miRNA-29b at the Bedside?February 16, 2009Start stocking the miRNA-29b in your medicine cabinet. A group of researchers from The Ohio State University recently cranked out some great data demonstrating how miRNAs work to regulate DNA methylation in acute myeloid leukemia (AML), outlining a potential therapeutic use of mir-29b. The study reveals how miR-29b works by targeting DNA Methyltransferases (DNMTs), the […]
The miRNA Importin BizFebruary 10, 2009For all we know about miRNA – how it’s made, what it does, how it folds, … – comparatively little is known about how the Argonaute (Ago) proteins allow miRNA to do what it does. Yet thanks to a group out of Germany, we now understand a bit more of the machinery that lets miRNA […]
Chromatin Maps Conserved Missing linc-RNAFebruary 3, 2009 Researchers in Boston figured that maybe they could find something interesting in all the non-protein, non-miRNA, non-siRNA genes. They did…linc-RNAs. Through a massive sequencing of ChIP data they uncovered a chromatin “signature” for actively transcribed regions between known protein coding genes, and used this signature to identify about 1700 previously un-annotated stretches of the genome at […]
Fixing Small RNA Detection in FFPE SamplesFebruary 2, 2009In situ hybridization (ISH) is great to tell how much miRNA is expressed where. But it’s not so easy to get a signal from low-abundance miRNAs in formalin-fixed tissue. Formaldehyde cross-links RNA to proteins, diminishing the ability of probes to recognize and bind to the RNA, and can modify some of the bases as well. […]
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 […]
CAGEd miRNAs: Taming Transcriptional InitiationJanuary 18, 2009Most primary miRNA transcripts remain a mystery because they’re generally degraded by the time they leave the comfort of the nucleus. Where do the transcripts start? Do they have a single “peak” of initiation, or are there a variety of sites where they’re likely to begin? Limitations in the currently available molecular biology tool set […]
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 […]
To Code or Not to Code…Is that the Question?December 10, 2008In the past few years, ncRNAs have progressed from interesting anomalies to what some researchers think constitute the majority of the mammalian transcriptome. However, as reviewed by John Mattick and coworkers at the University of Queensland and the Ludwig Institute for Cancer Research (both in Australia), it’s increasingly difficult to distinguish coding from noncoding RNAs […]
Let It SnoDecember 2, 2008It’s December, the time of year when much of the States is blanketed in a frosty mantle of the white stuff. But as recently reported in Molecular Cell, the ACA45 RNA appears to have pulled the ultimate snow job. Nikolaus Rajewsky, Gunter Meister, and colleagues revealed that ACA45, which was previously thought to function exclusively […]
miRNA Fights Cancer-Promoting Histone MethyltransferaseNovember 23, 2008What makes some tumors as gentle as purring kittens and others of the same cancer type as ferocious as saber-toothed tigers? A miRNA (miR-101) was recently shown to take a bite out of cancer by inhibiting the EZH2 histone methyltransferase. The study by Arul Chinnaiyan and co-workers at the University of Michigan Medical School, the […]