Sifting Through the Rubble: miRNA “Degradome” Sequencing for miRNA TargetsJanuary 26, 2009The 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 ProfilingJanuary 25, 2009Tissue 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 MappabilityJanuary 10, 2009ChIP-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 RNADecember 16, 2008What’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 SitesNovember 5, 2008DNA, 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 miRNAsOctober 24, 2008Proving 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 ResearchOctober 8, 2008A 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 TimeSeptember 28, 2008A 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 […]
Allele-Specific Modifications: A Tale of Two EpigenomesSeptember 24, 2008It 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 ResearchSeptember 8, 2008As 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. […]