Open AccessDNA rotational positioning in a regulatory nucleosome is determined by base sequence. An algorithm to model the preferred superhelix
Author(s) -
Benjamı́n Piña,
Mathias Truss,
Heiko H. Ohlenbusch,
J. P. M. Postma,
Miguel Beato
Publication year - 1990
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/18.23.6981
Subject(s) - nucleosome , superhelix , histone octamer , biology , histone , dna , sequence (biology) , base pair , computational biology , algorithm , genetics , biophysics , dna replication , dna supercoil , computer science
MMTV-LTR sequences -190/-45 position a histone octamer both in vivo and in vitro. Experimental evidence suggested that nucleosome rotational positioning is determined by the DNA sequence itself. We developed an algorithm that is able to predict the most favorable path of a given DNA sequence over a histone octamer, based on rotational preferences of different dinucleotides. Our analysis shows that these preferences are sufficient for explaining the observed rotational positioning of the MMTV-LTR nucleosome, at one base pair accuracy level. Computer-generated 3-D models of the experimentally calculated and predicted MMTV-LTR nucleosome show that the predicted orientation is fully compatible with the currently available data in terms of accessibility of relevant sequences to regulatory proteins.