title: Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis.
abstract: We used a power spectrum method to identify periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to prokaryotic and eukaryotic genomes and genomes. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in eubacteria. The 10-bp periodicity was also prevalent in the eukaryotes such as the worm Caenorhabditis elegans. Additionally, in the worm genome, a 68-bp periodicity in chromosome I, a 59-bp periodicity in chromosome II, and a 94-bp periodicity in chromosome III were found. In human chromosomes 21 and 22, approximately 167- or 84-bp periodicity was detected along the entire length of these chromosomes. Because the 167-bp is identical to the length of DNA that forms two complete helical turns in nucleosome organization, we speculated that the respective sequences may correspond to arrays of a special compact form of nucleosomes clustered in specific regions of the human chromosomes. This periodic element contained a high frequency of TGG. TGG-rich sequences are known to form a specific subset of folded DNA structures, and therefore, the sequences might have potential to form specific higher order structures related to the clustered occurrence of a specific form of the speculated nucleosomes.
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Fukushima
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
authors.forename: Makoto
authors.initials: M
authors.lastname: Kinouchi
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kudo
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001482:Base Composition; D017173:Caenorhabditis elegans / Q000235:genetics; D002875:Chromosomes / Q000235:genetics; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005057:Eukaryotic Cells / Q000378:metabolism*; D016678:Genome; D006801:Humans; D011387:Prokaryotic Cells / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA