title: Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.
abstract: In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3'UTR, a region affecting mRNA translation, localization and stability. (TA)n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TA)n repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3'-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in genomes and a strategy for its characterization inside human fragile sites.
authors: Dip. Informatica, Università di Pisa, Largo Pontecorvo, Pisa, Italy; Istituto Nazionale di Alta Matematica "Francesco Severi", Piazzale Aldo Moro, Città Universitaria, Roma, Italy.
authors: Giulia
authors: G
authors: Menconi
authors: Dept. Mathematics and Statistics, The University of Melbourne Victoria, Australia.
authors: Andrea
authors: A
authors: Bedini
authors: Dip. Biologia, Università di Pisa, Via Derna, Pisa, Italy.
authors: Roberto
authors: R
authors: Barale
authors: Dip. Biologia, Università di Pisa, Via Derna, Pisa, Italy.
authors: Isabella
authors: I
authors: Sbrana
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics* / Q000648:ultrastructure*; D016681:Genome, Fungal / Q000235:genetics*; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004271:DNA, Fungal