DiNuP: a systematic approach to identify regions of differential nucleosome positioning.
BACKGROUND
With the rapid development of high-throughput sequencing technologies, the genome-wide profiling of nucleosome positioning has become increasingly affordable. Many future studies will investigate the dynamic behaviour of nucleosome positioning in cells that have different states or that are exposed to different conditions. However, a robust method to effectively identify the regions of differential nucleosome positioning (RDNPs) has not been previously available.


RESULTS
We describe a novel computational approach, DiNuP, that compares nucleosome profiles generated by high-throughput sequencing under various conditions. DiNuP provides a statistical P-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the false discovery rate as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location, occupancy and fuzziness. RDNPs that were identified using publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription.


METHODS
DiNuP is implemented in Python and is freely available at http://www.tongji.edu.cn/~zhanglab/DiNuP.


BACKGROUND
yzhang@tongji.edu.cn


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Kai
K
Fu
Qianzi
Q
Tang
Jianxing
J
Feng
X Shirley
XS
Liu
Yong
Y
Zhang
D042002:Chromatin Assembly and Disassembly; D019295:Computational Biology / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009707:Nucleosomes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D012984:Software
D004271:DNA, Fungal; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins