ATAC-seq

ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) is a method for determining chromatin accessibility across the genome. It utilizes a hyperactive Tn5 transposase to insert sequencing adapters into open chromatin regions (Buenrostro et al. 2015). The principle of the assay is presented on Figure 1. High-throughput sequencing yields reads that indicate the regions of increased accessibility (Figure 2).

Fig 1. Overview of ATAC-seq

Fig 2. ATAC-seq Signal

flowchart LR
  subgraph QC
    D(Quality Control, Feature Agnostic)
    H(Quality Control, Feature Focused)
  end
  subgraph Analysis
    C(Feature Detection)
    E(Feature Annotation)
    F(Statistical Analysis)
    E(Feature Annotation)
  end

  A[Data] --> B([Data Processing])
  B([Data Processing]) --> C(Feature Detection)
  B([Data Processing]) --> D(Quality Control, Feature Agnostic)
  C(Feature Detection) --> E(Feature Annotation)
  C(Feature Detection) --> F(Statistical Analysis)
  C(Feature Detection) --> G(Visualisation)
  B([Data Processing]) --> G(Visualisation)
  E(Feature Annotation) --> I{Analysed}
  F(Statistical Analysis) --> I{Analysed}
  D(Quality Control, Feature Agnostic) --> H(Quality Control, Feature Focused)
  C(Feature Detection) --> H(Quality Control, Feature Focused)
  G(Visualisation) --> I{Analysed}
  H(Quality Control, Feature Focused) --> I{Analysed}

  style A fill:#8FB4F7,stroke:#2768F5
  style I fill:#DF8FF7,stroke:#C11DF2
  style QC fill:#D4D1C5,stroke:#87857C 
  style Analysis fill:#D4D1C5,stroke:#87857C 

(a)

Figure 1: ATAC-seq data analysis workflow.

ATAC-seq tutorials

Tutorials in this module:

• Data Processing and QC

• Peak Detection

• Differential Accessibility

• Peak Annotation

Additional ATAC-seq related tutorials:

• TF motifs

• Identifying Relevant TFs

References

Buenrostro, Jason D., Beijing Wu, Howard Y. Chang, and William J. Greenleaf. 2015. “ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.” Current Protocols in Molecular Biology 109 (January): 21.29.1–9. https://doi.org/10.1002/0471142727.mb2129s109.