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.

中文翻译：

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植物染色质可及性数据分析中的考虑。

转录控制主要通过转录因子蛋白与 DNA 中的调节元件的结合来实现。由于真核 DNA 与组蛋白复合，与 DNA 结合的转录因子会改变或消除组蛋白与 DNA 的接触，从而增加 DNA 区域对核酸酶的可及性。这种对核酸酶消化的超敏反应已被用于定义跨基因组的 DNA 结合事件和调控元件，并在细胞类型或条件之间比较这些属性。这些方法使得定义基因组中的调控元件以及预测给定细胞状态下转录因子及其靶基因的调控网络成为可能。随着越来越多地使用这些染色质可及性测定，重要的是要考虑如何分析结果数据以避免人为结果或误解。在这篇综述中，我们重点关注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。