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 […]
Developing Technologies for Improved In Vivo Epigenetic Imaging/AnalysisDecember 15, 2009The NIH is opening up its wallet again for epigenetic technology development. $3.5M will be allocated in 2010 for developing in vivo epigenetic imaging and analysis technologies. According to the grant description, the NIH has recognized that “… the technologies available to determine the epigenetic state of tissues in vivo are extremely limited. The specific […]
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, […]
Pre-miRNA Importin and Exportin Strong As EverDecember 2, 2009In today’s global economy, imports and exports can ebb and flow dramatically depending on economic conditions. But in the fine-tuned cellular economy, where supply-demand runs the show, miRNA Importin and Exportin operate with consistency that would have most economists envious. When pre-miRNAs are shipped from the nucleus to the cytoplasm. Exportin-5 escorts the ~65 nt […]
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 […]
Got miR-2861? Novel miRNA Is Linked to OsteoporosisNovember 18, 2009What can you do to keep your bones healthy and strong? In addition to sporting the ever-trendy milk mustache, you might want to avoid mutations in miR-2861, a newly discovered miRNA involved in osteoblast differentiation. A team of Chinese researchers identified miR-2861 by cloning miRNAs from primary mouse osteoblasts (the cells responsible for bone formation). […]
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 […]
MBD-Sequencing: The Latest Methylation Analysis Cocktail DeliversNovember 17, 2009Add 1 part enriched methylated DNA to 2 parts sequencing lanes, and you have a cocktail that delivers key insights without a data hangover. Last week, a team of Ohio scientists added the latest research recipe that is destined to become a lab fav in Nucleic Acids Research. The crew took the benefits of methylation […]