ATAC-Seq

ATAC-Seq

ATAC-Seq uses the Tn5 transposome to detect nucleosome-free regions of the genome. The method is commonly used, and optimized protocols are available for tissues, such as blood (Fast-ATAC)¹, neurons², biobank specimens³, and single cells (scATAC-seq⁴ and single-cell ATAC-seq⁵).

In this method, gDNA is incubated with Tn5 transposomes, which fragments it and adds adapters simultaneously, in open chromatin regions. Deep sequencing of the purified regions provides base-pair resolution of nucleosome-free regions in the genome.

Pros:

• Two-step protocol with no adapter ligation steps, gel purification, or crosslink reversal
• High signal-to-noise ratio compared to FAIRE-Seq

Cons:

• During mechanical sample processing, bound chromatin regions might open and be tagged by the transposome
• Only half of the molecules contain the adapters in the orientation required for PCR amplification
• Distance between adapter sites may not be optimal for PCR amplification⁶

• ATAC-Seq: Buenrostro J. D., Giresi P. G., Zaba L. C., Chang H. Y. and Greenleaf W. J. (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213-1218
• 1. Corces M. R., Buenrostro J. D., Wu B., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203
• 2. Milani P., Escalante-Chong R., Shelley B. C., et al. Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells. Sci Rep. 2016;6:25474
• 3. Scharer C. D., Blalock E. L., Barwick B. G., et al. ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naive SLE B cells. Sci Rep. 2016;6:27030
• 4. Buenrostro J. D., Wu B., Litzenburger U. M., et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015;523:486-490
• 5. Cusanovich D. A., Daza R., Adey A., et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015;348:910-914
• 6. Sos B. C., Fung H. L., Gao D. R., et al. Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biol. 2016;17:20

1. Chaitankar V., Karakulah G., Ratnapriya R., Giuste F. O., Brooks M. J., et al. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res. 2016;55:1-31
2. Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109

1. Bogdanovic O., Smits A. H., de la Calle Mustienes E., Tena J. J., Ford E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426
2. Corces M. R., Buenrostro J. D., Wu B., Greenside P. G., Chan S. M., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203
3. Miller C. L., Pjanic M., Wang T., et al. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci. Nat Commun. 2016;7:12092
4. Wu J., Huang B., Chen H., et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534:652-657
5. Ackermann A. M., Wang Z., Schug J., Naji A. and Kaestner K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab. 2016;5:233-244
6. Atianand M. K., Hu W., Satpathy A. T., et al. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell. 2016;165:1672-1685
7. Boukhaled G. M., Cordeiro B., Deblois G., et al. The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence. Cell Rep. 2016;16:1829-1837
8. de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116
9. Flynn R. A., Do B. T., Rubin A. J., et al. 7SK-BAF axis controls pervasive transcription at enhancers. Nat Struct Mol Biol. 2016;23:231-238
10. George J., Uyar A., Young K., et al. Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. Nat Commun. 2016;7:12166
11. Han D., Lu X., Shih A. H., et al. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016;63:711-719
12. Hay D., Hughes J. R., Babbs C., Davies J. O., Graham B. J., et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48:895-903
13. Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146
14. Kaufman C. K., Mosimann C., Fan Z. P., et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science. 2016;351:aad2197
15. Koues O. I., Collins P. L., Cella M., et al. Distinct Gene Regulatory Pathways for Human Innate versus Adaptive Lymphoid Cells. Cell. 2016;165:1134-1146
16. Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388
17. Proudhon C., Snetkova V., Raviram R., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169
18. Rendeiro A. F., Schmidl C., Strefford J. C., et al. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nat Commun. 2016;7:11938
19. Sebe-Pedros A., Ballare C., Parra-Acero H., et al. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell. 2016;165:1224-1237
20. Shih H. Y., Sciume G., Mikami Y., et al. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell. 2016;165:1120-1133
21. Smith J. D., Suresh S., Schlecht U., et al. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol. 2016;17:45
22. Wang L., Siegenthaler J. A., Dowell R. D. and Yi R. Foxc1 reinforces quiescence in self-renewing hair follicle stem cells. Science. 2016;351:613-617
23. Wang W., Org T., Montel-Hagen A., et al. MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis. Nat Commun. 2016;7:12376