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Open Access Research article

Analysis of nucleosome positioning determined by DNA helix curvature in the human genome

Hongde Liu, Xueye Duan, Shuangxin Yu and Xiao Sun*

Author Affiliations

State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China

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BMC Genomics 2011, 12:72  doi:10.1186/1471-2164-12-72

Published: 27 January 2011

Abstract

Background

Nucleosome positioning has an important role in gene regulation. However, dynamic positioning in vivo casts doubt on the reliability of predictions based on DNA sequence characteristics. What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predicted in the human genome and patterns of nucleosomes near some key sites are investigated.

Results

Curvature profiling revealed that in the vicinity of a transcription start site, there is also a nucleosome-free region. Near transcription factor binding sites, curvature profiling showed a trough, indicating nucleosome depletion. The trough of the curvature profile corresponds well to the high binding scores of transcription factors. Moreover, our analysis suggests that nucleosome positioning has a selective protection role. Target sites of miRNAs are occupied by nucleosomes, while single nucleotide polymorphism sites are depleted of nucleosomes.

Conclusions

The results indicate that DNA sequences play an important role in nucleosome positioning, and the positioning is important not only in gene regulation, but also in genetic variation and miRNA functions.