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...
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Public Library of Science (PLoS)
2010-02-01
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| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1000848&type=printable |
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| author | Mei Zhong Wei Niu Zhi John Lu Mihail Sarov John I Murray Judith Janette Debasish Raha Karyn L Sheaffer Hugo Y K Lam Elicia Preston Cindie Slightham LaDeana W Hillier Trisha Brock Ashish Agarwal Raymond Auerbach Anthony A Hyman Mark Gerstein Susan E Mango Stuart K Kim Robert H Waterston Valerie Reinke Michael Snyder |
| author_facet | Mei Zhong Wei Niu Zhi John Lu Mihail Sarov John I Murray Judith Janette Debasish Raha Karyn L Sheaffer Hugo Y K Lam Elicia Preston Cindie Slightham LaDeana W Hillier Trisha Brock Ashish Agarwal Raymond Auerbach Anthony A Hyman Mark Gerstein Susan E Mango Stuart K Kim Robert H Waterston Valerie Reinke Michael Snyder |
| author_sort | Mei Zhong |
| collection | DOAJ |
| 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 | Article |
| id | doaj-art-3935b829c33d42ab895b0ebada48e8f7 |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2010-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-3935b829c33d42ab895b0ebada48e8f72025-08-20T02:01:57ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042010-02-0162e100084810.1371/journal.pgen.1000848Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.Mei ZhongWei NiuZhi John LuMihail SarovJohn I MurrayJudith JanetteDebasish RahaKaryn L SheafferHugo Y K LamElicia PrestonCindie SlighthamLaDeana W HillierTrisha BrockAshish AgarwalRaymond AuerbachAnthony A HymanMark GersteinSusan E MangoStuart K KimRobert H WaterstonValerie ReinkeMichael SnyderTranscription 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.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1000848&type=printable |
| spellingShingle | Mei Zhong Wei Niu Zhi John Lu Mihail Sarov John I Murray Judith Janette Debasish Raha Karyn L Sheaffer Hugo Y K Lam Elicia Preston Cindie Slightham LaDeana W Hillier Trisha Brock Ashish Agarwal Raymond Auerbach Anthony A Hyman Mark Gerstein Susan E Mango Stuart K Kim Robert H Waterston Valerie Reinke Michael Snyder Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genetics |
| 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 |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1000848&type=printable |
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