title: Using RNA inverse folding to identify IRES-like structural subdomains.
abstract: Internal ribosome entry site (IRES) elements govern protein synthesis of mRNAs that bypass cap-dependent translation inhibition under stress conditions. Picornavirus IRES are cis-acting elements, organized in modular domains that recruit the ribosome to internal mRNA sites. The aim of this study was to retrieve short RNA sequences with the capacity to adopt RNA folding patterns conserved with IRES structural subdomains, likely corresponding to RNA modules. We have applied a new program, RNAiFold, an inverse folding algorithm that determines all sequences whose minimum free energy structure is identical to that of the structural domains of interest. Sequences differing by more than 1 nt were clustered. Then, BLASTing one randomly chosen sequence from each cluster of the RNAiFold output, we retrieved viral and cellular sequences among output hits. As a proof of principle, we present the data corresponding to a coding region of Drosophila melanogaster TAF6, a transcription factor-associated protein that contains a structural motif within its coding region potentially folding into an IRES-like subdomain. This RNA region shows a biased codon usage, as predicted from structural constraints at the RNA level, it harbors conserved IRES structural motifs in loops, and interestingly, it has the capacity to confer internal initiation of translation in tissue culture cells.
authors.affiliation: Biology Department; Boston College; Chestnut Hill, MA USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
authors.affiliation: Centro de Biologia Molecular Severo Ochoa; Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid; Madrid, Spain.
authors.forename: Gloria
authors.initials: G
authors.lastname: Lozano
authors.affiliation: Biology Department; Boston College; Chestnut Hill, MA USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
authors.affiliation: Centro de Biologia Molecular Severo Ochoa; Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid; Madrid, Spain.
authors.forename: Encarnacion
authors.initials: E
authors.lastname: Martinez-Salas
mesh_terms: D000465:Algorithms; D000818:Animals; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010849:Picornaviridae / Q000235:genetics; D059370:RNA Folding; D012333:RNA, Messenger / Q000378:metabolism*; D038621:Regulatory Sequences, Ribonucleic Acid; D015203:Reproducibility of Results; D012270:Ribosomes / Q000378:metabolism*; D035381:TATA-Binding Protein Associated Factors / Q000235:genetics; D035362:Transcription Factor TFIID / Q000235:genetics
chemical_list: D029721:Drosophila Proteins; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; D035381:TATA-Binding Protein Associated Factors; C084976:Taf6 protein, Drosophila; D035362:Transcription Factor TFIID
keywords: IRES elements; RNA structural domains; SHAPE analysis; inverse folding; translation control