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  • 1
    In: Nature Reviews Microbiology, 2010, Vol.8(3), p.185
    Description: Emerging models of the bacterial nucleoid show that nucleoid-associated proteins (NAPs) and transcription contribute in combination to the dynamic nature of nucleoid structure. NAPs and other DNA-binding proteins that display gene-silencing and anti-silencing activities are emerging as key antagonistic regulators of nucleoid structure. Furthermore, it is becoming clear that the boundary between NAPs and conventional transcriptional regulators is quite blurred and that NAPs facilitate the evolution of novel gene regulatory circuits. Here, NAP biology is considered from the standpoints of both gene regulation and nucleoid structure.
    Keywords: Dna Replication -- Physiological Aspects ; Dna Replication -- Research ; Bacterial Genetics -- Research ; Dna Binding Proteins -- Physiological Aspects ; Dna Binding Proteins -- Research ; Nucleosomes -- Physiological Aspects ; Nucleosomes -- Genetic Aspects;
    ISSN: 1740-1526
    E-ISSN: 17401534
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  • 2
    Language: English
    In: Molecular Microbiology, Sept, 2012, Vol.85, p.1072(18)
    Keywords: Transcription (Genetics) -- Genetic Aspects ; Transcription (Genetics) -- Analysis ; Bacterial Genetics -- Genetic Aspects ; Bacterial Genetics -- Analysis ; Preventive Medicine -- Analysis ; Dna Binding Proteins -- Genetic Aspects ; Dna Binding Proteins -- Analysis ; Genes -- Genetic Aspects ; Genes -- Analysis ; Rna -- Genetic Aspects ; Rna -- Analysis ; Salmonella -- Analysis
    ISSN: 0950-382X
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Molecular Microbiology, Sept, 2012, Vol.85, p.1072(18)
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.08162.x/abstract Byline: Shane C. Dillon(1), Elena Espinosa(3), Karsten Hokamp(2), David W. Ussery(4), Josep Casadesus(3), Charles J. Dorman(1) Summary We report the first investigation of the binding of the Salmonella enterica LeuO LysR-type transcription regulator to its genomic targets in vivo. Chromatin-immunoprecipitation-on-chip identified 178 LeuO binding sites on the chromosome of S. enterica serovar Typhimurium strain SL1344. These sites were distributed across both the core and the horizontally acquired genome, and included housekeeping genes and genes known to contribute to virulence. Sixty-eight LeuO targets were co-bound by the global repressor protein, H-NS. Thus, while LeuO may function as an H-NS antagonist, these functions are unlikely to involve displacement of H-NS. RNA polymerase bound 173 of the 178 LeuO targets, consistent with LeuO being a transcription regulator. Thus, LeuO targets two classes of genes, those that are bound by H-NS and those that are not bound by H-NS. LeuO binding site analysis revealed a logo conforming to the TN.sub.11A motif common to LysR-type transcription factors. It differed in some details from a motif that we composed for Escherichia coli LeuO binding sites; 1263 and 1094 LeuO binding site locations were predicted in the S. Typhimurium SL1344 and E. coli MG1655 genomes respectively. Despite differences in motif composition, many LeuO target genes were common to both species. Thus, LeuO is likely to be a more important global regulator than previously suspected. Author Affiliation: (1)Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine (2)Department of Genetics, School of Genetics and Microbiology, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland (3)Departamento de Genetica, Facultad de Biologia, Universidad de Sevilla, Apartado 1095, Seville 41080, Spain (4)Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark Correspondence: (*) E-mail cjdorman@tcd.ie; Tel. (+353) 1 8962013; Fax (+353) 1 6799294. Accepted 29 June, 2012. Supporting information: Additional Supporting Information may be found in the online version of this article
    Keywords: Transcription (Genetics) -- Genetic Aspects ; Transcription (Genetics) -- Analysis ; Bacterial Genetics -- Genetic Aspects ; Bacterial Genetics -- Analysis ; Preventive Medicine -- Analysis ; Dna Binding Proteins -- Genetic Aspects ; Dna Binding Proteins -- Analysis ; Genes -- Genetic Aspects ; Genes -- Analysis ; Rna -- Genetic Aspects ; Rna -- Analysis ; Salmonella -- Analysis
    ISSN: 0950-382X
    Source: Cengage Learning, Inc.
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  • 4
    In: Molecular Microbiology, June 2010, Vol.76(5), pp.1250-1265
    Description: The conjugative IncHI1 plasmid pSfR27 from 2a strain 2457T encodes the Sfh protein, a paralogue of the global transcriptional repressor H‐NS. Sfh allows pSfR27 to be transmitted to new bacterial hosts with minimal impact on host fitness, providing a ‘stealth’ function whose molecular mechanism has yet to be determined. The impact of the Sfh protein on the serovar Typhimurium transcriptome was assessed and binding sites for Sfh in the Typhimurium genome were identified by chromatin immunoprecipitation. Sfh did not bind uniquely to any sites. Instead, it bound to a subset of the larger H‐NS regulatory network. Analysis of Sfh binding in the absence of H‐NS revealed a greatly expanded population of Sfh binding sites that included the majority of H‐NS target genes. Furthermore, the presence of plasmid pSfR27 caused a decrease in H‐NS interactions with the Typhimurium chromosome, suggesting that the A + T‐rich DNA of this large plasmid acts to titrate H‐NS, removing it from chromosomal locations. It is proposed that Sfh acts as a molecular backup for H‐NS and that it provides its ‘stealth’ function by replacing H‐NS on the chromosome, thus minimizing disturbances to the H‐NS‐DNA binding pattern in cells that acquire pSfR27.
    Keywords: Fighter Planes -- Analysis ; Chromatin -- Analysis ; Preventive Medicine -- Analysis ; Salmonella Typhimurium -- Analysis ; Genomics -- Analysis;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 5
    In: Molecular Microbiology, September 2012, Vol.85(6), pp.1072-1089
    Description: We report the first investigation of the binding of the LeuO LysR‐type transcription regulator to its genomic targets . Chromatin‐immunoprecipitation‐on‐chip identified 178 LeuO binding sites on the chromosome of serovar Typhimurium strain SL1344. These sites were distributed across both the core and the horizontally acquired genome, and included housekeeping genes and genes known to contribute to virulence. Sixty‐eight LeuO targets were co‐bound by the global repressor protein, H‐NS. Thus, while LeuO may function as an H‐NS antagonist, these functions are unlikely to involve displacement of H‐NS. RNA polymerase bound 173 of the 178 LeuO targets, consistent with LeuO being a transcription regulator. Thus, LeuO targets two classes of genes, those that are bound by H‐NS and those that are not bound by H‐NS. LeuO binding site analysis revealed a logo conforming to the TNA motif common to LysR‐type transcription factors. It differed in some details from a motif that we composed for LeuO binding sites; 1263 and 1094 LeuO binding site locations were predicted in the . Typhimurium SL1344 and MG1655 genomes respectively. Despite differences in motif composition, many LeuO target genes were common to both species. Thus, LeuO is likely to be a more important global regulator than previously suspected.
    Keywords: Biology;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 15 May 2012, Vol.109(20), pp.E1277-86
    Description: More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ(70) (including phoP, slyA, and invF) from which we identified the -10 and -35 motifs of σ(70)-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and 〈20% were found throughout the Enterobacteriaceae. This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model.
    Keywords: Gene Expression Regulation, Bacterial -- Genetics ; RNA, Small Untranslated -- Genetics ; Regulatory Sequences, Ribonucleic Acid -- Genetics ; Salmonella Typhimurium -- Genetics ; Transcription, Genetic -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 7
    Language: English
    In: PLoS ONE, 2010, Vol.5(2), p.e9059
    Description: The SCL (TAL1) transcription factor is a critical regulator of haematopoiesis and its expression is tightly controlled by multiple cis -acting regulatory elements. To elaborate further the DNA elements which control its regulation, we used genomic tiling microarrays covering 256 kb of the human SCL locus to perform a concerted analysis of chromatin structure and binding of regulatory proteins in human haematopoietic cell lines. This approach allowed us to characterise further or redefine known human SCL regulatory elements and led to the identification of six novel elements with putative regulatory function both up and downstream of the SCL gene. They bind a number of haematopoietic transcription factors (GATA1, E2A LMO2, SCL, LDB1), CTCF or components of the transcriptional machinery and are associated with relevant histone modifications, accessible chromatin and low nucleosomal density. Functional characterisation shows that these novel elements are able to enhance or repress SCL promoter activity, have endogenous promoter function or enhancer-blocking insulator function. Our analysis opens up several areas for further investigation and adds new layers of complexity to our understanding of the regulation of SCL expression.
    Keywords: Research Article ; Biochemistry -- Transcription And Translation ; Cell Biology -- Gene Expression ; Genetics And Genomics -- Epigenetics ; Genetics And Genomics -- Gene Expression ; Genetics And Genomics -- Genomics
    E-ISSN: 1932-6203
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  • 8
    In: Environmental Microbiology, April 2014, Vol.16(4), pp.950-962
    Description: It is believed that the main role of plasmids that encode multiple antibiotic resistance is to confer their hosts the ability to survive in the presence of antimicrobial compounds. In the pathogenic bacterium , plasmids of the incompatibility group 1 account for a significant proportion of antibiotic resistance phenotypes. In this work, we show that plasmid 27 has a strong impact on the global transcriptome of  yphimurium strain 1344 when cells grow at low temperature and enter the stationary phase. Down‐regulated genes include pathogenicity islands, anaerobic respiration and metabolism determinants. Up‐regulated genes include factors involved in the response to nutrient starvation, antimicrobial resistance, iron metabolism and the heat shock response. Accordingly, cells harbouring 27 are more resistant to heat shock than plasmid‐free cells. The use of a different plasmid, , provided evidence that these plasmids facilitate adaptation of to environmental conditions outside their host(s). This is consistent with the fact that conjugative transfer of plasmids only occurs at low temperature. A significant number of the 27‐dependent alterations in gene expression could be correlated with expression of a plasmid‐encoded orthologue of the global modulator ‐, which is up‐regulated when cells grow at low temperature.
    Keywords: Drug Resistance, Multiple, Bacterial–Genetics ; Gene Expression Profiling–Genetics ; Gene Expression Regulation, Bacterial–Genetics ; Genes, Bacterial–Genetics ; Heat-Shock Response–Genetics ; Molecular Sequence Data–Genetics ; Oligonucleotide Array Sequence Analysis–Genetics ; Plasmids–Genetics ; Salmonella Typhimurium–Genetics ; Temperature–Genetics ; Bacteriology ; Plasmids ; Antimicrobial Agents ; Gene Expression;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 9
    Language: English
    In: PLoS ONE, 2010, Vol.5(8), p.e12339
    Description: It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons (“exon-intron marking”), linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.
    Keywords: Research Article ; Molecular Biology -- Chromatin Structure ; Molecular Biology -- Chromosome Structure ; Molecular Biology -- Histone Modification ; Molecular Biology -- Rna Splicing ; Molecular Biology -- Translation Mechanisms ; Molecular Biology -- Translational Regulation ; Molecular Biology -- Chromatin Structure ; Molecular Biology -- Chromosome Structure ; Molecular Biology -- Histone Modification ; Molecular Biology -- Rna Splicing ; Molecular Biology -- Translation Mechanisms ; Molecular Biology -- Translational Regulation
    E-ISSN: 1932-6203
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  • 10
    Language: English
    In: Microbial genomics, October 2017, Vol.3(10), pp.e000127
    Description: We have investigated the connection between the four-dimensional architecture of the bacterial nucleoid and the organism's global gene expression programme. By localizing the transcription machinery and the transcriptional outputs across the genome of the model bacterium serovar Typhimurium at different stages of the growth cycle, a surprising disconnection between gene dosage and transcriptional output was revealed. During exponential growth, gene output occurred chiefly in the Ori (origin), Ter (terminus) and NSL (non-structured left) domains, whereas the Left macrodomain remained transcriptionally quiescent at all stages of growth. The apparently high transcriptional output in Ter was correlated with an enhanced stability of the RNA expressed there during exponential growth, suggesting that longer mRNA half-lives compensate for low gene dosage. During exponential growth, RNA polymerase (RNAP) was detected everywhere, whereas in stationary phase cells, RNAP was concentrated in the Ter macrodomain. The alternative sigma factors RpoE, RpoH and RpoN were not required to drive transcription in these growth conditions, consistent with their observed binding to regions away from RNAP and regions of active transcription. Specifically, these alternative sigma factors were found in the Ter macrodomain during exponential growth, whereas they were localized at the Ori macrodomain in stationary phase.
    Keywords: RNA Polymerase ; Sigma Factors ; Bacterial Chromosome ; Chromatin Immunoprecipitation ; Transcriptomics ; DNA-Directed RNA Polymerases -- Biosynthesis ; Salmonella Typhimurium -- Genetics ; Sigma Factor -- Biosynthesis
    E-ISSN: 2057-5858
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