Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis.
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.
Fukushima
Atsushi
A
Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.
Ikemura
Toshimichi
T
Kinouchi
Makoto
M
Oshima
Taku
T
Kudo
Yoshihiro
Y
Mori
Hirotada
H
Kanaya
Shigehiko
S
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*
D004247:DNA