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

Liu H, Duan X, Yu S, Sun X - BMC Genomics (2011)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.

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.

Show MeSH
Patterns of nucleosomes near SNP sites. (A), single nucleotide variation (single); (B), insertions/deletions (in-del); (C), insertion SNP; (D), deletion SNP
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Figure 8: Patterns of nucleosomes near SNP sites. (A), single nucleotide variation (single); (B), insertions/deletions (in-del); (C), insertion SNP; (D), deletion SNP

Mentions: Patterns of nucleosomes near SNP sites were investigated (see Figure 8). SNP sites are grouped into four classes, single, insertion/deletion (indels), insertion, and deletion. Near the sites of indels, insertions, and deletions, the curvature profile shows a large trough (Figure 8B-D), indicating such mutation events favor linker-DNA. Importantly, a similar result was also observed using the experimental data. Although the trough near the single SNP sites is not as low as that near the other types of SNP (Figure 8A), nucleosome depletion is obvious. In the genome of Oryzias latipes, genetic variation downstream of a TSS occurs with an ~200-bp periodicity, and the insertion/deletion of more than 1 bp frequently occurs in the linker-DNA region [30], which is consistent with our findings in humans. Moreover, we found that nucleosomes are also depleted near SNP sites in the dog genome (Additional file 1: Figure s8).


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

Liu H, Duan X, Yu S, Sun X - BMC Genomics (2011)

Patterns of nucleosomes near SNP sites. (A), single nucleotide variation (single); (B), insertions/deletions (in-del); (C), insertion SNP; (D), deletion SNP
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037905&req=5

Figure 8: Patterns of nucleosomes near SNP sites. (A), single nucleotide variation (single); (B), insertions/deletions (in-del); (C), insertion SNP; (D), deletion SNP
Mentions: Patterns of nucleosomes near SNP sites were investigated (see Figure 8). SNP sites are grouped into four classes, single, insertion/deletion (indels), insertion, and deletion. Near the sites of indels, insertions, and deletions, the curvature profile shows a large trough (Figure 8B-D), indicating such mutation events favor linker-DNA. Importantly, a similar result was also observed using the experimental data. Although the trough near the single SNP sites is not as low as that near the other types of SNP (Figure 8A), nucleosome depletion is obvious. In the genome of Oryzias latipes, genetic variation downstream of a TSS occurs with an ~200-bp periodicity, and the insertion/deletion of more than 1 bp frequently occurs in the linker-DNA region [30], which is consistent with our findings in humans. Moreover, we found that nucleosomes are also depleted near SNP sites in the dog genome (Additional file 1: Figure s8).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.

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.

Show MeSH