The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome.
The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome.
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DOI：
10.11234/gi1990.20.199
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发表时间：
2008
期刊：
影响因子：
--
通讯作者：
Stephen C. J. Parker;E. Margulies;T. Tullius
中科院分区：
文献类型：
--
作者：
Stephen C. J. Parker;E. Margulies;T. Tullius
GC含量已被证明是人类基因组功能的一个重要方面。除了GC含量之外，基因组中还有一类区域具有特别高的GC含量，并且富含CG二核苷酸-称为CpG岛。CpG岛与具有生物学功能的基因组元件相关联。DNA结构也有助于生物功能。最近的研究发现，一些DNA结构特性与CpG岛功能相关。在这里，我们使用羟基自由基裂解模式作为衡量DNA结构，探讨GC含量和精细尺度DNA结构之间的关系。我们发现，GC含量和DNA序列的溶剂可访问的结构特性之间存在正相关性，并且这种相关性的强度随着基因组分辨率的增加而降低。我们证明了具有高度溶剂可及DNA结构的基因组区域倾向于重叠功能基因组元件。我们的研究结果表明，基因组中编码的精细尺度DNA结构特性对生物学功能很重要，高GC含量区域和一些CpG岛的高度溶剂可及性可能解释了它们的一些功能特性。
GC content has been shown to be an important aspect of human genomic function. Extending beyond the scope of GC content alone, there is a class of regions in the genome that have especially high GC content and are enriched for the CG dinucleotide--called CpG islands. CpG islands have been linked to biologically functional genomic elements. DNA structure also contributes to biological function. Recent studies found that some DNA structural properties are correlated with CpG island functionality. Here, we use hydroxyl radical cleavage patterns as a measure of DNA structure, to explore the relationship between GC content and fine-scale DNA structure. We show that there is a positive correlation between GC content and the solvent-accessible structural properties of a DNA sequence, and that the strength of this correlation decreases as genomic resolution increases. We demonstrate that regions of the genome that have highly solvent-accessible DNA structure tend to overlap functional genomic elements. Our results suggest that fine-scale DNA structural properties that are encoded in the genome are important for biological function, and that the highly solvent-accessible nature of high GC content regions and some CpG islands may account for some of their functional properties.