ATAC-Seq

Assay for Transposase Accessible Chromatin Sequencing (ATAC-Seq) is used for genome-wide mapping of open chromatin, where gene regulatory elements such as promoters, enhancers, and insulators are active.

Why study open chromatin?

• Generate genome-wide open chromatin signatures in different patient populations
• Identify transcription factors and gene regulatory elements that drive disease
• Gain mechanistic insight into the gene regulatory response to treatments
• Develop models of dynamic chromatin reorganization during different stages of cell differentiation and development

ATAC-Seq is a perfect first step for those exploring the role of epigenetics in cell systems or disease models as it doesn’t require prior knowledge of gene regulation mechanisms.

Sample Types

Active Motif’s services will generate ATAC-Seq data from the following sample types:

1. Human and animal tissues (including xenografts and human biopsies)
2. Primary cells (including T and B cells)
3. FACS sorted cells, including from rare cell populations

Learn More About ATAC-Seq

Figure 1: Active Motif’s ATAC-Seq assay reliably detects regions of open chromatin.
DNAse-Seq, which has long been the gold standard for generating genome-wide profiles of open chromatin, is shown in blue. The utility of DNAse-Seq has been limited since it requires tens of millions of cells and is technically challenging. Active Motif’s ATAC-Seq (shown in green), uses only 50,000 cells and provides data that is comparable to DNAse-Seq.

Figure 2: Active Motif’s ATAC-Seq assay distinguishes sample groups by identifying chromatin regions that are differentially open.
The example above shows ATAC-Seq data from 4 different samples, each performed in triplicate. Differentially open regions are highlighted in yellow.

Figure 3: Identifying important transcription factor binding sites using ATAC-Seq
The underlying DNA sequence of differentially open chromatin regions can be analyzed to identify the most enriched transcription factor binding sites. In this cell system the two most enriched binding motifs are also relevant to B cell biology. Fra1 is quickly upregulated upon B cell activation and PU.1 is a key regulator of B cell fate specification.

Figure 4: Distribution of Histone Modifications Relative to ATAC-Seq Peaks at Annotated Promoters
Comparison of ATAC-Seq data to different histone modification ChIP-Seq data sets reveals that ATAC-Seq peaks at promoters are most enriched for H3K4me3 and H3K9Ac.

Figure 5: Distribution of Histone Modifications Relative to ATAC-Seq Peaks Outside of Annotated Promoters
ATAC-Seq peaks outside promoters are enriched for all active marks including the enhancer marks H3K27Ac and H3K4me1.

Figure 6: Active Motif’s ATAC-Seq data generated from tissues
The images above show ATAC-Seq data generated using frozen mouse liver and lung tissue. The open chromatin profiles are similar to DNAse-Seq profiles generated by the ENCODE consortium.

Figure 7: Active Motif’s ATAC-Seq data shows high reproducibility
The experiment above was performed using a cell line that was left untreated or treated under three different conditions and each condition was performed in triplicate. The correlation coefficients are presented in the heat map. Replicates have coefficients of at least 0.96. The heat map shows that the samples cluster into four distinct groups as expected.

Figure 9: Active Motif’s optimized ATAC-Seq protocol results in increased number of peaks.
Human embryonic progenitor cells (4D20.8 cell line and primary cells), human primary endothelial cells, human mesenchymal stem cells, and rat primary neonatal cardiomyocytes were processed with either the standard ATAC-Seq protocol* (blue), Omni ATAC-Seq protocol^# (orange), or Active Motif’s ATAC-Seq protocol (purple). Samples processed with Active Motif’s ATAC-Seq protocol consistently identify more peaks in a variety of samples.