Bioinformatics, Vol 14, 271-278, Copyright © 1998 by Oxford University Press
T Dandekar, K Beyer, P Bork, MR Kenealy, K Pantopoulos, M Hentze, V Sonntag- Buck, G Flouriot, F Gannon and S Schreiber
MOTIVATION: The untranslated regions (UTRs) of mRNA upstream (5'UTR) and
downstream (3'UTR) of the open reading frame, as well as the mRNA
precursor, carry important regulatory sequences. To reveal unidentified
regulatory signals, we combine information from experiments with
computational approaches. Depending on available knowledge, three different
strategies are employed. RESULTS: Searching with a consensus template, new
RNAs with regulatory RNA elements can be identified in genomic screens. By
this approach, we identify new candidate regulatory motifs resembling
iron-responsive elements in the 5'UTRs of HemA, FepB and FrdB mRNA from
Escherichia coli. If an RNA element is not yet defined, it may be analyzed
by combining results from SELEX (selective enrichment of ligands by
exponential amplification) and a search of databases from RNA or genomic
sequences. A cleavage stimulating factor (CstF) binding element 3 of the
polyadenylation site in the mRNA precursor serves as a test example.
Alternatively, the regulatory RNA element may be found by studying
different RNA foldings and their correlation with simple experimental
tests. We delineate a novel instability element in the 3'UTR of the
estrogen receptor mRNA in this way. AVAILABILITY: Strategy, methods and
programs are available on request from T.Dandekar. CONTACT:
dandekar@embl-heidelberg.de
ARTICLES
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
European Molecular Biology Laboratory, Postfach 102209, D-69012 Heidelberg, Germany. dandekar@embl-heidelberg.de
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