Methods Enzymol. 2008;437:211-33.

Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR.

Efromovich S, Grainger D, Bodenmiller D, Spiro S.

Source

Department of Mathematical Sciences, University of Texas at Dallas, Richardson, Texas, USA.

Abstract

NsrR is a nitric oxide-sensitive regulator of transcription. In Escherichia coli, NsrR is a repressor of the hmp gene encoding the flavohemoglobin that detoxifies nitric oxide. Three other transcription units (ytfE, ygbA, and hcp-hcr) are known to be subject to regulation by NsrR. This chapter describes experimental and statistical protocols used to identify NsrR-binding sites in the E. coli chromosome using chromatin immunoprecipitation and microarray analysis. The methods are applicable, with suitable modifications, to any regulatory protein and any organism.

PMID:: 18433631; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

MeSH Terms

Substances

Grant Support

Wellcome Trust/United Kingdom

LinkOut - more resources

Molecular Biology Databases

NITRIC OXIDE - HSDB

Supplemental Content

Save items

Related citations in PubMed

The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase. [J Bacteriol. 2007]
The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase.
Filenko N, Spiro S, Browning DF, Squire D, Overton TW, Cole J, Constantinidou C. J Bacteriol. 2007 Jun; 189(12):4410-7. Epub 2007 Apr 20.
NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility. [Mol Microbiol. 2009]
NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility.
Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S. Mol Microbiol. 2009 Aug; 73(4):680-94. Epub 2009 Jul 27.
The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator. [J Bacteriol. 2006]
The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator.
Bodenmiller DM, Spiro S. J Bacteriol. 2006 Feb; 188(3):874-81.
Review Global regulators of transcription in Escherichia coli: mechanisms of action and methods for study. [Adv Appl Microbiol. 2008]
Review Global regulators of transcription in Escherichia coli: mechanisms of action and methods for study.
Grainger DC, Busby SJ. Adv Appl Microbiol. 2008; 65:93-113.
Review Characterization of the nitric oxide-reactive transcriptional activator NorR. [Methods Enzymol. 2008]
Review Characterization of the nitric oxide-reactive transcriptional activator NorR.
D'Autréaux B, Tucker N, Spiro S, Dixon R. Methods Enzymol. 2008; 437:235-51.

See reviews... See all...

Cited by 5 PubMed Central articles

Genome-wide identification of in vivo binding sites of GlxR, a cyclic AMP receptor protein-type regulator in Corynebacterium glutamicum. [J Bacteriol. 2011]
Genome-wide identification of in vivo binding sites of GlxR, a cyclic AMP receptor protein-type regulator in Corynebacterium glutamicum.
Toyoda K, Teramoto H, Inui M, Yukawa H. J Bacteriol. 2011 Aug; 193(16):4123-33. Epub 2011 Jun 10.
Review Iron-containing transcription factors and their roles as sensors. [Curr Opin Chem Biol. 2011]
Review Iron-containing transcription factors and their roles as sensors.
Fleischhacker AS, Kiley PJ. Curr Opin Chem Biol. 2011 Apr; 15(2):335-41. Epub 2011 Feb 1.
ChIP on Chip: surprising results are often artifacts. [BMC Genomics. 2010]
ChIP on Chip: surprising results are often artifacts.
Waldminghaus T, Skarstad K. BMC Genomics. 2010 Jul 5; 11:414. Epub 2010 Jul 5.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Gene
Gene records that cite the current articles. Citations in Gene are added manually by NCBI or imported from outside public resources.
Gene (GeneRIF)
Gene records that have the current articles as Reference into Function citations (GeneRIFs). NLM staff reviewing the literature while indexing MEDLINE add GeneRIFs manually.
Nucleotide (Weighted)
Nucleotide records associated with the current articles through the Gene database. These are the related sequences on the Gene record that are added manually by NCBI.
Protein (RefSeq)
NCBI protein Reference Sequences (RefSeqs) that are cited in the current articles, included in the corresponding Gene Reference into Function, or that include the PubMed articles as references.
Protein (Weighted)
Protein records associated with the current articles through related Gene database records. These are the related sequences on the Gene record that are added manually by NCBI.
Protein Clusters
Clusters of related proteins from the Protein Clusters database that cite the current articles. Sources of references in Protein Clusters include the associated Gene and Conserved Domain records as well as NCBI added citations.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Taxonomy via GenBank
Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).
GEO Profiles
Gene Expression Omnibus (GEO) Profiles of molecular abundance data. The current articles are references on the Gene record associated with the GEO profile.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Genome-wide identification of binding sites for the nitric oxide-sensitive trans...
Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR.
Methods Enzymol. 2008 ;437:211-33.

PubMed
[Perioperative fluid therapy--what new?].
[Perioperative fluid therapy--what new?].
Ugeskr Laeger. 2008 Apr 7 ;170(15):1237-9.

PubMed
Fatty acids and oxidative stress in psychiatric disorders.
Fatty acids and oxidative stress in psychiatric disorders.
BMC Psychiatry. 2008 Apr 17 ;8 Suppl 1:S5.

PubMed
Androgenic dependence of exophytic tumor growth in a transgenic mouse model of b...
Androgenic dependence of exophytic tumor growth in a transgenic mouse model of bladder cancer: a role for thrombospondin-1.
BMC Urol. 2008 Apr 23 ;8:7.

PubMed
Platelet-delivered factor VIII provides limited resistance to anti-factor VIII i...
Platelet-delivered factor VIII provides limited resistance to anti-factor VIII inhibitors.
J Thromb Haemost. 2008 Jul ;6(7):1160-6. Epub 2008 Jul 1 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: