Considerations in the analysis of plant chromatin accessibility data.
Considerations in the analysis of plant chromatin accessibility data.
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DOI：
10.1016/j.pbi.2020.01.003
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发表时间：
2020-04
影响因子：
9.5
通讯作者：
Deal RB
中科院分区：
文献类型：
--
作者：
Bubb KL;Deal RB
转录控制主要通过转录因子蛋白与DNA中的调控元件的结合来实现。由于真核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接触，导致DNA区域对核酸酶的可接近性增加。这种对核酸酶消化的超敏反应已被用于定义DNA结合事件和基因组间的调控元件，并比较细胞类型或条件之间的这些属性。这些方法使得确定基因组中的调控元件以及预测转录因子及其靶基因在给定细胞状态下的调控网络成为可能。随着这些染色质可及性测定的使用越来越多，重要的是要考虑如何分析所得数据，以避免人为结果或误解。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。
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.
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