Whole-genome analysis of temporal gene expression during foregut development.
We have investigated the cis-regulatory network that mediates temporal gene expression during organogenesis. Previous studies demonstrated that the organ selector gene pha-4/FoxA is critical to establish the onset of transcription of Caenorhabditis elegans foregut (pharynx) genes. Here, we discover...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2004-11-01
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| Series: | PLoS Biology |
| Online Access: | https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0020352&type=printable |
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| author | Jeb Gaudet Srikanth Muttumu Michael Horner Susan E Mango |
| author_facet | Jeb Gaudet Srikanth Muttumu Michael Horner Susan E Mango |
| author_sort | Jeb Gaudet |
| collection | DOAJ |
| description | We have investigated the cis-regulatory network that mediates temporal gene expression during organogenesis. Previous studies demonstrated that the organ selector gene pha-4/FoxA is critical to establish the onset of transcription of Caenorhabditis elegans foregut (pharynx) genes. Here, we discover additional cis-regulatory elements that function in combination with PHA-4. We use a computational approach to identify candidate cis-regulatory sites for genes activated either early or late during pharyngeal development. Analysis of natural or synthetic promoters reveals that six of these sites function in vivo. The newly discovered temporal elements, together with predicted PHA-4 sites, account for the onset of expression of roughly half of the pharyngeal genes examined. Moreover, combinations of temporal elements and PHA-4 sites can be used in genome-wide searches to predict pharyngeal genes, with more than 85% accuracy for their onset of expression. These findings suggest a regulatory code for temporal gene expression during foregut development and provide a means to predict gene expression patterns based solely on genomic sequence. |
| format | Article |
| id | doaj-art-d33fe779238b45e28413dc7384a3fba1 |
| institution | OA Journals |
| issn | 1544-9173 1545-7885 |
| language | English |
| publishDate | 2004-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj-art-d33fe779238b45e28413dc7384a3fba12025-08-20T02:00:54ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852004-11-01211e35210.1371/journal.pbio.0020352Whole-genome analysis of temporal gene expression during foregut development.Jeb GaudetSrikanth MuttumuMichael HornerSusan E MangoWe have investigated the cis-regulatory network that mediates temporal gene expression during organogenesis. Previous studies demonstrated that the organ selector gene pha-4/FoxA is critical to establish the onset of transcription of Caenorhabditis elegans foregut (pharynx) genes. Here, we discover additional cis-regulatory elements that function in combination with PHA-4. We use a computational approach to identify candidate cis-regulatory sites for genes activated either early or late during pharyngeal development. Analysis of natural or synthetic promoters reveals that six of these sites function in vivo. The newly discovered temporal elements, together with predicted PHA-4 sites, account for the onset of expression of roughly half of the pharyngeal genes examined. Moreover, combinations of temporal elements and PHA-4 sites can be used in genome-wide searches to predict pharyngeal genes, with more than 85% accuracy for their onset of expression. These findings suggest a regulatory code for temporal gene expression during foregut development and provide a means to predict gene expression patterns based solely on genomic sequence.https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0020352&type=printable |
| spellingShingle | Jeb Gaudet Srikanth Muttumu Michael Horner Susan E Mango Whole-genome analysis of temporal gene expression during foregut development. PLoS Biology |
| title | Whole-genome analysis of temporal gene expression during foregut development. |
| title_full | Whole-genome analysis of temporal gene expression during foregut development. |
| title_fullStr | Whole-genome analysis of temporal gene expression during foregut development. |
| title_full_unstemmed | Whole-genome analysis of temporal gene expression during foregut development. |
| title_short | Whole-genome analysis of temporal gene expression during foregut development. |
| title_sort | whole genome analysis of temporal gene expression during foregut development |
| url | https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0020352&type=printable |
| work_keys_str_mv | AT jebgaudet wholegenomeanalysisoftemporalgeneexpressionduringforegutdevelopment AT srikanthmuttumu wholegenomeanalysisoftemporalgeneexpressionduringforegutdevelopment AT michaelhorner wholegenomeanalysisoftemporalgeneexpressionduringforegutdevelopment AT susanemango wholegenomeanalysisoftemporalgeneexpressionduringforegutdevelopment |