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Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these—H-NS and Fis—bind to specific DNA sequences and structures. Because of their importance to global gene expression, t...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064808/ https://www.ncbi.nlm.nih.gov/pubmed/21097887 http://dx.doi.org/10.1093/nar/gkq934 |
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author | Kahramanoglou, Christina Seshasayee, Aswin S. N. Prieto, Ana I. Ibberson, David Schmidt, Sabine Zimmermann, Jurgen Benes, Vladimir Fraser, Gillian M. Luscombe, Nicholas M. |
author_facet | Kahramanoglou, Christina Seshasayee, Aswin S. N. Prieto, Ana I. Ibberson, David Schmidt, Sabine Zimmermann, Jurgen Benes, Vladimir Fraser, Gillian M. Luscombe, Nicholas M. |
author_sort | Kahramanoglou, Christina |
collection | PubMed |
description | Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these—H-NS and Fis—bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques. |
format | Text |
id | pubmed-3064808 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30648082011-03-28 Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli Kahramanoglou, Christina Seshasayee, Aswin S. N. Prieto, Ana I. Ibberson, David Schmidt, Sabine Zimmermann, Jurgen Benes, Vladimir Fraser, Gillian M. Luscombe, Nicholas M. Nucleic Acids Res Gene Regulation, Chromatin and Epigenetics Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these—H-NS and Fis—bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques. Oxford University Press 2011-03 2010-11-20 /pmc/articles/PMC3064808/ /pubmed/21097887 http://dx.doi.org/10.1093/nar/gkq934 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene Regulation, Chromatin and Epigenetics Kahramanoglou, Christina Seshasayee, Aswin S. N. Prieto, Ana I. Ibberson, David Schmidt, Sabine Zimmermann, Jurgen Benes, Vladimir Fraser, Gillian M. Luscombe, Nicholas M. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli |
title | Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli |
title_full | Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli |
title_fullStr | Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli |
title_full_unstemmed | Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli |
title_short | Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli |
title_sort | direct and indirect effects of h-ns and fis on global gene expression control in escherichia coli |
topic | Gene Regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064808/ https://www.ncbi.nlm.nih.gov/pubmed/21097887 http://dx.doi.org/10.1093/nar/gkq934 |
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