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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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Allele-Specific Modifications: A Tale of Two Epigenomes

September 24, 2008

It was the best of times, it was the worst of times-one parental allele was transcribing like gangbusters and the other was permanently stalled. Each of us carries a set of genetically distinct chromosomes from mom and dad, and increasing evidence indicates that the two parental genomes also have widespread epigenetic differences. But how can […]

Karolin Luger: Leading Ladies in Epigenetics Research

September 8, 2008

As a post-doctoral fellow in 1997, Karolin Luger burst onto the chromatin scene with the now classic Nature cover story, “Structure of the nucleosome core particle at 2.8 Å resolution” [Nature 1997, 389, 251−260]. A native of Austria, Dr. Luger joined the faculty at Colorado State University in 1999, where she is an HHM Investigator. […]

Joan Steitz: Leading Ladies in Epigenetics Research

September 4, 2008

In 1967, Joan Argetsinger Steitz received her Ph.D. from Harvard University, where she conducted her doctoral research on RNA bacteriophage in the lab of Dr. James Watson. As a post-doc at Cambridge, Dr. Steitz studied ribosome binding sites in mRNA. In 1970, she joined the faculty at Yale and began her groundbreaking and now famous […]

Can Batman Save Whole Methylome Analysis?

July 25, 2008

With all the hype around Batman-The Dark Knight, we missed one of the most recent heroic efforts to facilitate global methylation studies. The unveiling of a Bayesian tool for methylation analysis (Batman) enables researchers to estimate absolute methylation levels across a range of CpG dense regions using methylated DNA immunoprecipitation (MeDIP) approaches combined with either […]

Ligation Mediated RNA-RNA Analysis

July 21, 2008

Last week, researchers from the Karolinska Institute and the University of London released data on an innovative approach for studying RNA-RNA interactions. Data supporting the multitude of RNA functions in our cells continues to pour in, but challenges in analyzing the effecting complexes in cellular processes persist, so we tip our hats to this team […]

Webserver for Aligning Non-Coding RNA Structure-WAR

July 13, 2008

Finally a WAR with no conflict. We have to give a big electronic high five to the group from the University of Copenhagen who just introduced a very helpful web utility: WAR-Webserver for aligning structural RNAs is a very handy site that allows you to use the best algorithms for aligning and predicting the consensus […]

ChIPs and MeDIP: ChIP Antibody Selection Tips

July 9, 2008

Chromatin immunoprecipitation (ChIP) remains a powerful method to characterize in vivo binding of DNA hugging proteins like histones and transcription factors and more recently has been used effectively for DNA methylation studies. The ChIP technique has been around since the days of big hair and “Miami Vice,” so we won’t review it here much, but […]

PatMAn and the Magnificent Seven Methylation Classifiers

June 16, 2008

It seems pattern recognition and supervised learning techniques are being applied to epigenetics research a lot nowadays. These advanced computational techniques that have proven useful in everything from homeland security to financial modeling are lending a hand to some of the challenges in epigenetics research. Recently we’ve seen them applied to miRNA discovery and target […]

ChIP Tips

June 1, 2008

There’s a reason chromosome immunoprecipitation (ChIP) continues to be used in labs all over the world. It works well. In fact, there aren’t too many ways to map minute-by-minute changes at a single promoter, or alternatively, follow a single transcription factor over the entire human genome. ChIP is very versatile and can yield significant insights […]

Pursuit of the Moving miRNA Target

April 11, 2008

Since 3’ UTRs were found to contain docking sites for miRNAs, labs with computational muscle around the world have been chipping away the target predication dilemma, but like any game, it’s hard to win when you don’t know the rules. It’s even harder when the rules are being rewritten weekly which is why we have […]

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