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A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans

While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacteria...

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Autores principales: Engelmann, Ilka, Griffon, Aurélien, Tichit, Laurent, Montañana-Sanchis, Frédéric, Wang, Guilin, Reinke, Valerie, Waterston, Robert H., Hillier, LaDeana W., Ewbank, Jonathan J.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094335/
https://www.ncbi.nlm.nih.gov/pubmed/21602919
http://dx.doi.org/10.1371/journal.pone.0019055
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author Engelmann, Ilka
Griffon, Aurélien
Tichit, Laurent
Montañana-Sanchis, Frédéric
Wang, Guilin
Reinke, Valerie
Waterston, Robert H.
Hillier, LaDeana W.
Ewbank, Jonathan J.
author_facet Engelmann, Ilka
Griffon, Aurélien
Tichit, Laurent
Montañana-Sanchis, Frédéric
Wang, Guilin
Reinke, Valerie
Waterston, Robert H.
Hillier, LaDeana W.
Ewbank, Jonathan J.
author_sort Engelmann, Ilka
collection PubMed
description While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http://wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes.
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spelling pubmed-30943352011-05-19 A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans Engelmann, Ilka Griffon, Aurélien Tichit, Laurent Montañana-Sanchis, Frédéric Wang, Guilin Reinke, Valerie Waterston, Robert H. Hillier, LaDeana W. Ewbank, Jonathan J. PLoS One Research Article While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http://wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes. Public Library of Science 2011-05-13 /pmc/articles/PMC3094335/ /pubmed/21602919 http://dx.doi.org/10.1371/journal.pone.0019055 Text en Engelmann et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Engelmann, Ilka
Griffon, Aurélien
Tichit, Laurent
Montañana-Sanchis, Frédéric
Wang, Guilin
Reinke, Valerie
Waterston, Robert H.
Hillier, LaDeana W.
Ewbank, Jonathan J.
A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
title A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
title_full A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
title_fullStr A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
title_full_unstemmed A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
title_short A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
title_sort comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in c. elegans
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094335/
https://www.ncbi.nlm.nih.gov/pubmed/21602919
http://dx.doi.org/10.1371/journal.pone.0019055
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