title: Variation and constraints in species-specific promoter sequences.
abstract: A vast literature is nowadays devoted to the search of correlations between transcription related functions and the composition of sequences upstream the Transcription Start Site. Little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA in such regions. We have used suitable statistical indicators for identifying sequences that may play an important role in regulating transcription processes. In particular, we have analyzed base composition, periodicity and information content in sets of aligned promoters clustered according to functional information in order to obtain an insight on the main structural differences between promoters regulating genes with different functions. Our results show that when we select promoters according to some biological information, in a single species, at least in vertebrates, we observe structurally different classes of sequences. The highly variable and differentiated gene expression patterns may explain the great extent of structural differentiation observed in complex organisms. In fact, despite our analysis is focused on Homo sapiens, we provide also a comparison with other species, selected at different positions in the phylogenetic tree.
authors.affiliation: Center for the Study of Complex Dynamics (CSDC), University of Florence, Via G. Sansone 1, 50019 Sesto Fiorentino (Fi), Italy; Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Calistri
authors.affiliation: Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy.
authors.forename: Marcello
authors.initials: M
authors.lastname: Buiatti
authors.affiliation: Center for the Study of Complex Dynamics (CSDC), University of Florence, Via G. Sansone 1, 50019 Sesto Fiorentino (Fi), Italy; Department of Physics, University of Florence and INFN Florence, Via G. Sansone 1, 50019 Sesto Fiorentino (Fi), Italy. Electronic address: livi@fi.infn.it.
authors.forename: Roberto
authors.initials: R
authors.lastname: Livi
mesh_terms: D001482:Base Composition / Q000235:genetics*; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics*; D013045:Species Specificity
keywords: Base composition; CpG; Entropy; Gene regulation; Low-complexity sequence