State of Methylome Analysis: Genome-Wide Methylation Techniques ReviewFebruary 11, 2010The 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, 2010Figuring 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 ConversionJanuary 21, 2010Some 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 BSJanuary 13, 2010When 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 AnalysisJanuary 6, 2010Solving 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 ProbesDecember 8, 2009A 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 vivoDecember 3, 2009miR-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 SequencingDecember 1, 2009One 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. […]
Bulletproof Your Bisulfite Conversion: Key Considerations from the ExpertsDecember 1, 2009There’s a lot of talk out there about bisulfite conversion, how useful it is, how it’s the “Gold Standard,” how laborious it is, how rough it is on your samples, but the reality of it is that there probably isn’t any better way to prep your samples for single nucleotide resolution methylation profiling, so don’t […]
Sopping Up Regulatory Insights with miRNA SpongesNovember 17, 2009We’ve all seen those household cleaning commercials on the tele that show a super detergent that cuts through grease, whitens whites, and zaps pet odor effortlessly, so when we first got wind of miRNA sponges a few years back (Nature Methods, August 2007), we remember being interested but skeptical. But, if these vector-driven miRNA inhibitors […]