Shashikant Tanvi, Ettensohn Charles A
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
Methods Cell Biol. 2019;151:219-235. doi: 10.1016/bs.mcb.2018.11.002. Epub 2018 Dec 21.
Programs of gene transcription are controlled by cis-acting DNA elements, including enhancers, silencers, and promoters. Local accessibility of chromatin has proven to be a highly informative structural feature for identifying such regulatory elements, which tend to be relatively open due to their interactions with proteins. Recently, ATAC-seq (assay for transposase-accessible chromatin using sequencing) has emerged as one of the most powerful approaches for genome-wide chromatin accessibility profiling. This method assesses DNA accessibility using hyperactive Tn5 transposase, which simultaneously cuts DNA and inserts sequencing adaptors, preferentially in regions of open chromatin. ATAC-seq is a relatively simple procedure which can be applied to only a few thousand cells. It is well-suited to developing embryos of sea urchins and other echinoderms, which are a prominent experimental model for understanding the genomic control of animal development. In this chapter, we present a protocol for applying ATAC-seq to embryonic cells of sea urchins.
基因转录程序由顺式作用DNA元件控制，包括增强子、沉默子和启动子。染色质的局部可及性已被证明是识别此类调控元件的一个极具信息价值的结构特征，由于它们与蛋白质的相互作用，这些调控元件往往相对开放。最近，ATAC-seq（使用测序法检测转座酶可及染色质）已成为全基因组染色质可及性分析最强大的方法之一。该方法使用超活性Tn5转座酶评估DNA可及性，转座酶同时切割DNA并插入测序接头，优先插入开放染色质区域。ATAC-seq是一个相对简单的程序，仅适用于几千个细胞。它非常适合海胆和其他棘皮动物的发育胚胎，这些胚胎是理解动物发育基因组控制的一个重要实验模型。在本章中，我们介绍了将ATAC-seq应用于海胆胚胎细胞的实验方案。
