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


Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Boyle, AP; Song, L; Lee, B-K; London, D; Keefe, D; Birney, E; Iyer, VR; Crawford, GE; Furey, TS

Published Date

  • March 2011

Published In

Volume / Issue

  • 21 / 3

Start / End Page

  • 456 - 464

PubMed ID

  • 21106903

Pubmed Central ID

  • 21106903

Electronic International Standard Serial Number (EISSN)

  • 1549-5469

Digital Object Identifier (DOI)

  • 10.1101/gr.112656.110


  • eng

Conference Location

  • United States