Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.
Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.
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使用 ATAC-seq 进行活性调控元件的全基因组图谱。
DOI：
10.1007/978-1-0716-2899-7_1
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Greenleaf,WilliamJ
中科院分区：
文献类型：
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作者：
Marinov,GeorgiK;Shipony,Zohar;Kundaje,Anshul;Greenleaf,WilliamJ
真核生物中的活性顺式调节元件（cRE）的特点是核小体耗尽，因此具有更高的可及性。事实证明，这一特性对于在全基因组范围内识别 cRE 并跟踪它们在不同细胞状态下的动态非常有用，并且是许多利用可访问 DNA 的优先酶促切割/标记的方法的基础。 ATAC-seq（使用测序进行转座酶可及染色质分析）已成为最通用且适应性广泛的方法，并已被广泛采用作为绘制开放染色质区域的标准工具。在这里，我们主要在哺乳动物系统的背景下讨论当前进行 ATAC-seq 实验的最佳实践和重要考虑因素。
Activecis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs genome-wide and tracking their dynamics across different cellular states and is the basis of numerous methods taking advantage of the preferential enzymatic cleavage/labeling of accessible DNA. ATAC-seq (Assay forTransposase-AccessibleChromatin usingsequencing) has emerged as the most versatile and widely adaptable method and has been widely adopted as the standard tool for mapping open chromatin regions. Here, we discuss the current optimal practices and important considerations for carrying out ATAC-seq experiments, primarily in the context of mammalian systems.