Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

scientific article published on 28 May 2015

Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1038/SREP10469
P932PMC publication ID4447067
P698PubMed publication ID26020590
P5875ResearchGate publication ID277409362

P50authorGianluca De BellisQ51932877
Paolo LandiniQ57631601
Johannes GeiselmannQ59550672
Luca PetitiQ114422023
Elio RossiQ38800253
Clelia PeanoQ42876553
P2093author name stringJohannes Wolf
Thomas Egli
Stephan Lacour
Julien Demol
P2860cites workUltrafast and memory-efficient alignment of short DNA sequences to the human genomeQ21183894
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteriaQ24641843
Repression of small toxic protein synthesis by the Sib and OhsC small RNAsQ24648490
Regulator trafficking on bacterial transcription units in vivoQ24650920
The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulatorQ24653385
Conserved and variable functions of the sigmaE stress response in related genomesQ24811266
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR productsQ27860842
The Sequence Alignment/Map format and SAMtoolsQ27860966
Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigmQ28204689
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpDQ28255704
BEDTools: a flexible suite of utilities for comparing genomic featuresQ29547332
An efficient recombination system for chromosome engineering in Escherichia coliQ29615038
An integrated software system for analyzing ChIP-chip and ChIP-seq dataQ33382059
Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933Q33489852
Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coliQ33511247
Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in SalmonellaQ33584235
A previously uncharacterized gene, yjfO (bsmA), influences Escherichia coli biofilm formation and stress responseQ33928894
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarraysQ33937839
Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica serovar typhimuriumQ33994705
The RpoS-mediated general stress response in Escherichia coliQ34189650
A complex network of small non-coding RNAs regulate motility in Escherichia coliQ34296188
Activation and repression of transcription initiation in bacteriaQ34471533
Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity.Q35110872
In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elementsQ35120775
Complex regulation of the global regulatory gene csrA: CsrA-mediated translational repression, transcription from five promoters by Eσ⁷⁰ and Eσ(S), and indirect transcriptional activation by CsrAQ35296562
Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S.Q35607110
SoxS-dependent coregulation of ompN and ydbK in a multidrug-resistant Escherichia coli strain.Q54338279
The P1 promoter of the Escherichia coli rpoH gene is utilized by sigma 70 -RNAP or sigma s -RNAP depending on growth phase.Q54412452
Extensive functional overlap between sigma factors in Escherichia coli.Q54458231
Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12.Q54495569
Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.Q54517417
Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coliQ72915782
Characterization of the Escherichia coli sigma E regulonQ73684799
Promoter recognition and discrimination by EsigmaS RNA polymeraseQ77333834
RpoS- and OxyR-independent induction of HPI catalase at stationary phase in Escherichia coli and identification of rpoS mutations in common laboratory strainsQ35625190
General pathway for turning on promoters transcribed by RNA polymerases containing alternative sigma factorsQ36513675
The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase.Q36736448
Design and analysis of ChIP-seq experiments for DNA-binding proteinsQ37003887
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.Q37581716
SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences.Q37583338
Dynamics of microbial growth and cell composition in batch cultureQ37922220
sigmaS, a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition.Q38193405
Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coliQ38230079
Negative regulation by RpoS: a case of sigma factor competitionQ38332573
Identification of conserved, RpoS-dependent stationary-phase genes of Escherichia coli.Q39568776
Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coliQ40871460
Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivityQ41863185
Biofilm formation-gene expression relay system in Escherichia coli: modulation of sigmaS-dependent gene expression by the CsgD regulatory protein via sigmaS protein stabilizationQ42010076
Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase.Q42603337
Identification and analysis of the rpoS-dependent promoter of katE, encoding catalase HPII in Escherichia coliQ42658948
Molecular analysis of the regulation of csiD, a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on sigma s and requires activation by cAMP-CRP.Q42674368
What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma(S).Q43544098
Substitutions in region 2.4 of sigma70 allow recognition of the sigmaS-dependent aidB promoter.Q45126633
Control of RpoS in global gene expression of Escherichia coli in minimal media.Q46324887
RpoS regulation of gene expression during exponential growth of Escherichia coli K12.Q46833743
Specific growth rate and not cell density controls the general stress response in Escherichia coliQ47376881
Chemical Characterization, Spatial Distribution and Function of a Lipoprotein (Murein-Lipoprotein) of the E. coli Cell Wall. The Specific Effect of Trypsin on the Membrane StructureQ47787110
Expression dynamics of RpoS/Crl-dependent genes in Escherichia coliQ47983286
Role of the alternative sigma factors sigmaE and sigmaS in survival of Salmonella enterica serovar Typhimurium during starvation, refrigeration and osmotic shockQ50074789
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P407language of work or nameEnglishQ1860
P921main subjectEscherichia coliQ25419
P304page(s)10469
P577publication date2015-05-28
P1433published inScientific ReportsQ2261792
P1476titleCharacterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis
P478volume5

Reverse relations

cites work (P2860)
Q56888271A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
Q89997489BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus
Q47124668Broad-scale redistribution of mRNA abundance and transcriptional machinery in response to growth rate in Salmonella enterica serovar Typhimurium.
Q39159738Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology
Q57024870Dimethyl adenosine transferase (KsgA) contributes to cell-envelope fitness in Salmonella Enteritidis
Q99237710Diversity in E. coli (p)ppGpp Levels and Its Consequences
Q64264203Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology
Q41746387Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12
Q64067281Hfq-dependent mRNA unfolding promotes sRNA-based inhibition of translation
Q58700745Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes
Q34526027Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent to sdiA.
Q33704735Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation.
Q42423878Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli
Q41951797SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals
Q54208178Single-target regulators form a minor group of transcription factors in Escherichia coli K-12.
Q90132296Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli
Q93039158Structural basis for inhibition of a response regulator of σS stability by a ClpXP antiadaptor
Q39037038Tail-Anchored Inner Membrane Protein ElaB Increases Resistance to Stress While Reducing Persistence in Escherichia coli
Q36114219The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium.
Q57183085The small RNA, SdsR, acts as a novel type of toxin in Escherichia coli
Q28277062The target spectrum of SdsR small RNA in Salmonella
Q40987640The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase
Q92732858Trouble is coming: Signaling pathways that regulate general stress responses in bacteria

Search more.