home > bioproject > PRJDB675
identifier PRJDB675
type bioproject
organism Bacillus subtilis
title Genome footprinting by high-throughput sequencing (GeF-seq) resolves DNA-binding sites of targeted proteins with an accuracy comparable to in vitro DNase I footprinting
description Chromatin immunoprecipitation (ChIP) is a common method to map protein-binding sites in vivo. Combining this method with microarray (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows us to detect protein-binding sites scattered across the entire genome. An enduring challenge for these methods, however, is how to increase theirpositional resolution. Here, we describe a new method, “Genome Footprinting by high-throughput sequencing (GeF-seq)”, to attain high-resolution mapping of protein-binding sites by combining in vivo DNase I digestion and ChIP-seq. We used GeF-seq to determine the binding site of Bacillus subtilis transition state regulator, AbrB, across the genome. GeF-seq can resolve closely positioned binding sites that appear as single peak in the ChAP-chip and ChAP-seq methods. The binding sites of AbrB determined by GeF-seq are comparable to the resolution achieved by in vitroDNase I footprinting. The results enable us not only to confirm a minimal element in AbrB recognition sequences, previously determined as the AbrB binding motif (TGGNA) by in vitro analysis, but also to find new types of AbrB recognition sequences.
data type Other
sra-run  DRR003185
sra-submission  DRA000758
biosample  SAMD00010730
sra-study  DRP000789
sra-sample  DRS002605
sra-experiment  DRX002517
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2012-10-01T08:15:54+0000
dateModified 2014-01-30T06:52:41+0000
datePublished 2014-01-30T06:52:41+0000