ATAC

ATAC, in the context of biology, most often refers to ATAC-seq, the assay for transposase-accessible chromatin using sequencing. Introduced in 2013, ATAC-seq is a rapid method for map-ping open chromatin across the genome, enabling discovery of regulatory elements such as promoters and enhancers.

Principle and workflow: The method uses a hyperactive Tn5 transposase loaded with sequencing adapters to perform tagmentation in permeabilized nuclei. The enzyme preferentially cuts and inserts adapters into regions of accessible chromatin, producing small DNA fragments that reflect open chromatin. After transposition, the DNA is purified, PCR-amplified to add full adapters and indices, and then sequenced. The resulting reads are aligned to a reference genome, and regions with enriched signal are identified as accessible chromatin via peak calling. Fragment length distributions provide information about nucleosome positioning, and single-cell adaptations enable ATAC-seq at the single-cell level.

Applications and variants: ATAC-seq is widely used to annotate regulatory landscapes, study development, lineage specification, and disease-related changes in chromatin accessibility. Variants such as Omni-ATAC improve data quality in challenging samples. Single-cell ATAC-seq (scATAC-seq) reveals heterogeneity in chromatin accessibility across cell populations, enabling integrative analyses with transcriptomics to link regulatory elements to gene expression.

Strengths and limitations: ATAC-seq requires relatively few cells, is quick and cost-effective, and works with a range of tissue types. Limitations include transposase sequence bias, potential mitochondrial DNA contamination, and the need for careful normalization and controls in data analysis.

Other uses of the acronym ATAC exist in different fields, but this article focuses on the sequencing method.