Document Details

Document Type : Article In Journal 
Document Title :
Using deformation energy to analyze nucleosome positioning in genomes
Using deformation energy to analyze nucleosome positioning in genomes
 
Document Language : English 
Abstract : By modulating the accessibility of genomic regions to regulatory proteins, nucleosome positioning plays important roles in cellular processes. Although intensive efforts have beenmade, the rules for determining nucleosome positioning are far fromsatisfaction yet. In this study, we developed a biophysical model to predict nucleosomal sequences based on the deformation energy ofDNA sequences, and validated it against the experimentally determined nucleosome positions in the Saccharomyces cerevisiae genome, achieving very high success rates. Furthermore, using the deformation energy model, we analyzed the distribution of nucleosomes around the following three types of DNA functional sites: (1) double strand break (DSB), (2) single nucleotide polymorphism (SNP), and (3) origin of replication (ORI).We have found from the analyzed energy spectra that a remarkable “trough” or “valley” occurs around each of these functional sites, implying a depletion of nucleosome density, fully in accordance with experimental observations. These findings indicate that the deformation energy may play a key role for accurately predicting nucleosome positions, and that it can also provide a quantitative physical approach for in-depth understanding the mechanism of nucleosome positioning. 
ISSN : 0888-7543 
Journal Name : Genomics 
Volume : 107 
Issue Number : 2 
Publishing Year : 1437 AH
2016 AD 
Article Type : Article 
Added Date : Monday, July 10, 2017 

Researchers

Researcher Name (Arabic)Researcher Name (English)Researcher TypeDr GradeEmail
Chen WeiWei, Chen ResearcherDoctorate 
Pengmian FengFeng, Pengmian ResearcherDoctorate 
Hui DingDing, Hui ResearcherDoctorate 
Hao LincLinc, Hao ResearcherDoctorate 
Kuo-Chen ChouChou, Kuo-Chen ResearcherDoctorate 

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