Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

  1. Gregory E. Crawford1,
  2. Ingeborg E. Holt1,
  3. James Whittle1,
  4. Bryn D. Webb1,
  5. Denise Tai1,
  6. Sean Davis1,
  7. Elliott H. Margulies1,
  8. YiDong Chen1,
  9. John A. Bernat2,
  10. David Ginsburg2,
  11. Daixing Zhou3,
  12. Shujun Luo3,
  13. Thomas J. Vasicek3,
  14. Mark J. Daly4,
  15. Tyra G. Wolfsberg1, and
  16. Francis S. Collins1,5
  1. 1 National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
  2. 2 University of Michigan, Department of Human Genetics, Ann Arbor, Michigan 48109, USA
  3. 3 Solexa, Inc., Hayward, California 94545, USA
  4. 4 Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA

Abstract

A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear chromatin is a powerful and well-established method of identifying many different types of regulatory elements, but in the past it has been limited to analysis of single loci. We have recently described a protocol to generate a genome-wide library of DNase HS sites. Here, we report high-throughput analysis, using massively parallel signature sequencing (MPSS), of 230,000 tags from a DNase library generated from quiescent human CD4+ T cells. Of the tags that uniquely map to the genome, we identified 14,190 clusters of sequences that group within close proximity to each other. By using a real-time PCR strategy, we determined that the majority of these clusters represent valid DNase HS sites. Approximately 80% of these DNase HS sites uniquely map within one or more annotated regions of the genome believed to contain regulatory elements, including regions 2 kb upstream of genes, CpG islands, and highly conserved sequences. Most DNase HS sites identified in CD4+ T cells are also HS in CD8+ T cells, B cells, hepatocytes, human umbilical vein endothelial cells (HUVECs), and HeLa cells. However, ∼10% of the DNase HS sites are lymphocyte specific, indicating that this procedure can identify gene regulatory elements that control cell type specificity. This strategy, which can be applied to any cell line or tissue, will enable a better understanding of how chromatin structure dictates cell function and fate.

Footnotes

  • Article published online ahead of print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.4074106.

  • 5 Corresponding author. E-mail francisc{at}exchange.nih.gov. fax (301) 496-0837.

    • Accepted September 16, 2005.
    • Received April 27, 2005.
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