Skip to main content
SpringerLink
Log in

Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq

  • Protocol
  • First Online:
Chromatin Accessibility

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2611))

Abstract

Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs genome-wide and tracking their dynamics across different cellular states and is the basis of numerous methods taking advantage of the preferential enzymatic cleavage/labeling of accessible DNA. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) has emerged as the most versatile and widely adaptable method and has been widely adopted as the standard tool for mapping open chromatin regions. Here, we discuss the current optimal practices and important considerations for carrying out ATAC-seq experiments, primarily in the context of mammalian systems.

Georgi K. Marinov and Zohar Shipony authors contributed equally to this work.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Luger K, Mäder AW, Richmond RK et al. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260

    Article  CAS  PubMed  Google Scholar 

  2. Wu C (1980) The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286(5776):854–860

    Article  CAS  PubMed  Google Scholar 

  3. Keene MA, Corces V, Lowenhaupt K et al. (1981) DNase I hypersensitive sites in Drosophila chromatin occur at the 5′ ends of regions of transcription. Proc Natl Acad Sci U S A 78:143–146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. McGhee JD, Wood WI, Dolan M et al. (1981) A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion. Cell 27:45–55

    Article  CAS  PubMed  Google Scholar 

  5. Dorschner MO, Hawrylycz M, Humbert R et al. (2004) High-throughput localization of functional elements by quantitative chromatin profiling. Nat Methods 1:219–225

    Article  CAS  PubMed  Google Scholar 

  6. Sabo PJ, Humbert R, Hawrylycz M et al. (2004) Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc Natl Acad Sci U S A 101:4537–4542

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sabo PJ, Kuehn MS, Thurman R et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3:511–518

    Article  CAS  PubMed  Google Scholar 

  8. Crawford GE, Holt IE, Whittle J et al. (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16:123–131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Boyle AP, Davis S, Shulha HP et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311–322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Thurman RE, Rynes E, Humbert R et al. (2012) The accessible chromatin landscape of the human genome. Nature 489:75–82

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kelly TK, Liu Y, Lay FD et al. (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22:2497–2506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Krebs AR, Imanci D, Hoerner L, Gaidatzis D et al. (2017) Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol Cell 67:411–422.e4

    Google Scholar 

  13. Shipony Z, Marinov GK, Swaffer MP et al. (2018) Long-range single-molecule mapping of chromatin accessibility in eukaryotes. bioRxiv 504662

    Google Scholar 

  14. Wang Y, Wang A, Liu Z et al. (2019) Single-molecule long-read sequencing reveals the chromatin basis of gene expression. Genome Res 29:1329–1342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Aughey GN, Estacio Gomez A, Thomson J et al. (2018) CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo. Elife 7:pii: e32341

    Google Scholar 

  16. Chereji RV, Eriksson PR, Ocampo J, Clark DJ (2019) DNA accessibility is not the primary determinant of chromatin-mediated gene regulation bioRxiv 639971

    Google Scholar 

  17. Ponnaluri VKC, Zhang G, Estéve PO et al. (2017) NicE-seq: high resolution open chromatin profiling. Genome Biol 18(1):122

    Article  PubMed  PubMed Central  Google Scholar 

  18. Umeyama T, Ito T (2017) DMS-seq for in vivo genome-wide mapping of protein-DNA interactions and nucleosome centers. Cell Rep 21:289–300

    Article  CAS  PubMed  Google Scholar 

  19. Timms RT, Tchasovnikarova IA, Lehner PJ (2019) Differential viral accessibility (DIVA) identifies alterations in chromatin architecture through large-scale mapping of lentiviral integration sites. Nat Protoc 14:153–170

    Article  CAS  PubMed  Google Scholar 

  20. Buenrostro JD, Giresi PG, Zaba LC et al. (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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Buenrostro JD, Wu B, Litzenburger UM et al. (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486–490

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cusanovich DA, Daza R, Adey A et al. (2015) Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348:910–914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Corces MR, Trevino AE, Hamilton EG et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14:959–962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Corces MR, Buenrostro JD, Wu B et al. (2016) Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet 48:1193–1203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Picelli S, Björklund AK, Reinius B et al. (2014) Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res 24:2033–2040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lu Z, Hofmeister BT, Vollmers C et al. (2017) Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res 45:e41

    Article  PubMed  Google Scholar 

  27. Maher KA, Bajic M, Kajala K et al. (2018) Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cell 30:15–36

    Article  CAS  PubMed  Google Scholar 

  28. Bajic M, Maher KA, Deal RB (2018) Identification of open chromatin regions in plant genomes using ATAC-seq. Methods Mol Biol 1675:183–201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Deal RB, Henikoff S (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18:1030–1040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Daugherty AC, Yeo RW, Buenrostro JD et al. (2017) Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Res 27:2096–2107

    Google Scholar 

  31. Schep AN, Buenrostro JD, Denny SK et al. (2015) Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res 25:1757–1770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Cusanovich DA, Reddington JP, Garfield DA et al. (2018) The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 555:538–542

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Cao J, Cusanovich DA, Ramani V et al. (2018) Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361:1380–1385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank members of the Greenleaf and Kundaje labs for many helpful discussions. This work was supported by NIH grants UM1HG009436 and P50HG007735 (to W.J.G.). WJG is a Chan Zuckerberg investigator. Z.S. is supported by EMBO Long-Term Fellowship EMBO ALTF 1119-2016 and by Human Frontier Science Program Long-Term Fellowship HFSP LT 000835/2017-L. G.K.M. was supported by the Stanford School of Medicine Dean’s Fellowship.

Author information

Authors and Affiliations

  1. Department of Genetics, Stanford University, Stanford, CA, USA

    Georgi K. Marinov & Zohar Shipony

  2. Department of Genetics, Stanford University, Stanford, CA, USA

    Anshul Kundaje

  3. Department of Computer Science, Stanford University, Stanford, CA, USA

    Anshul Kundaje

  4. Department of Genetics, Stanford University, Stanford, CA, USA

    William J. Greenleaf

  5. Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA

    William J. Greenleaf

  6. Department of Applied Physics, Stanford University, Stanford, CA, USA

    William J. Greenleaf

  7. Chan Zuckerberg Biohub, San Francisco, CA, USA

    William J. Greenleaf

Authors
  1. Georgi K. Marinov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zohar Shipony
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anshul Kundaje
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. William J. Greenleaf
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Georgi K. Marinov or William J. Greenleaf .

Editor information

Editors and Affiliations

  1. Stanford University, Stanford, CA, USA

    Georgi K. Marinov

  2. Stanford University, Stanford, CA, USA

    William J. Greenleaf

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Marinov, G.K., Shipony, Z., Kundaje, A., Greenleaf, W.J. (2023). Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq. In: Marinov, G.K., Greenleaf, W.J. (eds) Chromatin Accessibility. Methods in Molecular Biology, vol 2611. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2899-7_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2899-7_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2898-0

  • Online ISBN: 978-1-0716-2899-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation