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Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites

Author

Listed:
  • Xianfu Yi
  • Yu-Dong Cai
  • Zhisong He
  • WeiRen Cui
  • Xiangyin Kong

Abstract

Background: The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs) have been suggested to play a role in nucleosome positioning in vivo. Principal Findings: Here, the minimum redundancy maximum relevance (mRMR) feature selection algorithm, the nearest neighbor algorithm (NNA), and the incremental feature selection (IFS) method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs) in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test. Conclusions: Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.

Suggested Citation

  • Xianfu Yi & Yu-Dong Cai & Zhisong He & WeiRen Cui & Xiangyin Kong, 2010. "Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-7, September.
    • Handle: RePEc:plo:pone00:0012495
    DOI: 10.1371/journal.pone.0012495
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    1. Ramakrishna K. Chodavarapu & Suhua Feng & Yana V. Bernatavichute & Pao-Yang Chen & Hume Stroud & Yanchun Yu & Jonathan A. Hetzel & Frank Kuo & Jin Kim & Shawn J. Cokus & David Casero & Maria Bernal & , 2010. "Relationship between nucleosome positioning and DNA methylation," Nature, Nature, vol. 466(7304), pages 388-392, July.
    2. Eran Segal & Yvonne Fondufe-Mittendorf & Lingyi Chen & AnnChristine Thåström & Yair Field & Irene K. Moore & Ji-Ping Z. Wang & Jonathan Widom, 2006. "A genomic code for nucleosome positioning," Nature, Nature, vol. 442(7104), pages 772-778, August.
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