@article{Boyle01032011,
author = {Boyle, Alan P. and Song, Lingyun and Lee, Bum-Kyu and London, Darin and Keefe, Damian and Birney, Ewan and Iyer, Vishwanath R. and Crawford, Gregory E. and Furey, Terrence S.}, 
title = {High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells},
volume = {21}, 
number = {3}, 
pages = {456-464}, 
year = {2011}, 
doi = {10.1101/gr.112656.110}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/21/3/456.abstract}, 
eprint = {http://genome.cshlp.org/content/21/3/456.full.pdf+html}, 
journal = {Genome Research} 
}