TY  - JOUR
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
Y1  - 2011/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 456 
EP  - 464 
DO  - 10.1101/gr.112656.110 
VL  - 21 
IS  - 3 
UR  - http://genome.cshlp.org/content/21/3/456.abstract 
N2  - 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. 
ER  -