Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation

Most genetic variations associated with human complex traits are located in non-coding genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a comprehensive catalog of functional non-coding genomic elements, most of which are involved in epigenetic regulation of gene expression. Genome-wide maps of open chromatin regions can facilitate functional analysis of cis- and trans-regulatory elements via their connections with trait-associated sequence variants. Currently, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is considered the most accessible and cost-effective strategy for genome-wide profiling of chromatin accessibility. Single-cell ATAC-seq (scATAC-seq) technology has also been developed to study cell type-specific chromatin accessibility in tissue samples containing a heterogeneous cellular population. However, due to the intrinsic nature of scATAC-seq data, which are highly noisy and sparse, accurate extraction of biological signals and devising effective biological hypothesis are difficult. To overcome such limitations in scATAC-seq data analysis, new methods and software tools have been developed over the past few years. Nevertheless, there is no consensus for the best practice of scATAC-seq data analysis yet. In this review, we discuss scATAC-seq technology and data analysis methods, ranging from preprocessing to downstream analysis, along with an up-to-date list of published studies that involved the application of this method. We expect this review will provide a guideline for successful data generation and analysis methods using appropriate software tools and databases for the study of chromatin accessibility at single-cell resolution.