The Introduction of ATAC-Seq

CD Genomics is now able to provide Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. The method is a fast and sensitive alternative to DNase-seq (DNase I hypersensitive sites sequencing) or MNase-seq (micrococcal nuclease sensitive sites sequencing). By using our service, you can detect genome-wide profiles of open and accessible regions of chromatin that are indicative of active regulatory regions.

The eukaryotic genome is highly packaged to fit into the very limited nuclear space. As a result, access to genomic information is tightly regulated based on cellular state. What regions of the genome are accessible reveals a great deal about the state of the cell. ATAC-seq is a technique to locate accessible chromatin regions.

Key Features and Advantages

  • Gain mechanistic insight into gene regulation, cellular response to treatment or disease
  • Identify which transcription factors are driving cell fate, disease, or response
  • Limited patient samples
  • Low requirements on the amount of the biological sample, and the whole protocol requires 3 hours in total

Project Workflow

The key part of the ATAC-seq procedure is the action of the transposase Tn5 on the genomic DNA of the sample. Transposases are enzymes catalyzing the movement of transposons to other parts of the genome. While naturally occurring transposases have a low level of activity, ATAC-seq employs a mutated hyperactive transposase. The high activity allows for highly efficient cutting of exposed DNA and simultaneous ligation of specific sequences, called adapters. Adapter-ligated DNA fragments are then isolated, amplified by PCR and used for next generation sequencing. The experimental pipeline of ATAC-seq is demonstrated in Figure 1.

ATAC-seq WorkflowFigure 1. Schematic workflow of ATAC-seq process.

Data Analysis
Regions of the genome where DNA was accessible during the experiment will contain significantly more sequencing reads (since that is where the transposase preferentially acts), and form peaks in the ATAC-seq signal that are detectable with peak calling tools. These regions can be further categorized into the various regulatory element types - promoters, enhancers, insulators, etc.- by taking into account further information, like their distance from a Transcription Start Site or data from other experiments. Inside the regions where the ATAC-seq signal is enriched, one can also observe sub-regions with depleted signal. These subregions, typically only a few base pairs long, are considered to be "footprints" of DNA-binding proteins. These proteins will protect the DNA strand from transposase cleavage and will consequently cause a depletion in the signal.
  • Quality control
  • Reference genome mapping
  • Peak calling
  • Annotation
  • Differential analysis
  • Motif discovery
An ATAC-seq experiment can also be used to infer nucleosome positions.
Sample Requirements
  • Sample type: Human, mouse and rat tissues, Live cells, not genomic DNA.
  • cell number : ≥ 1×105 cells, an accurate cell number is key to the success of the experiment.
  • Healthy cells in a homogeneous single-cell suspension work the best.
Sequencing Strategy and Recommended Depth
  • Illumina HiSeq PE50 or PE150.
  • For some applications such as nucleosome mapping, paired end sequencing is preferred. Illumina HiSeq PE150.
  • ≥50M Reads.

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For Research Use Only. Not for use in diagnostic procedures.
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