Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA

Biopolymers
H Lowman, M Bina

Abstract

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)...Continue Reading

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Citations

Aug 22, 2001·Biopolymers·M Bina, E Crowely
Dec 25, 1992·Nucleic Acids Research·J D Lauderdale, A Stein
Jun 10, 2010·PloS One·Clayton K CollingsJohn N Anderson
Aug 14, 2012·Advances in Biological Regulation·Dilshad H KhanJames R Davie
Feb 22, 2012·Trends in Plant Science·Robert J Schmitz, Joseph R Ecker
Feb 11, 2018·Genome Biology·Răzvan V CherejiSteven Henikoff
Jan 22, 2020·Molecular Biology and Evolution·Jullien M FlynnAndrew G Clark
Apr 10, 2018·Biophysical Journal·Răzvan V Chereji, David J Clark
Apr 9, 2010·The Journal of Physical Chemistry. B·Arvind Marathe, Manju Bansal
Apr 11, 1997·Journal of Molecular Biology·H R WidlundM Kubista

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