ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

Abstract

This unit describes Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome.

Keywords: ATAC-seq; chromatin accessibility; transposase.

Conflict of interest statement

Competing financial interests

Stanford University has filed a provisional patent application on the methods described, and J.D.B., H.Y.C. and W.J.G. are named as inventors.

Copyright © 2015 John Wiley & Sons, Inc.

Figures

Figure 1

(A) Library preparation schematic. (B) Transposition results in fragmented DNA. Prior to amplification, adapters have to be completed with a 72°C extension step. During the subsequent PCR additional sequence is incorporated into the adapters, which include common sequencing ends and a sequencing barcode.

Figure 2

Fragment sizes for amplified ATAC-seq libraries, determined by (A) Gel electrophoresis and (B) Bioanalyzer. Bioanalyzer image contrast has been enhanced from its original image for clarity. (C) Insert sizes determined by high-throughput sequencing. Adapters are an additional 124 bps and are not included when measuring fragment size in this panel.