Premium
Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA
Author(s) -
Lowman Henry,
Bina Minou
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360300902
Subject(s) - nucleosome , histone , dna , satellite dna , linker dna , satellite , base pair , biophysics , chemistry , genetics , biology , chromosome , physics , gene , astronomy
Previous studies demonstrated 16 well‐defined nucleosome locations (A–P) on a tandemly repeated prototype 234 base pair (bp) mouse satellite repeat unit. We have aligned the A–P fragments to search for DNA sequence elements that might contribute to nucleosome placement at these positions. Our results demonstrate a strikingly regular, uninterrupted, periodic pattern for the AA dinucleotide occurrences along the entire length of the aligned fragments. The periodicity of the AA occurrences is about 9.7 bp. The pattern exhibits a local minimum at position 74, near the nucleosome dyad axis of symmetry. Other dinucleotides—including AC : GT, CA : TG, and CC : GG—are also placed periodically, but their patterns of occurrence are less regular and less frequent than AA. The calculated spacings between consecutive preferred nucleosome locations on mouse satellite DNA are nearly identical, corresponding to multiples of 9.7 bp. The correlation between the periodicity of dinucleotide occurrences and the average spacing of nucleosome positions suggests that the preferred nucleosome locations recur at intervals that may correspond to the DNA helical repeat in the mouse satellite nucleosomes, and that the histone octamers sample (or slip along) the duplex in steps of 9.7 bp during nucleosome formation on mouse satellite DNA.