- ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a powerful and relatively recent genomic technique used to study chromatin accessibility.
- It identifies regions of open chromatin, which are typically associated with regulatory elements such as enhancers, promoters, and transcription factor binding sites.
- The method is based on the principle that DNA regions not tightly bound by nucleosomes are more accessible to enzymes. This accessibility is indicative of active gene regulatory elements and can provide insights into gene expression regulation, cell-type-specific epigenetic landscapes, and the dynamics of chromatin structure in development and disease.
- The core of ATAC-seq lies in the use of a hyperactive Tn5 transposase enzyme that simultaneously cuts accessible DNA and inserts sequencing adapters in a process known as “tagmentation.” Since the enzyme preferentially targets open chromatin, the resulting DNA fragments are enriched in regulatory regions. These fragments are then amplified by PCR and sequenced using high-throughput sequencing platforms. The resulting data can be mapped to a reference genome to reveal accessible regions, with fragment size distribution offering additional information about nucleosome positioning.
- ATAC-seq is notable for its efficiency, requiring a relatively low number of cells and minimal input DNA compared to older methods such as DNase-seq or FAIRE-seq. This makes it particularly suitable for rare cell populations, single-cell applications (scATAC-seq), and clinical samples.
- Furthermore, the method is fast, with library preparation achievable in just a few hours. The versatility and sensitivity of ATAC-seq have made it a widely adopted tool in epigenetics, developmental biology, cancer research, and immunology, enabling researchers to link chromatin accessibility with gene regulation at unprecedented resolution.
