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

Journal Article (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

  • PMC3044859

Electronic International Standard Serial Number (EISSN)

  • 1549-5469

Digital Object Identifier (DOI)

  • 10.1101/gr.112656.110


  • eng

Conference Location

  • United States