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Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using c...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824807/ https://www.ncbi.nlm.nih.gov/pubmed/20174564 http://dx.doi.org/10.1371/journal.pgen.1000848 |
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author | Zhong, Mei Niu, Wei Lu, Zhi John Sarov, Mihail Murray, John I. Janette, Judith Raha, Debasish Sheaffer, Karyn L. Lam, Hugo Y. K. Preston, Elicia Slightham, Cindie Hillier, LaDeana W. Brock, Trisha Agarwal, Ashish Auerbach, Raymond Hyman, Anthony A. Gerstein, Mark Mango, Susan E. Kim, Stuart K. Waterston, Robert H. Reinke, Valerie Snyder, Michael |
author_facet | Zhong, Mei Niu, Wei Lu, Zhi John Sarov, Mihail Murray, John I. Janette, Judith Raha, Debasish Sheaffer, Karyn L. Lam, Hugo Y. K. Preston, Elicia Slightham, Cindie Hillier, LaDeana W. Brock, Trisha Agarwal, Ashish Auerbach, Raymond Hyman, Anthony A. Gerstein, Mark Mango, Susan E. Kim, Stuart K. Waterston, Robert H. Reinke, Valerie Snyder, Michael |
author_sort | Zhong, Mei |
collection | PubMed |
description | Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes. We identified thousands of binding sites for PHA-4 during formation of the embryonic pharynx, and also found a role for this factor during the starvation response. Many binding sites were found to shift dramatically between embryos and starved larvae, from developmentally regulated genes to genes involved in metabolism. These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles. |
format | Text |
id | pubmed-2824807 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-28248072010-02-19 Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response Zhong, Mei Niu, Wei Lu, Zhi John Sarov, Mihail Murray, John I. Janette, Judith Raha, Debasish Sheaffer, Karyn L. Lam, Hugo Y. K. Preston, Elicia Slightham, Cindie Hillier, LaDeana W. Brock, Trisha Agarwal, Ashish Auerbach, Raymond Hyman, Anthony A. Gerstein, Mark Mango, Susan E. Kim, Stuart K. Waterston, Robert H. Reinke, Valerie Snyder, Michael PLoS Genet Research Article Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes. We identified thousands of binding sites for PHA-4 during formation of the embryonic pharynx, and also found a role for this factor during the starvation response. Many binding sites were found to shift dramatically between embryos and starved larvae, from developmentally regulated genes to genes involved in metabolism. These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles. Public Library of Science 2010-02-19 /pmc/articles/PMC2824807/ /pubmed/20174564 http://dx.doi.org/10.1371/journal.pgen.1000848 Text en Zhong 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 Zhong, Mei Niu, Wei Lu, Zhi John Sarov, Mihail Murray, John I. Janette, Judith Raha, Debasish Sheaffer, Karyn L. Lam, Hugo Y. K. Preston, Elicia Slightham, Cindie Hillier, LaDeana W. Brock, Trisha Agarwal, Ashish Auerbach, Raymond Hyman, Anthony A. Gerstein, Mark Mango, Susan E. Kim, Stuart K. Waterston, Robert H. Reinke, Valerie Snyder, Michael Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response |
title | Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response |
title_full | Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response |
title_fullStr | Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response |
title_full_unstemmed | Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response |
title_short | Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response |
title_sort | genome-wide identification of binding sites defines distinct functions for caenorhabditis elegans pha-4/foxa in development and environmental response |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824807/ https://www.ncbi.nlm.nih.gov/pubmed/20174564 http://dx.doi.org/10.1371/journal.pgen.1000848 |
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