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ATAC-Seq for Chromatin Accessibility Analysis

What is ATAC-Seq

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.

Applications of ATAC-Seq

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

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."

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.

Dr. Greenleaf and his team developed ATAC-Seq
Surveying the Chromatin Landscape with ATAC-Seq

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

ATAC-Seq Protocol

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
How Does ATAC-Seq Work
Single-Cell ATAC-Seq

Single-Cell ATAC-Seq

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

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.

Single-Cell ATAC-Seq of Arabidopsis thaliana

Single-Cell ATAC-Seq of A. thaliana

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

Featured ATAC-Seq Publications

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.

Science. 2015;348(6237):910-914.

Buenrostro JD, Wu B, Litzenburger UM, et al. Single-cell chromatin accessibility reveals principles of regulatory variation.

Nature. 2015;523(7561):486-490.

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.

Featured Products

Tagment DNA TDE1 Enzyme and Buffer Kits
Tagment DNA TDE1 Enzyme and Buffer Kits

Use these components in ATAC-Seq experiments to analyze chromatin accessibility.

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NextSeq 1000 & 2000 Systems
NextSeq 1000 & 2000 Systems

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications, with higher efficiency and fewer restraints.

Learn More
NovaSeq Reagent Kits
NovaSeq Reagent Kits

Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.

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ATAC-Seq Workflow

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Related Methods & Applications

DNA Methylation Analysis
DNA Methylation Analysis

Characterizing DNA methylation patterns can help you gain valuable insight into gene regulation and identify potential biomarkers.

ChIP-Seq
ChIP-Seq

Combining chromatin immunoprecipitation with DNA sequencing, ChIP-Seq is a powerful method for identifying genome-wide binding sites for transcription factors and other proteins.

Cancer Epigenetics
Cancer Epigenetics

Studies of epigenetic alterations in cancer, such as altered transcription factor binding, can provide insight into important tumorigenic pathways.

Complex Disease Genomics
Complex Disease Genomics

Complex diseases result from a combination of genetic and environmental factors, and are often heavily influenced by gene regulation and epigenetic patterns.

Cellular & Molecular Biology
Cellular & Molecular Biology

Broaden cell and molecular biology research beyond the conventional methods of protein-interaction and single-gene functional studies.

RNA Sequencing
RNA Sequencing

RNA-Seq is a highly sensitive and accurate tool for measuring gene expression and studying both coding and noncoding regions of the transcriptome.

References

  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.