Best practices for the ATAC-seq assay and its data analysis

Eukaryotic nuclear DNA is hierarchically packaged into chromatin, with different regions condensed at different levels across the genome. Accessible chromatin regions are permissive to transcription factor binding, acting as regulatory regions that modulate gene expression. Chromatin accessibility is dynamic and often varies depending on cell or tissue types, developmental stages, and health status. Therefore, chromatin accessibility profiling can provide important biological insights into the regulatory landscape of the genome. Several methods have been developed to profile chromatin accessibility genome-wide, among which assay of transposase accessible chromatin sequencing (ATAC-seq) has become increasingly popular due to its simplicity and high sensitivity. Herein, we discuss the current best practices for ATAC-seq assays, including experimental design, sample preparation, data generation, and quality control (QC). We also provide the recommendations on bioinformatics software for comprehensive data analyses, from data quality assessment to reconstruction of gene regulatory networks (GRNs).