Abstract
BackgroundSignificant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well.ResultsExtraction of the patterns from the isochore DNA sequences by Shannon N-gram extension reveals that while the general motif YRRRRRYYYYYR is characteristic for all isochore types, the dominant positioning patterns of the isochores vary between TAAAAATTTTTA and CGGGGGCCCCCG due to the large differences in G+C composition. This is observed in human, mouse and chicken isochores, demonstrating that the variations of the positioning patterns are largely G+C dependent rather than species-specific. The species-specificity of nucleosome positioning patterns is revealed by dinucleotide periodicity analyses in isochore sequences. While human sequences are showing CG periodicity, chicken isochores display AG (CT) periodicity. Mouse isochores show very weak CG periodicity only.ConclusionsNucleosome positioning pattern as revealed by Shannon N-gram extension is strongly dependent on G+C content and different in different isochores. Species-specificity of the pattern is subtle. It is reflected in the choice of preferentially periodical dinucleotides.
Highlights
Significant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well
One possible way to tackle this problem is to analyze the oligonucleotide composition of DNA sequences, which may reflect to some degree the hidden positioning patterns
The occurrence of CG dinucleotides is higher in G+C rich isochores, which is not surprising
Summary
Significant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well. The nucleosome positioning signal in human genome sequences is rather weak. It lacks the periodical AA and TT dinucleotides, the main component of the nucleosome positioning pattern in most of other genomes [1,2]. The mouse genome is featureless in terms of dinucleotide periodicities [2]. This lack of periodicities, diagnostic of the presence of a nucleosome positioning signal, makes the extraction of a nucleosome signal from such “silent” genomes problematic. One possible way to tackle this problem is to analyze the oligonucleotide composition of DNA sequences, which may reflect to some degree the hidden positioning patterns. Recent Shannon N-gram extension analysis [3] of eukaryotic genomes [4] revealed that the majority of the genomes are characterized by the same hidden sequence motif GRAAATTTYC which, according
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