Open AccessNucleosome packaging and nucleosome positioning of genomic DNA
Author(s) -
Peggy T. Lowary,
Jonathan Widom
Publication year - 1997
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.94.4.1183
Subject(s) - nucleosome , histone octamer , histone , dna , linker dna , chromatosome , genomic dna , genetics , biology , dna sequencing , histone methylation , biophysics , computational biology , gene , microbiology and biotechnology , dna methylation , gene expression
The goals of this study were to assess the extent to which bulk genomic DNA sequences contribute to their own packaging in nucleosomes and to reveal the relationship between nucleosome packaging and positioning. Using a competitive nucleosome reconstitution assay, we found that at least 95% of bulk DNA sequences have an affinity for histone octamer in nucleosomes that is similar to that of randomly synthesized DNA; they contribute little to their own packaging at the level of individual nucleosomes. An equation was developed that relates the measured free energy to the fractional occupancy of specific nucleosome positions. Evidently, the bulk of eukaryotic genomic DNA is also not evolved or constrained for significant sequence-directed nucleosome positioning at the level of individual nucleosomes. Implications for gene regulationin vivo are discussed.