Nucleic Acids Research, Vol 27, Issue 3 848-853, Copyright © 1999 by Oxford University Press
A Stein and M Bina
Evidence is provided that the nucleotide triplet con-sensus non-T(A/T)G
(abbreviated to VWG) influences nucleosome positioning and nucleosome
alignment into regular arrays. This triplet consensus has been recently
found to exhibit a fairly strong 10 bp periodicity in human DNA,
implicating it in anisotropic DNA bendability. It is demonstrated that the
experimentally determined preferences for nucleosome positioning in native
SV40 chromatin can, to a large extent, be pre-dicted simply by counting the
occurrences of the period-10 VWG consensus. Nucleosomes tend to form in
regions of the SV40 genome that contain high counts of period-10 VWG and/or
avoid regions with low counts. In contrast, periodic occurrences of the
dinucleotides AA/TT, implicated in the rotational positioning of DNA in
nucleosomes, did not correlate with the preferred nucleosome locations in
SV40 chromatin. Periodic occurrences of AA did correlate with preferred
nucleosome locations in a region of SV40 DNA where VWG occurrences are low.
Regular oscillations in period-10 VWG counts with a dinucleosome period
were found in vertebrate DNA regions that aligned nucleosomes into regular
arrays in vitro in the presence of linker histone. Escherichia coli and
plasmid DNA, which fail to align nucleosomes in vitro, lacked these regular
VWG oscillations.
ARTICLES
A signal encoded in vertebrate DNA that influences nucleosome positioning and alignment
Department of Biological Sciences and Department of Chemistry, Purdue University, West Lafayette, IN 47907-1392, USA. astein@bilbo.bio.purdue.edu
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