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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Publication ,  Journal Article
Heintzman, ND; Stuart, RK; Hon, G; Fu, Y; Ching, CW; Hawkins, RD; Barrera, LO; Van Calcar, S; Qu, C; Ching, KA; Wang, W; Weng, Z; Green, RD ...
Published in: Nat Genet
March 2007

Eukaryotic gene transcription is accompanied by acetylation and methylation of nucleosomes near promoters, but the locations and roles of histone modifications elsewhere in the genome remain unclear. We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers are marked by monomethylation, but not trimethylation, of H3K4. We developed computational algorithms using these distinct chromatin signatures to identify new regulatory elements, predicting over 200 promoters and 400 enhancers within the 30-Mb region. This approach accurately predicted the location and function of independently identified regulatory elements with high sensitivity and specificity and uncovered a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2). Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome.

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Published In

Nat Genet

DOI

ISSN

1061-4036

Publication Date

March 2007

Volume

39

Issue

3

Start / End Page

311 / 318

Location

United States

Related Subject Headings

  • Solute Carrier Family 22 Member 5
  • Promoter Regions, Genetic
  • Organic Cation Transport Proteins
  • Models, Genetic
  • Humans
  • Histones
  • Genomics
  • Genome, Human
  • Enhancer Elements, Genetic
  • Developmental Biology
 

Citation

APA
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ICMJE
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Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., … Ren, B. (2007). Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet, 39(3), 311–318. https://doi.org/10.1038/ng1966
Heintzman, Nathaniel D., Rhona K. Stuart, Gary Hon, Yutao Fu, Christina W. Ching, R David Hawkins, Leah O. Barrera, et al. “Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.Nat Genet 39, no. 3 (March 2007): 311–18. https://doi.org/10.1038/ng1966.
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007 Mar;39(3):311–8.
Heintzman, Nathaniel D., et al. “Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.Nat Genet, vol. 39, no. 3, Mar. 2007, pp. 311–18. Pubmed, doi:10.1038/ng1966.
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007 Mar;39(3):311–318.

Published In

Nat Genet

DOI

ISSN

1061-4036

Publication Date

March 2007

Volume

39

Issue

3

Start / End Page

311 / 318

Location

United States

Related Subject Headings

  • Solute Carrier Family 22 Member 5
  • Promoter Regions, Genetic
  • Organic Cation Transport Proteins
  • Models, Genetic
  • Humans
  • Histones
  • Genomics
  • Genome, Human
  • Enhancer Elements, Genetic
  • Developmental Biology