NCS: Incorporating positioning data to quantify nucleosome stability in yeast

Jung Hsien Chiang, Chan Hsien Lin

Research output: Contribution to journalArticle

Abstract

Motivation: With the spreading technique of mass sequencing, nucleosome positions and scores for their intensity have become available through several previous studies in yeast, but relatively few studies have specifically aimed to determine the score of nucleosome stability. Based on mass sequencing data, we proposed a nucleosome center score (NCS) for quantifying nucleosome stability by measuring shifts of the nucleosome center, and then mapping NCS scores to nucleosome positions in Brogaard et al.'s study.Results: We demonstrated the efficiency of NCS by known preference of A/T-based tracts for nucleosome formation, and showed that central nucleosomal DNA is more sensitive to A/T-based tracts than outer regions, which corresponds to the central histone tetramer-dominated region. We also found significant flanking preference around nucleosomal DNA for A/T-based dinucleotides, suggesting that neighboring sequences could affect nucleosome stability. Finally, the difference between results of NCS and Brogaard et al.'s scores was addressed and discussed.

Original languageEnglish
Pages (from-to)761-767
Number of pages7
JournalBioinformatics
Volume30
Issue number6
DOIs
Publication statusPublished - 2014 Mar 1

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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