%0 Journal Article
%T Sequence periodicity of Escherichia coli is concentrated in intergenic regions
%A Sergey Hosid
%A Edward N Trifonov
%A Alexander Bolshoy
%J BMC Molecular Biology
%D 2004
%I BioMed Central
%R 10.1186/1471-2199-5-14
%X Here we demonstrate that practically only ApA/TpT dinucleotides contribute to overall dinucleotide periodicity in Escherichia coli. The noncoding sequences reveal this periodicity much more prominently compared to protein-coding sequences. The sequence periodicity of ApC/GpT, ApT and GpC dinucleotides along the Escherichia coli K-12 is found to be located as well mainly within the intergenic regions.The observed concentration of the dinucleotide sequence periodicity in the intergenic regions of E. coli suggests that the periodicity is a typical property of prokaryotic intergenic regions. We suppose that this preferential distribution of dinucleotide periodicity serves many biological functions; first of all, the regulation of transcription.DNA sequence periodicity with the period about 10¨C11 base pairs (bp) has been long known in eukaryotic DNA sequences. It was discovered recently in prokaryotic sequences as well [1-6]. The periodicity in Eubacteria sequences usually shows the period close to 11 bp [1]. This period is clearly different from the structural helical period of 10.5¨C10.6 bp/turn [7,8]. The difference was interpreted [1,2] as a possible reflection of the sequence dependent writhe of prokaryotic DNA. In the work [9] it was demonstrated that the periodicity in the bacterial genomes, in E. coli as well, is distributed in a non-uniform way, in scattered segments of the size 100¨C150 bases. It was also known for a long time that quite a few DNA promoter regions of E. coli possess the sequence periodicity of AA and TT dinucleotides [10].The sequence periodicity of AA/TT dinucleotides is frequently associated with sequence-dependent DNA curvature, which is known to play an important role in the initiation of transcription of many genes (for reviews, see [11-15]). Using different models and approaches for prediction of intrinsic DNA curvature it was shown that many E. coli promoters have upstream curved sequences [16,17]. Pedersen et al. [18] showed that promoter
%U http://www.biomedcentral.com/1471-2199/5/14