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Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.

Publication ,  Journal Article
Xi, H; Shulha, HP; Lin, JM; Vales, TR; Fu, Y; Bodine, DM; McKay, RDG; Chenoweth, JG; Tesar, PJ; Furey, TS; Ren, B; Weng, Z; Crawford, GE
Published in: PLoS Genet
August 2007

The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type-specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites is an accurate method for identifying the location of functional regulatory elements. We used a high throughput method called DNase-chip to identify 3,904 DNaseI HS sites from six cell types across 1% of the human genome. A significant number (22%) of DNaseI HS sites from each cell type are ubiquitously present among all cell types studied. Surprisingly, nearly all of these ubiquitous DNaseI HS sites correspond to either promoters or insulator elements: 86% of them are located near annotated transcription start sites and 10% are bound by CTCF, a protein with known enhancer-blocking insulator activity. We also identified a large number of DNaseI HS sites that are cell type specific (only present in one cell type); these regions are enriched for enhancer elements and correlate with cell type-specific gene expression as well as cell type-specific histone modifications. Finally, we found that approximately 8% of the genome overlaps a DNaseI HS site in at least one the six cell lines studied, indicating that a significant percentage of the genome is potentially functional.

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Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

August 2007

Volume

3

Issue

8

Start / End Page

e136

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Research Design
  • Repressor Proteins
  • Regulatory Elements, Transcriptional
  • Organ Specificity
  • Molecular Sequence Data
  • Microarray Analysis
  • K562 Cells
  • Insulator Elements
  • Humans
 

Citation

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Xi, H., Shulha, H. P., Lin, J. M., Vales, T. R., Fu, Y., Bodine, D. M., … Crawford, G. E. (2007). Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet, 3(8), e136. https://doi.org/10.1371/journal.pgen.0030136
Xi, Hualin, Hennady P. Shulha, Jane M. Lin, Teresa R. Vales, Yutao Fu, David M. Bodine, Ronald D. G. McKay, et al. “Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.PLoS Genet 3, no. 8 (August 2007): e136. https://doi.org/10.1371/journal.pgen.0030136.
Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 2007 Aug;3(8):e136.
Xi, Hualin, et al. “Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.PLoS Genet, vol. 3, no. 8, Aug. 2007, p. e136. Pubmed, doi:10.1371/journal.pgen.0030136.
Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RDG, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 2007 Aug;3(8):e136.

Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

August 2007

Volume

3

Issue

8

Start / End Page

e136

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Research Design
  • Repressor Proteins
  • Regulatory Elements, Transcriptional
  • Organ Specificity
  • Molecular Sequence Data
  • Microarray Analysis
  • K562 Cells
  • Insulator Elements
  • Humans