University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington, USA.
Emory University, Department of Biology, Atlanta, GA, USA.
Curr Opin Plant Biol. 2020 Apr;54:69-78. doi: 10.1016/j.pbi.2020.01.003. Epub 2020 Feb 26.
Transcriptional control is exerted primarily through the binding of transcription factor proteins to regulatory elements in DNA. By virtue of eukaryotic DNA being complexed with histones, transcription factor binding to DNA alters or eliminates histone-DNA contacts, leading to increased accessibility of the DNA region to nuclease enzymes. This hypersensitivity to nuclease digestion has been used to define DNA binding events and regulatory elements across genomes, and to compare these attributes between cell types or conditions. These approaches make it possible to define the regulatory elements in a genome as well as to predict the regulatory networks of transcription factors and their target genes in a given cell state. As these chromatin accessibility assays are increasingly used, it is important to consider how to analyze the resulting data to avoid artifactual results or misinterpretation. In this review, we focus on some of the key technical and computational caveats associated with plant chromatin accessibility data, including strategies for sample preparation, sequencing, read mapping, and downstream analyses.
转录控制主要通过转录因子蛋白与 DNA 中的调节元件结合来发挥作用。由于真核生物 DNA 与组蛋白复合，转录因子与 DNA 的结合改变或消除了组蛋白-DNA 的接触，从而增加了 DNA 区域对核酸酶的可及性。这种对核酸酶消化的超敏性已被用于定义整个基因组中的 DNA 结合事件和调节元件，并在细胞类型或条件之间比较这些属性。这些方法使得能够定义基因组中的调节元件，并预测给定细胞状态下转录因子及其靶基因的调节网络。随着这些染色质可及性测定的应用越来越广泛，考虑如何分析所得数据以避免人为结果或误解变得非常重要。在这篇综述中，我们重点介绍了与植物染色质可及性数据相关的一些关键技术和计算注意事项，包括样品制备、测序、读取映射和下游分析的策略。
