ATAC-Seq for Chromatin Accessibility Analysis

A rapid, sensitive method for profiling accessible chromatin across the genome

what is ATAC-Seq illustration

What is ATAC-Seq?

The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility across the genome. By sequencing regions of open chromatin, ATAC-Seq can help you uncover how chromatin packaging and other factors affect gene expression.

ATAC-Seq does not require prior knowledge of regulatory elements, making it a powerful epigenetic discovery tool. It has been used to better understand chromatin accessibility, transcription factor binding, and gene regulation in complex diseases, embryonic development, T-cell activation, and cancer.1,2 ATAC-Seq can be performed on bulk cell populations or on single cells at high resolution.

ATAC-Seq Protocol

How Does ATAC-Seq Work?

In ATAC-Seq, genomic DNA is exposed to Tn5, a highly active transposase. Tn5 simultaneously fragments DNA, preferentially inserts into open chromatin sites, and adds sequencing primers (a process known as tagmentation). The sequenced DNA identifies the open chromatin and data analysis can provide insight into gene regulation.

Additionally, ATAC-Seq can be combined with other methods, such as RNA sequencing, for a multiomic approach to studying gene expression.3 Subsequent experiments often include ChIP-Seq, Methyl-Seq, or Hi-C-Seq to further characterize forms of epigenetic regulation.

Key applications of ATAC-Seq

Chromatin accessibility analysis with ATAC-Seq can provide valuable insights into the regulatory landscape of the genome. Popular applications include:

  • Nucleosome mapping
  • Transcription factor binding analysis
  • Novel enhancer identification
  • Exploration of disease-relevant regulatory mechanisms
  • Cell type–specific regulation analysis
  • Evolutionary studies
  • Comparative epigenomics
  • Biomarker discovery

Coverage recommendations for ATAC-Seq

The minimum required sequencing coverage for ATAC-Seq varies according to research objectives. This table provides some guidelines for common applications.

We recommend using paired-end reads for ATAC-Seq. Compared to single-read sequencing, paired-end reads offer:

  • Higher unique alignment rates
  • Removal of PCR duplicates
  • More complete information about accessible sequences
  • Ability to categorize reads as nucleosome-free, mono-nucleosomal, or di-nucleosomal
Learn more about paired-end sequencing
Research Goal Recommended Depth
Identification of open chromatin differences in human samples ≥ 50 M paired-end reads
Transcription factor foot printing to construct gene regulatory network > 200 M paired-end reads
Single-cell analysis 25–50 K paired-end reads per nucleus/cell

As experimental needs can vary, we encourage you to consult the scientific literature to determine the right level of coverage for your project.

ATAC-Seq allows you to ask questions about the epigenetic variability in complex or rare tissues and epigenomic landscape in populations of cells that haven’t been observable at the genome-wide level before.

Additional resources

Assaying genome-wide chromatin accessibility with ATAC-Seq

In this webinar, you'll learn how to use ATAC-Seq for genome-wide chromatin accessibility profiling and how it fits in with other chromatin accessibility profiling methods.

Profiling the transcriptome and epigenome

This technical note describes simultaneous profiling of the transcriptome and epigenome from single cells using 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expressions.

The regulatory landscape of A. thaliana

Join us for this webinar on single-cell ATAC-Seq of Arabidopsis thaliana. The speakers discuss an analytical framework to infer the regulatory networks that govern plant development.

  1. Cusanovich DA, Reddington JP, Garfield DA, et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. 2018; 555:538-542. 13.
  2. Gate RE, Cheng CS, Aiden AP, et al. Genetic determinants of co-accessible chromatin regions in activated T-cells across humans. Nat Genet. 2018; 50:1140-1150.
  3. Cao J, Cusanovich DA, Ramani V, et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science. 2018;361:1380-1385.