Prions Take Epigenetics to the ExtremeOctober 28, 2010Yeah, we know that somewhere between the X-games and base-jumping light beer ads, the term “Extreme” got a little played out. But, in their Perspective piece in Science, Randal Halfmann and Susan Lindquist make the case that certain proteins with unique folding properties, called prions, deserve the “extreme” label. Prions are proteins that are stably […]
Pardon the Epigenetic DisruptionOctober 28, 2010One of the great things about stem cells is how they seem to do just about anything. These days, stem cells have more Apps than an iPad, and in the new issue of Science we find one more: using stem cells to screen for “epigenetic disruptors”. The proposed idea is to use the built-in developmental […]
Take a Look: NCBI Epigenomics Sample BrowserOctober 26, 2010Our friends at the NCBI clued us in to one of their newest free tools that should prove to be a big help to anyone wanting to sort through next-gen sequencing data from epigenomic studies. NCBI’s new Sample Browser, located on its Epigenomics page, lets users search, access and analyze sequencing data from various publicly […]
Chromatin Remodelers In Search of Mr. RightOctober 26, 2010For the first time, the molecular machines known as “chromatin remodelers” have been found to spend much of their time rapidly searching for their nucleosome soulmates. And, just like desperate singles at a Speed Dating party, they keep at it until they find the right one. Chromatin remodelers help organize the genome, control DNA accessibility, […]
The miRNA Trade Deficit in CancerOctober 25, 2010Balancing imports and exports can be a tough task for any entity. It turns out cancer cells have a major issues when it comes to exporting pre-miRNA between the nucleus and cytoplasm that can have a pretty nasty impact on cellular homeostasis. miRNA expression profiles in tumors typically show a down regulation of miRNA expression. […]
Comparative Epigenomics Branches OutOctober 19, 2010When you’re comparing epigenomes, it’s easy to miss the forest for the trees. Because the epigenetic “fruit” on each nucleotide can vary with factors like cell type, differentiation state, and the environment, it’s often tricky to spot patterns on the epigenome-wide scale. In a recent Nature Biotechnology commentary, Aleksandar Milosavlijevic of the NIH Epigenomics Roadmap […]
How to Tame the MethylomeOctober 18, 2010So many ways to analyze genomic DNA methylation, so little time (and money). With so many choices available these days it’s not easy to figure out the best method to use for methylome studies. A new survey of two Nature Biotechnology papers by Stephan Beck from the UK’s University College London puts together the vital […]
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 […]