So you have performed some differential gene expression experiments and have discovered a (few) non-coding RNAs that are of conspicuous interest… What now? Unless you are lucky and someone else has already characterised your needle in a haystack, odds are little is known about this transcript. You might be tempted to paste that .fasta file into mfold and say: “Look! It folds into an RNA secondary structure!” yet this won’t tell you much, besides that your RNA might look like a Christmas tree in February. This video explains how you can find out which regions of your RNA transcript of interest might be responsible for its biological function.
Tag Archives: RNA structure
Last year, the massive ENCODE consortium disclosed that over 80% of the human genome appears to be functional through several detailed biochemical experiments. Their findings fuelled an already heated debate regarding the biological pertinence of similar findings. Many old-school biochemists and proponents of the “selfish” DNA hypothesis (who I collectively refer to as junk DNAy-sayers) dismiss the use of such data to support the notion that the majority of the genome is functional.
Amidst the nit-picking, bickering, and refutations, one logical argument stands out that somewhat confounds the ENCODE findings: the lack of detectable evolutionary conservation. Indeed, the statement that > 80% of the human genome sequence is biologically functional lies in stark contrast to the fact that < 9% of it is observed to be conserved throughout mammalian evolution. But is this estimate really accurate? Continue reading