title: A new parameter to study compositional properties of non-coding regions in eukaryotic genomes.
abstract: Genomes are characterized by global and local compositional properties that are interesting in an evolutionary perspective but also provide useful information for the identification of some functional elements. Following previous studies, in this work we investigated compositional properties of non-coding sequences in four eukaryotic genomes (C. elegans, D. melanogaster, M. musculus, H. sapiens). We developed a procedure based on Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) to identify pentamers that are over-represented in introns (intron vocabulary) and to define a new parameter (LD) that reflects oligonucleotide composition of a given sequence. We analyzed genomic sequences and we found that all non-coding parts of a genome are characterized by similar LD values. Furthermore, we used the new parameter to analyze potentially regulatory regions. We extracted non-redundant sets of promoter sequences for D. melanogaster and H. sapiens and we studied their compositional (G+C content and LD parameter) and conformational (bendability propensity) properties. We found that regions immediately surrounding transcription start sites are distinguishable because of their %G+C, LD and bendability values.
authors.affiliation: Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Bultrini
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Pizzi
mesh_terms: D000818:Animals; D001482:Base Composition; D017173:Caenorhabditis elegans / Q000235:genetics; D016002:Discriminant Analysis; D004331:Drosophila melanogaster / Q000235:genetics; D005091:Exons; D006801:Humans; D007438:Introns; D016014:Linear Models; D051379:Mice; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D025341:Principal Component Analysis; D011401:Promoter Regions, Genetic; D022661:RNA, Untranslated / Q000737:chemistry* / Q000235:genetics*; D013045:Species Specificity
chemical_list: D022661:RNA, Untranslated