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

被引：22

作者：

Efromovich, Sam ^{[1
]}

Grainger, David ^{[2
]}

Bodenmiller, Diane ^{[3
]}

Spiro, Stephen ^{[4
]}

机构：

[1] Univ Texas Dallas, Dept Math Sci, Richardson, TX 75083 USA

[2] Univ Birmingham, Sch Biosci, Birmingham, W Midlands, England

[3] Georgia Inst Technol, Sch Biol, Atlanta, GA 30332 USA

[4] Univ Texas Dallas, Dept Mol & Cell Biol, Richardson, TX 75083 USA

来源：

GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B | 2008年 / 437卷

基金：

英国惠康基金;

关键词：

D O I：

10.1016/S0076-6879(07)37012-2

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. colichromosome using chromatin immunoprecipitation and microarray analysis. The methods are applicable, with suitable modifications, to any regulatory protein and any organism.

引用

页码：211 / 233

页数：23

共 35 条

[1] Maintenance of nitric oxide and redox homeostasis by the Salmonella flavohemoglobin Hmp [J].

Bang, Iel-Soo ;

Liu, Limin ;

Vazquez-Torres, Andres ;

Crouch, Marie-Laure ;

Stamler, Jonathan S. ;

Fang, Ferric C. .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2006, 281 (38) :28039-28047

[2] Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome [J].

Bieda, M ;

Xu, XQ ;

Singer, MA ;

Green, R ;

Farnham, PJ .

GENOME RESEARCH, 2006, 16 (05) :595-605

[3] The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator [J].

Bodenmiller, DM ;

Spiro, S .

JOURNAL OF BACTERIOLOGY, 2006, 188 (03) :874-881

[4] ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data [J].

Buck, MJ ;

Nobel, AB ;

Lieb, JD .

GENOME BIOLOGY, 2005, 6 (11)

[5] ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments [J].

Buck, MJ ;

Lieb, JD .

GENOMICS, 2004, 83 (03) :349-360

[6] Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA [J].

Cairrao, F ;

Cruz, A ;

Mori, H ;

Arraiano, CM .

MOLECULAR MICROBIOLOGY, 2003, 50 (04) :1349-1360

[7] Nitric oxide formation by Escherichia coli -: Dependence on nitrite reductase, the NO-sensing regulator FNR, and flavohemoglobin Hmp [J].

Corker, H ;

Poole, RK .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (34) :31584-31592

[8] A non-haem iron centre in the transcription factor NorR senses nitric oxide [J].

D'Autréaux, B ;

Tucker, NP ;

Dixon, R ;

Spiro, S .

NATURE, 2005, 437 (7059) :769-772

[9] One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products [J].

Datsenko, KA ;

Wanner, BL .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (12) :6640-6645

[10] Data-driven and optimal denoising of a signal and recovery of its derivative using multiwavelets [J].

Efromovich, S ;

Lakey, J ;

Pereyra, MC ;

Tymes, N .

IEEE TRANSACTIONS ON SIGNAL PROCESSING, 2004, 52 (03) :628-635

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