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Review Article

全基因组识别蛋白质-DNA相互作用的方法

卷 26, 期 42, 2019

页: [7641 - 7654] 页: 14

弟呕挨: 10.2174/0929867325666180530115711

价格: $65

摘要

背景：转录因子是DNA结合蛋白，在许多基本生物学过程中起关键作用。弄清它们与DNA的相互作用对于鉴定其靶基因和了解调节网络至关重要。由于实验和计算方法的最新进展，全基因组识别其结合位点变得可行。 ChIP芯片，ChIP-seq和ChIP-exo是三种用于划定全基因组转录因子结合位点的技术。 目的：本文旨在概述这三种技术，包括它们的实验程序，计算方法和流行的分析工具。 结论：ChIP芯片，ChIP-seq和ChIP-exo是研究全基因组体内蛋白质-DNA相互作用的主要技术。由于下一代测序技术的飞速发展，不赞成使用基于阵列的ChIP芯片，而ChIP-seq已成为在整个基因组中鉴定转录因子结合位点的最广泛使用的技术。新开发的ChIP-exo进一步提高了单核苷酸的空间分辨率。已经开发了许多工具来分析ChIP芯片，ChIP-seq和ChIP-exo数据。但是，不同的程序可能采用不同的机制或基础算法，因此每个程序都将固有地包括自己的一组统计假设和偏差。因此，为给定实验选择最合适的分析程序需要仔细考虑。而且，大多数程序仅具有命令行界面，因此其安装和使用将需要Unix / Linux的基本计算专业知识。

关键词: 转录因子，转录因子结合位点，染色质免疫沉淀，微阵列，下一代测序，ChIP芯片，ChIP-seq，ChIP-exo，数据分析。

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