RT Journal
A1 Boyle, Alan P.
A1 Song, Lingyun
A1 Lee, Bum-Kyu
A1 London, Darin
A1 Keefe, Damian
A1 Birney, Ewan
A1 Iyer, Vishwanath R.
A1 Crawford, Gregory E.
A1 Furey, Terrence S.
T1 High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
JF Genome Research 
JO Genome Research 
YR 2011 
FD March 01 
VO 21 
IS 3 
SP 456 
OP 464 
DO 10.1101/gr.112656.110 
UL http://genome.cshlp.org/content/21/3/456.abstract 
AB 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.