Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes
Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes
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DOI：
10.1007/978-1-4939-3578-9_12
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发表时间：
2016-01-01
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影响因子：
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通讯作者：
Sung, Myong-Hee
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文献类型：
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作者：
Baek, Songjoon;Sung, Myong-Hee
高通量测序技术使生物学家能够以核苷酸分辨率生成染色质特征的全基因组图谱。酶如核酸酶或转座酶由于其靶向可接近的染色质进行切割或插入的能力而作为染色质探测剂是有用的。在几百个碱基对的范围内，核酶对可接近的染色质的优先作用允许在体内绘制细胞状态特异性可接近性。这些可接近区域包含功能上重要的调控位点，包括启动子和增强子，其经历主动重塑以使细胞适应动态环境。DNase-seq和最近的ATAC-seq是两种越来越受欢迎的检测方法。已经提出了对来自这些测定的DNA文库进行深度测序，称为基因组足迹法，以使得能够在核苷酸水平上在基因组上全面构建蛋白质占用谱。最近的研究已经发现基因组足迹的局限性，这减少了可检测蛋白质的范围。此外，识别与观察到的足迹结合的假定因素仍然具有挑战性。尽管有这些警告，该方法仍然比ChIP-seq或FAIRE-seq等替代技术具有显着优势。在这里，我们描述了用于分析染色质可及性和基因组足迹的计算方法和工具。适当的实验设计和分析特定的数据分析确保检测灵敏度和最大限度地检索信息。基于酶的染色质分析方法代表了一种强大的和不断发展的方法，有助于我们了解基因组是如何调节的。
High-throughput sequencing technologies have made it possible for biologists to generate genome-wide profiles of chromatin features at the nucleotide resolution. Enzymes such as nucleases or transposes have been instrumental as a chromatin-probing agent due to their ability to target accessible chromatin for cleavage or insertion. On the scale of a few hundred base pairs, preferential action of the nuclear enzymes on accessible chromatin allows mapping of cell state-specific accessibility in vivo. Such accessible regions contain functionally important regulatory sites, including promoters and enhancers, which undergo active remodeling for cells adapting in a dynamic environment. DNase-seq and the more recent ATAC-seq are two assays that are gaining popularity. Deep sequencing of DNA libraries from these assays, termed genomic footprinting, has been proposed to enable the comprehensive construction of protein occupancy profiles over the genome at the nucleotide level. Recent studies have discovered limitations of genomic footprinting which reduce the scope of detectable proteins. In addition, the identification of putative factors that bind to the observed footprints remains challenging. Despite these caveats, the methodology still presents significant advantages over alternative techniques such as ChIP-seq or FAIRE-seq. Here we describe computational approaches and tools for analysis of chromatin accessibility and genomic footprinting. Proper experimental design and assay-specific data analysis ensure the detection sensitivity and maximize retrievable information. The enzyme-based chromatin profiling approaches represent a powerful and evolving methodology which facilitates our understanding of how the genome is regulated.