Overview

It is widely accepted that expression of most eukaryotic genes is controlled at both transcriptional and post-transcriptional stages. Experimental investigations have revealed a large amount of various signals located in eukaryotic mRNAs (commonly within 5'- or 3'-untranslated regions, UTRs). It has been found that these signals can control expression rate in a tissue-, stress- or developmental stage-specific manner. The analysis of translation signals is rather difficult, because the conformation of mRNA molecule in the cytoplasm may vary depending on the nucleotide sequence and/or the interaction with ubiquitous translational factors or with specific proteins. Elements of the secondary structure may be involved in formation of translational signals, or at least the local secondary structure may affect the signal activity. It is the reason why most posttranscriptional signals remain hidden within mRNA segments of various lengths possessing specific regulatory activities in model experiments. Published data commonly provide description of mRNA elements influencing gene expression pattern in different model constructions and expression systems. Despite this, information is generally insufficient for the accurate prediction of a signal; it can be beneficial to compare the nucleotide sequence of mRNA of interest with the mRNA sequence seqments possessing regulatory activities. We developed a database TRSIG (TRanslational SIGnals) compiling the published experimental data on mRNA segments influencing mRNA translation efficiency. Implementation of TRSIG is based on a BLAST search for the local similarity between the mRNA of interest and the TRSIG sequence collection to make testable assumptions on the translational control. Two criteria were used for the selection of data from the literature: (1) mRNA seqment should control translation of the reporter mRNA in a specific manner; (2) mRNA segment should be relatively small (preferably less than 200 nucleotides) to increase BLAST search accuracy.