NDLI: High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.

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High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Chumsakul, Onuma Nakamura, Kensuke Kurata, Tetsuya Sakamoto, Tomoaki Hobman, Jon L. Ogasawara, Naotake Oshima, Taku Ishikawa, Shu
Description	Country affiliation: Japan Author Affiliation: Chumsakul O ( Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan.)
Abstract	Accurate identification of the DNA-binding sites of transcription factors and other DNA-binding proteins on the genome is crucial to understanding their molecular interactions with DNA. Here, we describe a new method: Genome Footprinting by high-throughput sequencing (GeF-seq), which combines in vivo DNase I digestion of genomic DNA with ChIP coupled with high-throughput sequencing. We have determined the in vivo binding sites of a Bacillus subtilis global regulator, AbrB, using GeF-seq. This method shows that exact DNA-binding sequences, which were protected from in vivo DNase I digestion, were resolved at a comparable resolution to that achieved by in vitro DNase I footprinting, and this was simply attained without the necessity of prediction by peak-calling programs. Moreover, DNase I digestion of the bacterial nucleoid resolved the closely positioned AbrB-binding sites, which had previously appeared as one peak in ChAP-chip and ChAP-seq experiments. The high-resolution determination of AbrB-binding sites using GeF-seq enabled us to identify bipartite TGGNA motifs in 96% of the AbrB-binding sites. Interestingly, in a thousand binding sites with very low-binding intensities, single TGGNA motifs were also identified. Thus, GeF-seq is a powerful method to elucidate the molecular mechanism of target protein binding to its cognate DNA sequences.
File Format	HTM / HTML
ISSN	13402838
e-ISSN	17561663
DOI	10.1093/dnares/dst013
Journal	DNA Research
Issue Number	4
Volume Number	20
Language	English
Publisher	Oxford University Press
Publisher Date	2013-08-01
Publisher Place	Great Britain (UK)
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Molecular Biology Bacillus Subtilis Metabolism Bacterial Proteins Conserved Sequence Dna-binding Proteins Sequence Analysis, Dna Transcription Factors Chemistry Genetics Binding Sites Chromatin Immunoprecipitation Dna Footprinting Deoxyribonuclease I High-throughput Nucleotide Sequencing Molecular Sequence Data Nucleotide Motifs Protein Binding Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Molecular Biology

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