Analysis and development of the computer methods of nucleosome localization on DNA fragments with different AT-content.
Trinucleotide parameter sets published previously were used for the development of the predictive method for the determining the nucleosome positions along the DNA. The choice of the type of parameter sets used depends upon AT-content of the fragment. Some limitations are imposed on these predictions due to the presence of A(n), T(n) tracts (in our case n>5 or =5) within the 145 bp fragment leading to the displacement or even the prohibition for the corresponding site to be occupied by nucleosomes. The predicted nucleosome positioning site with the large potential may influence on the choice of the proximal nucleosome positions with the weaker bending potentials as is revealed by the comparison with the micrococcal nuclease digestion map. Trinucleotide methods may be considered as advantageous in the comparison with the dinucleotide ones.
Fedoseyeva
V B
VB
Institute of Molecular Genetics, RAS, Kurchatov sq.2, Moscow 123182, Russia. fvb@img.ras.ru
Alexandrov
A A
AA
D020856:AT Rich Sequence / Q000235:genetics*; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D002875:Chromosomes; D003198:Computer Simulation; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D008836:Micrococcal Nuclease / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism
D002843:Chromatin; D009707:Nucleosomes; D004247:DNA; D008836:Micrococcal Nuclease