12/20/2017 ATAC-seq - Wikipedia

ATACseq
ATACseq (Assay for Transposase-Accessible Chromatin using sequencing)
is a technique used in molecular biology to study chromatin accessibility. The
technique was first described in 2013,[1] as an alternative or complementary
method to MNase-seq (sequencing of micrococcal nuclease sensitive sites),
FAIRE-seq and DNAse-seq. It aims to identify accessible DNA regions,
equivalent to DNase I hypersensitive sites.

Contents
Description
Usage and computational analysis
Advantages
References
External source

Description
The key part of the ATAC-seq procedure is the action of the transposase Tn5 on
the genomic DNA of the sample.[2] Transposases are enzymes catalyzing the
movement of transposons to other parts in 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 [1](see external reference for
explanatory image).

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Usageandcomputationalanalysis
Transposons are believed to incorporate preferentially into genomic regions
free of nucleosomes (nucleosome-free regions) or stretches of exposed DNA in
general.[1] Thus enrichment of sequences from certain loci in the genome
indicates absence of DNA-binding proteins or nucleosome in the region.

An ATAC-seq experiment will typically produce millions of next generation

sequencing reads that can be successfully mapped on the reference genome.
After elimination of duplicates, each sequencing read points to a position on
the genome where one transposition (or cutting) event took place during the
experiment. One can then assign a cut count for each genomic position and
create a signal with base-pair resolution.

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 integrating further genomic and epigenomic data such as information
about histone modifications or evidence for active transcription.[1] 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.

An ATAC-seq experiment can also be used to infer nucleosome positions.[3]

Advantages
The advantages of ATAC-seq include:

1. Low requirements on the amount of the biological sample. 50,000 cells are
sufcient for this technique, as opposed to others like MNase-seq or
DNase-seq that require at least 1,000-fold more material.[2]

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2. Speed: The whole protocol requires 3 hours in total.[2]

References
1. Buenrostro, Jason D; Giresi, Paul G; Zaba, Lisa C; Chang, Howard Y;
Greenleaf, William J (6 October 2013). "Transposition of native chromatin
for fast and sensitive epigenomic proling of open chromatin, DNA-binding
proteins and nucleosome position" (https://www.ncbi.nlm.nih.gov/pmc/artic
les/PMC3959825). Nature Methods. 10 (12): 12131218.
doi:10.1038/nmeth.2688 (https://doi.org/10.1038%2Fnmeth.2688).
PMC3959825 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959825)
. PMID24097267 (https://www.ncbi.nlm.nih.gov/pubmed/24097267).
2. Buenrostro, Jason D.; Wu, Beijing; Chang, Howard Y.; Greenleaf, William
J. (January 2015). "ATAC-seq: A Method for Assaying Chromatin
Accessibility Genome-Wide". Current Protocols in Molecular Biology:
21.29.121.29.9. doi:10.1002/0471142727.mb2129s109 (https://doi.org/1
0.1002%2F0471142727.mb2129s109).
3. Schep, Alicia N.; Buenrostro, Jason D.; Denny, Sarah K.; Schwartz, Katja;
Sherlock, Gavin; Greenleaf, William J. (2015-08-27). "Structured
nucleosome ngerprints enable high-resolution mapping of chromatin
architecture within regulatory regions" (http://genome.cshlp.org/content/ea
rly/2015/08/27/gr.192294.115). Genome Research. 25: gr.192294.115.
doi:10.1101/gr.192294.115 (https://doi.org/10.1101%2Fgr.192294.115).
ISSN1088-9051 (https://www.worldcat.org/issn/1088-9051).
PMC4617971 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617971)
. PMID26314830 (https://www.ncbi.nlm.nih.gov/pubmed/26314830).

Externalsource
ATAC-seq probes open-chromatin state (gure) (http://www.nature.com/n
meth/journal/v10/n12/g_tab/nmeth.2688_F1.html)
ATAC-seq: Fast and sensitive epigenomic proling (http://greenleaf.stanfor
d.edu/portfolio_details_buenrostro_2013_nature_methods.html)
Too good to be true?! What can Nextera do for you? (http://bitesizebio.co
m/13567/too-good-to-be-true-what-can-nextera-do-for-you/)

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