms point us in the right direction, but their indirect nature is a little like going to trial with only circumstantial evidence. Researchers from University of Kentucky published a new paper demonstrating how RIP-Chip techniques can […]

Targeted Bisulfite Sequencing with Padlock Probes

December 8, 2009

A rising star in the epigenetics field, Dr. Kun Zhang joined the UCSD faculty in 2007 after a post-doc with George Church at Harvard. Engaging in a little friendly competition with his former mentor, Zhang published a technique for targeted bisulfite sequencing using padlock probes (Nat. Biotechnol. 2009, 27, 353) at the same time the […]

LNA miR-122 Inhibitors Put HCV in Lockdown in vivo

December 3, 2009

miR-122 is a talented regulator. Sure it can negatively regulate gene expression by binding 3’ UTRs of target mRNAs, but it’s also shown that it can bind 5’ UTRs in the HCV genome just as well, and act as a positive regulator, giving the virus a hand with replicating its genome. Facilitating viral replication? Well, […]

ChIPing Away at Small Samples with Direct Sequencing

December 1, 2009

One rarely hears mention of deep sequencing without “more” being dropped into the sentence. More coverage, more depth,…more sample? That’s right. As valuable as next generation sequencing platforms have become, those library construction protocols demand a fair amount of sample. Often more than can be coaxed out of a biopsy, or other small cell population. […]

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