nature.com

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays - Nature Methods

  • ️Stamatoyannopoulos, John A
  • ️Wed Jun 21 2006

Abstract

Localized accessibility of critical DNA sequences to the regulatory machinery is a key requirement for regulation of human genes. Here we describe a high-resolution, genome-scale approach for quantifying chromatin accessibility by measuring DNase I sensitivity as a continuous function of genome position using tiling DNA microarrays (DNase-array). We demonstrate this approach across 1% (∼30 Mb) of the human genome, wherein we localized 2,690 classical DNase I hypersensitive sites with high sensitivity and specificity, and also mapped larger-scale patterns of chromatin architecture. DNase I hypersensitive sites exhibit marked aggregation around transcriptional start sites (TSSs), though the majority mark nonpromoter functional elements. We also developed a computational approach for visualizing higher-order features of chromatin structure. This revealed that human chromatin organization is dominated by large (100–500 kb) 'superclusters' of DNase I hypersensitive sites, which encompass both gene-rich and gene-poor regions. DNase-array is a powerful and straightforward approach for systematic exposition of the cis-regulatory architecture of complex genomes.

This is a preview of subscription content, access via your institution

Access options

Subscribe to this journal

Receive 12 print issues and online access

$259.00 per year

only $21.58 per issue

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF

Prices may be subject to local taxes which are calculated during checkout

Additional access options:

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

References

  1. Felsenfeld, G. Chromatin as an essential part of the transcriptional mechanism. Nature 355, 219–224 (1992).

    Article  CAS  Google Scholar 

  2. Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448–453 (2003).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Keene, M.A., Corces, V., Lowenhaupt, K. & Elgin, S.C. DNase I hypersensitive sites in Drosophila chromatin occur at the 5′ ends of regions of transcription. Proc. Natl. Acad. Sci. USA 78, 143–146 (1981).

    Article  CAS  Google Scholar 

  5. McGhee, J.D., Wood, W.I., Dolan, M., Engel, J.D. & Felsenfeld, G. 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 (1981).

    Article  CAS  Google Scholar 

  6. Gross, D.S. & Garrard, W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988).

    Article  CAS  Google Scholar 

  7. Li, Q., Peterson, K.R., Fang, X. & Stamatoyannopoulos, G. Locus control regions. Blood 100, 3077–3086 (2002).

    Article  CAS  Google Scholar 

  8. Weintraub, H. & Groudine, M. Chromosomal subunits in active genes have an altered conformation. Science 193, 848–856 (1976).

    Article  CAS  Google Scholar 

  9. Felsenfeld, G. et al. Chromatin boundaries and chromatin domains. Cold Spring Harb. Symp. Quant. Biol. 69, 245–250 (2004).

    Article  CAS  Google Scholar 

  10. Sproul, D., Gilbert, N. & Bickmore, W.A. The role of chromatin structure in regulating the expression of clustered genes. Nat. Rev. Genet. 6, 775–781 (2005).

    Article  CAS  Google Scholar 

  11. The Encode Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636–640 (2004).

  12. Elgin, S.C. The formation and function of DNase I hypersensitive sites in the process of gene activation. J. Biol. Chem. 263, 19259–19262 (1988).

    CAS  PubMed  Google Scholar 

  13. Dorschner, M.O. et al. High-throughput localization of functional elements by quantitative chromatin profiling. Nat. Methods 1, 219–225 (2004).

    Article  CAS  Google Scholar 

  14. Lee, G.R., Fields, P.E., Griffin, T.J. & Flavell, R.A. Regulation of the Th2 cytokine locus by a locus control region. Immunity 19, 145–153 (2003).

    Article  CAS  Google Scholar 

  15. Lee, G.R., Spilianakis, C.G. & Flavell, R.A. Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. Nat. Immunol. 6, 42–48 (2005).

    Article  CAS  Google Scholar 

  16. Loots, G.G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136–140 (2000).

    Article  CAS  Google Scholar 

  17. Ansel, K.M. et al. Deletion of a conserved Il4 silencer impairs T helper type 1-mediated immunity. Nat. Immunol. 5, 1251–1259 (2004).

    Article  CAS  Google Scholar 

  18. Smale, S.T. & Kadonaga, J.T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72, 449–479 (2003).

    Article  CAS  Google Scholar 

  19. West, A.G. & Fraser, P. Remote control of gene transcription. Hum. Mol. Genet. 14 (Spec. No. 1), R101–111 (2005).

    Article  CAS  Google Scholar 

  20. Yelin, R. et al. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21, 379–386 (2003).

    Article  CAS  Google Scholar 

  21. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509 (2004).

    Article  CAS  Google Scholar 

  22. Katayama, S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564–1566 (2005).

    Article  Google Scholar 

  23. Hinrichs, A.S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590–D598 (2006).

    Article  CAS  Google Scholar 

  24. Percival, D.B. Wavelet methods for time series analysis (Cambridge University Press, Cambridge, 2000).

    Book  Google Scholar 

  25. Korenberg, J.R. et al. Down syndrome phenotypes: the consequences of chromosomal imbalance. Proc. Natl. Acad. Sci. USA 91, 4997–5001 (1994).

    Article  CAS  Google Scholar 

  26. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000).

    Article  CAS  Google Scholar 

  27. Sabo, P.J. et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc. Natl. Acad. Sci. USA 101, 16837–16842 (2004).

    Article  CAS  Google Scholar 

  28. Sabo, P.J. et al. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. USA 101, 4537–4542 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the US National Institute of General Medical Sciences and the National Human Genome Research Institute to J.A.S. and W.S.N.

Author information

Author notes

  1. Peter J Sabo and Michael S Kuehn: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genome Sciences, University of Washington, 1705 NE Pacific St., Box 357730, Seattle, 98195, Washington, USA

    Peter J Sabo, Michael S Kuehn, Robert Thurman, Jeff Goldy, Andrew Haydock, Molly Weaver, Anthony Shafer, Kristin Lee, Fidencio Neri, Richard Humbert, Michael O Dorschner, William S Noble & John A Stamatoyannopoulos

  2. Division of Medical Genetics, Department of Medicine, University of Washington, 1705 NE Pacific St., Box 357730, Seattle, 98195, Washington, USA

    Michael S Kuehn, Robert Thurman, Brett E Johnson, Ericka M Johnson, Hua Cao, Man Yu, Elizabeth Rosenzweig & Patrick A Navas

  3. Nimblegen Systems, Inc., 1 Science Court, Madison, 53711, Wisconsin, USA

    Michael A Singer, Todd A Richmond & Roland D Green

  4. Department of Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

    Michael McArthur

  5. Allen Institute for Brain Sciences, 551 N. 34th Street, Seattle, 98103, Washington, USA

    Michael Hawrylycz

Authors

  1. Peter J Sabo

    You can also search for this author in PubMed Google Scholar

  2. Michael S Kuehn

    You can also search for this author in PubMed Google Scholar

  3. Robert Thurman

    You can also search for this author in PubMed Google Scholar

  4. Brett E Johnson

    You can also search for this author in PubMed Google Scholar

  5. Ericka M Johnson

    You can also search for this author in PubMed Google Scholar

  6. Hua Cao

    You can also search for this author in PubMed Google Scholar

  7. Man Yu

    You can also search for this author in PubMed Google Scholar

  8. Elizabeth Rosenzweig

    You can also search for this author in PubMed Google Scholar

  9. Jeff Goldy

    You can also search for this author in PubMed Google Scholar

  10. Andrew Haydock

    You can also search for this author in PubMed Google Scholar

  11. Molly Weaver

    You can also search for this author in PubMed Google Scholar

  12. Anthony Shafer

    You can also search for this author in PubMed Google Scholar

  13. Kristin Lee

    You can also search for this author in PubMed Google Scholar

  14. Fidencio Neri

    You can also search for this author in PubMed Google Scholar

  15. Richard Humbert

    You can also search for this author in PubMed Google Scholar

  16. Michael A Singer

    You can also search for this author in PubMed Google Scholar

  17. Todd A Richmond

    You can also search for this author in PubMed Google Scholar

  18. Michael O Dorschner

    You can also search for this author in PubMed Google Scholar

  19. Michael McArthur

    You can also search for this author in PubMed Google Scholar

  20. Michael Hawrylycz

    You can also search for this author in PubMed Google Scholar

  21. Roland D Green

    You can also search for this author in PubMed Google Scholar

  22. Patrick A Navas

    You can also search for this author in PubMed Google Scholar

  23. William S Noble

    You can also search for this author in PubMed Google Scholar

  24. John A Stamatoyannopoulos

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to John A Stamatoyannopoulos.

Ethics declarations

Competing interests

R.D.G. is an employee of NimbleGen Systems, a manufacturer of microarrays, which potentially stands to benefit from the results published in this article.

Supplementary information

About this article

Cite this article

Sabo, P., Kuehn, M., Thurman, R. et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3, 511–518 (2006). https://doi.org/10.1038/nmeth890

Download citation

  • Received: 12 April 2006

  • Accepted: 22 May 2006

  • Published: 21 June 2006

  • Issue Date: July 2006

  • DOI: https://doi.org/10.1038/nmeth890

Associated content