SYSTEMATIC GENOMIC SCREENING AND ANALYSIS OF MESSENGER-RNA IN UNTRANSLATED REGIONS AND MESSENGER-RNA PRECURSORS - COMBINING EXPERIMENTAL AND COMPUTATIONAL APPROACHES

Motivation: The untranslated regions (UTRs) of mRNA upstream (5'UTR) a nd downstream (3'UTR) of the open reading frame, as well as the mRNA p recursor, carry important regulatory sequences. To reveal unidentified regulatory signals, we combine information,from experiments with comp utational approaches. Depending on available knowledge, three differen t strategies are employed. Results: Searching with a consensus templat e, new RNAs with regulatory RNA elements can be identified in genomic screens. By this approach, we identify new candidate regulatory motifs resembling ii-on-responsive elements in the 5'UTRs of HemA, FepB and Fr-dB mRNA from Escherichia coli. If an RNA element is nor yet defined , it may be analyzed by combining results fi-om SELEX (selective enric hment of ligands by exponential amplification) and a search of databas es from RNA ol genomic sequences. A cleavage stimulating factor (CstF) binding element 3 of the polyadenylation site in the mRNA precursor s erves as a test example. Alternatively, the regulatory RNA element may be found by studying different RNA foldings and their correlation wit h simple experimental tests. We delineate a novel instability element in the 3'UTR of the estrogen receptor mRNA in this way.