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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Publication ,  Journal Article
Boyle, AP; Song, L; Lee, B-K; London, D; Keefe, D; Birney, E; Iyer, VR; Crawford, GE; Furey, TS
Published in: Genome Res
March 2011

Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find that footprints for specific transcription factors correlate with ChIP-seq enrichment and can accurately identify functional versus nonfunctional transcription factor motifs. We also find that footprints reveal a unique evolutionary conservation pattern that differentiates functional footprinted bases from surrounding DNA. Finally, detailed analysis of CTCF footprints suggests multiple modes of binding and a novel DNA binding motif upstream of the primary binding site.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

March 2011

Volume

21

Issue

3

Start / End Page

456 / 464

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • Protein Footprinting
  • Protein Binding
  • Promoter Regions, Genetic
  • Molecular Sequence Data
  • Humans
  • Genomics
  • Genome
  • Deoxyribonuclease I
 

Citation

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Boyle, A. P., Song, L., Lee, B.-K., London, D., Keefe, D., Birney, E., … Furey, T. S. (2011). High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res, 21(3), 456–464. https://doi.org/10.1101/gr.112656.110
Boyle, Alan P., Lingyun Song, Bum-Kyu Lee, Darin London, Damian Keefe, Ewan Birney, Vishwanath R. Iyer, Gregory E. Crawford, and Terrence S. Furey. “High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.Genome Res 21, no. 3 (March 2011): 456–64. https://doi.org/10.1101/gr.112656.110.
Boyle AP, Song L, Lee B-K, London D, Keefe D, Birney E, et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011 Mar;21(3):456–64.
Boyle, Alan P., et al. “High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.Genome Res, vol. 21, no. 3, Mar. 2011, pp. 456–64. Pubmed, doi:10.1101/gr.112656.110.
Boyle AP, Song L, Lee B-K, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011 Mar;21(3):456–464.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

March 2011

Volume

21

Issue

3

Start / End Page

456 / 464

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • Protein Footprinting
  • Protein Binding
  • Promoter Regions, Genetic
  • Molecular Sequence Data
  • Humans
  • Genomics
  • Genome
  • Deoxyribonuclease I