title: Nucleosome DNA sequence structure of isochores.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  Extraction 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.
  
  
  CONCLUSIONS
  Nucleosome 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.
authors.affiliation: Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
authors.forename: Zakharia M
authors.initials: ZM
authors.lastname: Frenkel
authors.forename: Thomas
authors.initials: T
authors.lastname: Bettecken
authors.forename: Edward N
authors.initials: EN
authors.lastname: Trifonov
mesh_terms: D000818:Animals; D001482:Base Composition; D002645:Chickens; D006801:Humans; D032085:Isochores / Q000737:chemistry*; D051379:Mice; D009702:Nucleoside Diphosphate Sugars / Q000737:chemistry; D009707:Nucleosomes / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D016415:Sequence Alignment
chemical_list: D032085:Isochores; D009702:Nucleoside Diphosphate Sugars; D009707:Nucleosomes; D009841:Oligonucleotides