Erring on the Side of Calling: Sequencing Mismatches Highlight RNA EditingJuly 1, 2009To err is enzymatic; to identify errors previously thought to be technical, but are actually biologically relevant, is divine. Most researchers view the sequencing errors from reverse transcription, sequencing reaction, or base calling part of the job. After all, with the mountains of sequence pouring off these platforms, one would expect and accept a few […]
Don’t Go Away Mad (Just GOmir)July 1, 2009Figuring out the targets of your favorite miRNA is no simple matter, and if it ranks somewhere between cleaning the bathroom and a trip to the dentist on your list, then you’ll want to check out a new java-based tool called GOmir which makes the miRNA target analysis experience a little less painful. A group […]
Lincd In: Large Intervening Non-Coding RNAs Expand their NetworksJune 25, 2009Last February, a team of standouts from the publication factory in Boston (aka Broad Institute), published work highlighting over 1,500 previously un-annotated genomic sequences that housed large intervening non-coding RNAs known as lincRNAs. These transcripts showed similar expression patterns as mRNA and they exhibited more conservation than neutral sequences, indicating they were probably functional, but […]
tasiRNAs Get the Word OutJune 24, 2009Spreading gossip around the water cooler is OK, but some news just has to be shouted from the mountaintops. These days, that means it’ll be posted to our blog, Twitter feed, and Facebook status box. Researchers at the Cold Spring Harbor Laboratory, Institut des Sciences du Végétal, and Institut de Biologie Moléculaire des Plantes report […]
Zeroing in on miRNA Targets with HITS-CLIPJune 24, 2009With only a modest, 6-8 nucleotide seed region required for pairing, miRNAs theoretically aren’t too fussy when it comes to which mRNAs they pair up with. But don’t let this apparent “beer goggle” regulation fool you. When it comes down to miRNA binding in vivo, miRNAs might be a little more discriminating than previously suggested. […]
miRNA qRT-PCR Data Normalization Gets MeanJune 23, 2009Although qRT-PCR has become a popular way to profile miRNAs, it has a dirty little secret that nobody likes to talk much about; data normalization. Without convenient “housekeeping genes” to use as internal references, like you would with mRNAs, researchers have had to settle for second rate options to normalize data from miRNA experiments. A […]
If You Can’t Be With the One You Target, Target the One You’re WithJune 11, 2009It’s not news that miRNAs are out of whack in cancers. So it shouldn’t be surprising that re-expressing an oncogene-targeting miRNA might halt tumor progression. But what if the miR didn’t even have to target a specific oncogene to show off its anti-proliferative mojo? Son and father research duo (we’re pretty sure they dominated the […]
Methylation and HDAC Inhibitors Rouse Cancer-Fighting miRNAs into ActionJune 11, 2009Recent advances in epigenetic therapy are promising, but their mechanisms of action and impact elsewhere in the epigenome remain a bit of a mystery. Armed with microarrays and ChIP assays, a talented team of Japanese researchers took a closer look at these approaches and found DNA methylation inhibitors and histone deacetylase (HDAC) inhibitors kill gastric […]
miRNA-Mediated Viral Attenuation Gives Vaccines a BoostJune 7, 2009With all the recent talk of swine flu and pandemics, you might be wondering how the development of new flu vaccines is coming along. In an example of impeccable timing, researchers at the Mount Sinai School of Medicine now report that they’ve attenuated, two strains of the influenza A virus, the culprit behind swine, avian, […]
miRNA Discovery: Algorithms, Sequencing and Life Outside miRBaseMay 12, 2009Back in the early days, they were these interesting “genes” with names like “lin” and “let” that appeared highly involved in developmental timing, so much so that they were called small temporal RNAs (stRNAs). A lot more has changed in the field of miRNA discovery than naming mechanisms since those early days when the first […]
