Accessible chromatin often represents gene regulatory elements, including promoters and enhancers, essential for gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is one of the most popular techniques to investigate chromatin accessibility across the genome. Here we describe, step by step, a series of optimized experimental methods and bioinformatics pipelines for ATAC-seq analysis. As an example, we present an analysis of murine spermatogenic cells: a method to isolate germ cells, a reaction step using Tn5 transposase to insert sequencing adapters into accessible DNA, a library preparation method for high-throughput sequencing, and bioinformatics analysis of sequencing data. Overall, we introduce a framework of ATAC-seq analysis that can be applied to any cell population to identify cell-type-specific gene regulatory elements and their cis-regulatory networks.
CITATION STYLE
Tatara, M., Ikeda, T., Namekawa, S. H., & Maezawa, S. (2023). ATAC-Seq Analysis of Accessible Chromatin: From Experimental Steps to Data Analysis. In Methods in Molecular Biology (Vol. 2577, pp. 65–81). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2724-2_5
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