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.
Chromatin accessibility analysis with ATAC-Seq can provide valuable insights into the regulatory landscape of the genome. Popular applications include:
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.
"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."
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.
Learn how Dr. Greenleaf and his team developed ATAC-Seq and why he believes that it might one day provide new insights into the development and treatment of cancer and autoimmune disease.Read Interview
We recommend the following ATAC-Seq protocol: Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21.29.1-21.29-9.
Note that the TDE1 Enzyme and Buffer Kits are now available separately from Illumina (Cat. No. 20034197 and 20034198). All other steps in the protocol, including the enzyme and buffer concentration, remain the same.View Protocol
Single-cell ATAC-Seq combines compartmentalization and barcoding of single cells with Tn5 tagmentation. The Tn5 transposase tags open chromatin regions with sequencing adapters. The tagged DNA fragments are then purified, amplified, and sequenced.Learn more about single-cell sequencing
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:
|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.
Join Dr. Josh Cuperus, Steve Hoffman, PhD, and Adriana Suarez, PhD as they discuss single-cell ATAC-Seq of Arabidopsis thaliana roots to understand chromatin accessibility. They examine the regulatory landscape and provide an analytical framework to infer the regulatory networks that govern plant development.View Webinar
Buenrostro JD, Giresi PG, Zaba LC, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Nat Methods. 2013;10(12):1213-1218.
Klein HU, McCabe C, Gjoneska E, et al. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains.
Nat Neurosci. 2019;22(1):37-46.
Lau CM, Adams NM, Geary CD, et al. Epigenetic control of innate and adaptive immune memory.
Nat Immunol. 2018;19(9):963-972.
Cusanovich DA, Daza R, Ade A, et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing.
Buenrostro JD, Wu B, Litzenburger UM, et al. Single-cell chromatin accessibility reveals principles of regulatory variation.
Lareau CA, Duarte FM, Chew JG, et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.
Nat Biotechnol. 2019;37(8):916-924.