title: Sequence-dependent DNA helical rise and nucleosome stability.
abstract: BACKGROUND
  Nucleosomes are the basic structural units of eukaryotic chromatin and play a key role in regulation of gene expression. After resolution of the nucleosome structure, the bipartite nature of this particle has revealed itself and has disclosed the presence, on the histone surface, of a symmetric distribution of positive charges, able to interact with their negative DNA phosphate counterpart.
  
  
  RESULTS
  We analyzed helical steps in known nucleosomal DNA sequences, observing a significant relationship between their symmetric distribution and nucleosome stability. Synthetic DNA sequences able to form stable nucleosomes were used to compare distances on the left and on the right side of the nucleosomal dyad axis, where DNA phosphates and charged residues of the (H3H4)2-tetramer interact. We observed a linear relationship between coincidence of distances and nucleosome stability, i. e., the more symmetric these distances the more stable the nucleosome.
  
  
  CONCLUSIONS
  Curves related to this symmetric distribution along the DNA sequence identify preferential sites for positioning of the dyad axis, which we termed palinstases. The comparison of our data with known nucleosome positions in archaeal and eukaryotic sequences shows many coincidences of location. Sequences that impair nucleosome formation and DNase I hypersensitive sites yield curves with a lower degree of symmetry. Analysis performed on DNA tracts of promoters close to the transcription start and termination sites identified peculiar patterns: in particular low affinity for nucleosome binding at the transcription start site and a high affinity exactly at the transcription termination site, suggesting a major role of nucleosomes in the termination of transcription.
authors: Dept. of Genetics and Molecular Biology, Sapienza University, P.A. Moro 3, 00161 Rome, Italy. francesco.pedone@uniroma1.it
authors: Francesco
authors: F
authors: Pedone
authors: Daniele
authors: D
authors: Santoni
mesh_terms: D001105:Archaea / Q000235:genetics; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D056890:Eukaryota / Q000235:genetics; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*; D009711:Nucleotides / Q000737:chemistry; D011401:Promoter Regions, Genetic / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D009707:Nucleosomes; D009711:Nucleotides; D012335:RNA, Ribosomal; D004247:DNA