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

Publication ,  Journal Article
Crawford, GE; Holt, IE; Whittle, J; Webb, BD; Tai, D; Davis, S; Margulies, EH; Chen, Y; Bernat, JA; Ginsburg, D; Zhou, D; Luo, S; Vasicek, TJ ...
Published in: Genome Res
January 2006

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, approximately 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.

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Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

January 2006

Volume

16

Issue

1

Start / End Page

123 / 131

Location

United States

Related Subject Headings

  • Umbilical Veins
  • Sequence Tagged Sites
  • Sequence Analysis, DNA
  • Regulatory Elements, Transcriptional
  • Organ Specificity
  • Lymphocytes
  • Humans
  • Hepatocytes
  • Hela Cells
  • HeLa Cells
 

Citation

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MLA
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Crawford, G. E., Holt, I. E., Whittle, J., Webb, B. D., Tai, D., Davis, S., … Collins, F. S. (2006). Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res, 16(1), 123–131. https://doi.org/10.1101/gr.4074106
Crawford, Gregory E., Ingeborg E. Holt, James Whittle, Bryn D. Webb, Denise Tai, Sean Davis, Elliott H. Margulies, et al. “Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).Genome Res 16, no. 1 (January 2006): 123–31. https://doi.org/10.1101/gr.4074106.
Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123–31.
Crawford, Gregory E., et al. “Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).Genome Res, vol. 16, no. 1, Jan. 2006, pp. 123–31. Pubmed, doi:10.1101/gr.4074106.
Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123–131.

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

January 2006

Volume

16

Issue

1

Start / End Page

123 / 131

Location

United States

Related Subject Headings

  • Umbilical Veins
  • Sequence Tagged Sites
  • Sequence Analysis, DNA
  • Regulatory Elements, Transcriptional
  • Organ Specificity
  • Lymphocytes
  • Humans
  • Hepatocytes
  • Hela Cells
  • HeLa Cells