miRNA Sponges Making a Big SplashOctober 15, 2010A few years back synthetic miRNA decoys, nicknamed “miRNA sponges”, were developed as an innovative new way to inhibit miRNA activity by bumping up the number of miRNA targets to “soak up” a specific miRNA. Now recent reports are popping up showing evidence that naturally occurring miRNA sponges have been around all along, we just […]
miRNAs Host New Variety ShowOctober 5, 2010If variety is the spice of life, then miRNAs are a bowl of 3-alarm Texas chili. A new study in the journal RNA used NextGen sequencing techniques to reveal that miRNAs show quite a bit of sequence variety, even within individual miRNA species. The research, conducted by Lik Wee Lee and colleagues at the Institute […]
Who Says Dnmt1 is Only a Maintenance Methyltransferase?October 5, 2010While investigating the in vitro activity of DNA methyltransferases on annealed oligonucleotide substrates, Australian researchers recently found that murine DNA methyltransferase I will quite happily methylate non-CpG sites in DNA bubbles. Jason Ross and Peter Molloy from the CSIRO, in collaboration with Japanese researchers from the Institute for Protein Research in Osaka, observed a high […]
Do Transcription Factors Occupy All their Binding Motifs in the Genome? Not quite.October 4, 2010A British team of researchers recently decided to take closer look at the role of DNA methylation in conserved consensus motifs. Dr. Roger Foo from the Department of Medicine, University of Cambridge was nice enough to share a bit about their approach that recently published in BMC Genomics (Sept 2010) last week. Transcription factors recognise […]
O-allylhydroxylamine Threatens Bisulfite’s Gold Standard StatusSeptember 23, 2010Let’s get ready to rumble! A new reagent, O-allylhydroxylamine, has entered the ring to challenge bisulfite conversion as the undisputed champion of DNA methylation analysis. In the latest issue of Nucleic Acids Research, chemists from Ludwig-Maximillians University in Germany introduced a new chemical reagent that could be a game-changer for distinguishing between cytosine (C) and […]
Heterogeneous DNA Methylation and Biomarkers: It’s ComplicatedSeptember 23, 2010The state of the economy, global climate change, DNA methylation…These are all complicated issues. Well, we found one well-written review article by Thomas Mikeska, Ida Candiloro, and Alexander Dobrovic at the Peter MacCallum Cancer Centre and the University of Melbourne in Australia that tries to put one of those topics, DNA methylation in perspective, at […]
miRNAs Go with the FlowSeptember 23, 2010Many of us dread the inevitable needle prick at the doctor’s office to draw blood, not to mention even more invasive diagnostic tests (colonoscopy, anyone?). Wouldn’t it be easier if we could just spit or pee in a cup, and from the spectrum of miRNAs in the fluid, our doctor could tell us whether or […]
DNA Methylation Holds Steady in Body Mass IndexSeptember 17, 2010Mules are well known for being stubborn creatures, but they aren’t alone. It seems that resistance to change is something they may have in common with body weight and certain stretches of your epigenome. Andrew Feinberg and M. Daniele Fallin at Johns Hopkins University led several teams in a study that shows, for the first […]
Grabbing Histones By The TailSeptember 15, 2010For those old-school scientists who are still using erector sets and Lincoln logs to model the interactions between histone tails and proteins, we’ve found a new interactive tool that’ll bring your histone analysis into the 21st century. A team from the Structural Genomics Consortium (a collaboration between the University of Oxford and the University of […]
In the Dark Lanes of the Library, Beware of miRNA Sequencing BiasSeptember 9, 2010Advanced sequencing techniques have enabled the characterization and discovery of miRNAs to explode like an Icelandic volcano. But no matter how fancy your sequencing box is, the quality of your data still relies on the strength of your miRNA library preparation protocol. A group of curious scientists from the Beijing Genomics Institute and the Chinese […]