BACKGROUND The 5' untranslated regions of mRNA play an important role in their translation. RESULTS Here, we describe the development of four methods of profiling mRNA 5' ends using the Illumina sequencing platform; the first method utilizes SMART (Switching Mechanism At 5' end of RNA Transcript) technology, while the second involves replacing the 5' cap structure with RNA oligomers via ligat...

Despite significant progress, the general functional and evolutionary significance of the untranslated regions (UTRs) of eukaryotic transcripts remain mysterious. Particularly mysterious is the common occurrence of spliceosomal introns in transcript UTRs because UTR splicing is not necessary for restoration of transcript coding sequence. In general, it is not known to what extent such splicing ...

Virus production in the deep-sea environment has been found to be high, and viruses have been suggested to play significant roles in the overall functioning of this ecosystem. Nevertheless, little is known about these viruses, including the mechanisms that control their production, which makes them one of the least understood biological entities on Earth. Previously, we isolated the filamentous...

The role of natural selection in biology is well appreciated. Recently, however, a critical role for physical principles of network self-organization in biological systems has been revealed. Here, we employ a systems level view of genome-scale sequence and expression data to examine the interplay between these two sources of order, natural selection and physical self-organization, in the evolut...

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through the binding of the 3' untranslated region (3'UTR) of specific mRNAs. MiRNAs are post-transcriptional regulators and determine the repression of translation processes or the degradation of mRNA targets. Recently, another kind of miRNA-mediated regulation of translation (repression or activation) involving the bind...