Abstract
BackgroundNucleosome 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.ResultsCurvature 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.ConclusionsThe 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.
Highlights
Nucleosome positioning has an important role in gene regulation
To test how representative the pattern derived from the crystal structures was, 634 well-positioned nucleosome DNA sequences were collected from Zhao et al.’s experimental dataset [2]
The results indicate that the importance of DNA sequences in determining nucleosome positions, providing a default pattern
Summary
Nucleosome positioning has an important role in gene regulation. 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. Positioning has important roles in gene regulation, because packing DNA into nucleosomes can limit the accessibility of the sequences [2,3,4]. High-resolution genome-wide nucleosome maps are available for the genomes of yeast, worms, flies, and humans [2,5,6,7]. Studies of these nucleosome position datasets have revealed some interesting characteristics, especially for promoter sequences. Low nucleosome occupancy is a significant feature of a functional transcription factor binding site (TFBS) [8]
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