CGC Bibliography Paper 5641

Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis.

Fukushima A, Ikemura T, Kinouchi M, Oshima T, Kudo Y, Mori H, Kanaya S

Medline:

12468102

Citation:

Gene 300: 203-211 2002

Type:

ARTICLE

Genes:

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. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in cubacteria. The 10-bp periodicity was also prevalent in the eukaryotes such as the worrn 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