Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy.

ABSTRACT:

Background

An organism's DNA sequence is one of the key factors guiding the positioning of nucleosomes within a cell's nucleus. Sequence-dependent bending anisotropy dictates how DNA is wrapped around a histone octamer. One of the best established sequence patterns consistent with this anisotropy is the periodic occurrence of AT-containing dinucleotides (WW) and GC-containing dinucleotides (SS) in the nucleosomal locations where DNA is bent in the minor and major grooves, respectively. Although this simple pattern has been observed in nucleosomes across eukaryotic genomes, its use for prediction of nucleosome positioning was not systematically tested.

Results

We present a simple computational model, termed the W/S scheme, implementing this pattern, without using any training

SUBMITTER: Cui F 

PROVIDER: S-EPMC4261538 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature