High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Genome Res
; 21(3): 456-64, 2011 Mar.
Article
de En
| MEDLINE
| ID: mdl-21106903
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.
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Facteurs de transcription
/
Prise d'empreintes protéiques
/
Protéines de liaison à l'ADN
Type d'étude:
Prognostic_studies
Limites:
Humans
Langue:
En
Journal:
Genome Res
Sujet du journal:
BIOLOGIA MOLECULAR
/
GENETICA
Année:
2011
Type de document:
Article
Pays d'affiliation:
États-Unis d'Amérique