Skip to main content

Genome-Wide Mapping of DNase I Hypersensitive Sites in Plants

  • Protocol
  • First Online:
Plant Functional Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1284))

Abstract

Genomic regions associated with regulatory proteins are known to be highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). DNase-seq has become a powerful technique for genome-wide mapping of chromatin accessibility in eukaryotes with a sequenced genome. We have developed a DNase-seq procedure in plants. This procedure was adapted from the protocol originally developed for mammalian cell lines. It includes plant nuclei isolation, digestion of purified nuclei with DNase I, recovery of DNase-trimmed DNA fragments, DNase-seq library development, Illumina sequencing and data analysis. We also introduce a barcoding system for library preparation. We have conducted DNase-seq in both Arabidopsis thaliana and rice, and developed genome-wide open chromatin maps in both species. These DHS datasets have been used to detect footprints from regulatory protein binding and to reveal genome-wide nucleosome positioning patterns.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

Similar content being viewed by others

References

  1. Orphanides G, Reinberg D (2002) A unified theory of gene expression. Cell 108:439–451

    Article  CAS  PubMed  Google Scholar 

  2. Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128:707–719

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  4. Kodama Y, Nagaya S, Shinmyo A, Kato K (2007) Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin. Plant Cell Physiol 48:459–470

    Article  CAS  PubMed  Google Scholar 

  5. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Hua C, Man Y, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, O’Dorschner M, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3:511–518

    Article  CAS  PubMed  Google Scholar 

  6. Hesselberth JR, Chen XY, Zhang ZH, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6:283–289

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Crawford GE, Holt IE, Mullikin JC, Tai D, Green ED, Wolfsberg TG, Collins FS (2004) Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc Natl Acad Sci U S A 101:992–997

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA (2004) Genome-wide identification of DNasel hypersensitive sites using active chromatin sequence libraries. Proc Natl Acad Sci U S A 101:4537–4542

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA (2011) Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol 12:R43

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  Google Scholar 

  11. Zhang WL, Wu YF, Schnable JC, Zeng ZX, Freeling M, Crawford GE, Jiang JM (2012) High-resolution mapping of open chromatin in the rice genome. Genome Res 22:151–162

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Shu H, Gruissem W, Hennig L (2013) Measuring Arabidopsis chromatin accessibility using DNase I-polymerase chain reaction and DNase I-chip assays. Plant Physiol 162:1794–1801

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Omidbakhshfard MA, Winck FV, Arvidsson S, Riano-Pachon DM, Mueller-Roeber B (2014) A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana. J Integr Plant Biol 56:527–538

    Article  CAS  PubMed  Google Scholar 

  14. Pajoro A, Madrigal P, Muino JM, Matus JT, Jin J, Mecchia MA, Debernardi JM, Palatnik JF, Balazadeh S, Arif M, O’Maoiléidigh DS, Wellmer F, Krajewski P, Riechmann JL, Angenent GC, Kaufmann K (2014) Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol 15:R41

    Article  PubMed Central  PubMed  Google Scholar 

  15. Wu Y, Zhang W, Jiang J (2014) Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genet 10:e1004378

    Article  PubMed Central  PubMed  Google Scholar 

  16. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311–322

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Song LY, Crawford GE (2010) DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc 2010:pdb prot5384

    Google Scholar 

  18. Zhang WL, Zhang T, Wu YF, Jiang JM (2012) Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24:2719–2731

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed Central  PubMed  Google Scholar 

  21. McArthur M, Gerum S, Stamatoyannopoulos G (2001) Quantification of DNasel-sensitivity by real-time PCR: quantitative analysis of DNasel-hypersensitivity of the mouse beta-globin LCR. J Mol Biol 313:27–34

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by grant DBI-0923640 from the National Science Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jiming Jiang .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Zhang, W., Jiang, J. (2015). Genome-Wide Mapping of DNase I Hypersensitive Sites in Plants. In: Alonso, J., Stepanova, A. (eds) Plant Functional Genomics. Methods in Molecular Biology, vol 1284. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2444-8_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2444-8_4

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2443-1

  • Online ISBN: 978-1-4939-2444-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics