染色质免疫沉淀测序（ChIP-Seq）数据分析：使用SISSRs峰检测工具鉴定蛋白质-DNA结合位点
ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.
作者信息
Narlikar Leelavati, Jothi Raja
机构信息
National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
出版信息
Methods Mol Biol. 2012;802:305-22. doi: 10.1007/978-1-61779-400-1_20.
Abstract
Protein-DNA interactions play key roles in determining gene-expression programs during cellular development and differentiation. Chromatin immunoprecipitation (ChIP) is the most widely used assay for probing such interactions. With recent advances in sequencing technology, ChIP-Seq, an approach that combines ChIP and next-generation parallel sequencing is fast becoming the method of choice for mapping protein-DNA interactions on a genome-wide scale. Here, we briefly review the ChIP-Seq approach for mapping protein-DNA interactions and describe the use of the SISSRs peak-finder, a software tool for precise identification of protein-DNA binding sites from sequencing data generated using ChIP-Seq.
摘要
蛋白质与DNA的相互作用在细胞发育和分化过程中决定基因表达程序方面起着关键作用。染色质免疫沉淀（ChIP）是用于探测此类相互作用的最广泛使用的检测方法。随着测序技术的最新进展，ChIP-Seq（一种将ChIP与下一代平行测序相结合的方法）正迅速成为在全基因组范围内绘制蛋白质与DNA相互作用图谱的首选方法。在这里，我们简要回顾用于绘制蛋白质与DNA相互作用图谱的ChIP-Seq方法，并描述SISSRs峰查找器的使用，这是一种用于从使用ChIP-Seq生成的测序数据中精确识别蛋白质与DNA结合位点的软件工具。
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