genomics / epigenetics · BEGINNER LESSON
ATAC-seq
ATAC-seq, or assay for transposase-accessible chromatin using sequencing, is a DNA sequencing method that maps open chromatin regions. It uses the Tn5 transposase to insert sequencing adaptors into accessible DNA so those regions can be read and measured.
What ATAC-seq is and what it measures
ATAC-seq measures chromatin accessibility, meaning how open or closed DNA is inside the nucleus. Chromatin is DNA plus proteins; when it is open, regulatory proteins such as transcription factors can bind more easily. ATAC-seq identifies genomic regions that are accessible in a given cell population, so it is used to compare different cell types, tissues, or conditions. It is especially useful when only a small number of cells are available. [0,1,2]
[1] Investigating chromatin accessibility during development and ... [2] ATAC-seq Optimization for Cancer Epigenetics Research - PMC [3] www.ncbi.nlm.nih.gov › pmc › articlesProtocol for Bulk-ATAC sequencing in head and neck squamous ...
How the method works
The core step is tagmentation: the hyperactive Tn5 transposase preferentially enters open chromatin, cuts the DNA, and inserts sequencing adaptors at the same time. The tagged DNA fragments are then purified, amplified by PCR, and read by high-throughput or next-generation sequencing. When the reads are aligned to a genome, accessible regions appear as peaks, and read depth in a peak generally rises with accessibility. With enough sequencing depth, protected subregions inside peaks can suggest where transcription factors were bound. [0,1,2]
[1] Investigating chromatin accessibility during development and ... [2] ATAC-seq Optimization for Cancer Epigenetics Research - PMC [3] www.ncbi.nlm.nih.gov › pmc › articlesProtocol for Bulk-ATAC sequencing in head and neck squamous ...
Limits and interpretation
ATAC-seq is fast and works with low input, but it has limits. It cannot by itself tell whether an accessible region is an enhancer, silencer, or promoter. It can also contain many mitochondrial reads, and Tn5 can introduce sequence or structural bias. Bulk ATAC-seq averages over many cells, so it does not show cell-by-cell differences unless it is adapted for single-cell analysis. [0,1,2]
[1] Investigating chromatin accessibility during development and ... [2] ATAC-seq Optimization for Cancer Epigenetics Research - PMC [3] www.ncbi.nlm.nih.gov › pmc › articlesProtocol for Bulk-ATAC sequencing in head and neck squamous ...
SEE THE IDEA
ATAC-seq workflow
DNA regions that are less packed and easier for proteins to reach.
Enzyme that cuts accessible DNA and inserts sequencing adaptors.
Fragments are copied and then read by next-generation sequencing.
Aligned reads form peaks that mark accessible regions.
Open chromatin is tagged by Tn5, converted into a sequencing library, and then readout as peaks after alignment.
ATAC-seq turns accessible DNA into sequence reads that can be plotted as regions of chromatin accessibility. [0,1,2]
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.