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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Genome Res. 2010 Nov 24;
Authors: Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS
Regulation of gene transcription in diverse cell types is largely determined by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNaseI 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 vs. non-functional 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.
PMID: 21106903 [PubMed - as supplied by publisher]
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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Genome Res. 2010 Nov 24;
Authors: Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS
Regulation of gene transcription in diverse cell types is largely determined by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNaseI 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 vs. non-functional 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.
PMID: 21106903 [PubMed - as supplied by publisher]
More...
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