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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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HistoneHits: A Must Have Compilation of Histone Mods for the Chromatin Researcher Who Has Everything

February 19, 2009

We often wonder what is in the top chromatin researchers iPod playlists. What gets them through those late night, seemingly countless ChIP assays. Although we hope Vanilla Ice’s “Ice Ice Baby,” or Young MC’s “Bust a Move,” are represented, we know each of us has our own Greatest Hits. Recently, a team at Johns Hopkins […]

Fixing Small RNA Detection in FFPE Samples

February 2, 2009

In situ hybridization (ISH) is great to tell how much miRNA is expressed where. But it’s not so easy to get a signal from low-abundance miRNAs in formalin-fixed tissue. Formaldehyde cross-links RNA to proteins, diminishing the ability of probes to recognize and bind to the RNA, and can modify some of the bases as well. […]

Sifting Through the Rubble: miRNA “Degradome” Sequencing for miRNA Targets

January 26, 2009

The miRNA target prediction field has developed rapidly over the last few years. New entrants like miRanda, PicTar, DIANA, and RNA22 have acted as oracles to the target seeking research community, but have often left scientists with more questions than answers, so experimental validation is still required. Taking advantage of the fact that Arognaute-mediated mRNA […]

LCM to Data: Navigating the Small Sample Obstacle Course in DNA Methylation Profiling

January 25, 2009

Tissue heterogeneity has pestered researchers desiring a closer look at tissue-specific genomics and epigenomics. Sure, laser capture microdissection (LCM) platforms have been really helpful in isolating very small and specific regions of tissue, but that’s only half the battle. Working with minute amounts of LCM samples, particularly when they’re derived from the battered formalin-fixed paraffin-embedded […]

Summitting With PeakSeq.It’s About Mappability

January 10, 2009

ChIP-seq continues to assault bioinformatics teams with avalanches of data, but the upside of using this powerful approach brings some challenges along with it. Modeling background accurately requires a few tweaks, so before you get all excited about the double black diamond peaks that you’re seeing in regulatory motifs, you might want to factor in […]

Bisulfite Sequencing the “Other” Nucleic Acid: Methylated RNA

December 16, 2008

What’s good for the goose is good for the gander, so why shouldn’t bisulfite sequencing be used to study RNA cytosine methylation? Until recently, the harsh reaction conditions required for bisulfite deamination were considered detrimental to RNA stability. However, Matthias Schaefer and colleagues developed an RNA bisulfite sequencing procedure that reproducibly and quantitatively detected cytosine […]

New Method HITS RNA-Protein Interaction Sites

November 5, 2008

DNA, it has turned out, isn’t all it was wound up to be. In recent years we learned that the molecule of life, the discovery of the 20th century, did not-could not-by itself explain the huge differences in complexity between a human and a worm. Forced to look elsewhere, scientists turned to RNA; however, methodological […]

Two Studies Reveal Proteome-Wide Effects of miRNAs

October 24, 2008

Proving that great minds think alike, two independent research groups have used similar methods to examine the impact of individual miRNAs on the proteome. In a Nature report by Steven Gygi, David Bartel, and co-workers at Harvard Medical School, the Whitehead Institute for Biomedical Research, and the Massachusetts Institute of Technology, researchers used a quantitative […]

Susan Clark: Leading Ladies in Epigenetics Research

October 8, 2008

A native of Australia, Susan J. Clark obtained her PhD in 1982 from the University of Adelaide. For the next 8 years, Dr. Clark worked in the biotech industry before returning to basic research where she was instrumental in developing the bisulphite sequencing method for DNA methylation analysis in the early 90s. Dr. Clark is […]

DNA Methylation Detection Goes Small Time

September 28, 2008

A sensitive new nanotechnology assay might represent a “quantum leap” in DNA methylation detection. The technique, which was developed by Vasudev Bailey and co-workers at The Johns Hopkins University School of Medicine, uses quantum dots-fluorescent nanocrystals of a semiconductor material-to selectivel detect and quantify minute amounts of methylated DNA. As in methylation-specific PCR (MSP), sample […]

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