In vivo validation of a computationally predicted conserved Ath5 Target Gene Set
Author SummaryTo establish regulatory gene networks that drive key biological processes is of crucial importance to identify the genes that are directly controlled by transcriptional regulators. Ideally, this can be accomplished by identifying the direct transcription factor binding site in the cis-...
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| Hauptverfasser: | , , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
September 21, 2007
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| In: |
PLoS Genetics
Year: 2007, Jahrgang: 3, Heft: 9, Pages: 1661-1670 |
| ISSN: | 1553-7404 |
| DOI: | 10.1371/journal.pgen.0030159 |
| Online-Zugang: | Verlag, kostenfrei, Volltext: http://dx.doi.org/10.1371/journal.pgen.0030159 Verlag, kostenfrei, Volltext: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0030159 
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| Verfasserangaben: | Filippo Del Bene, Laurence Ettwiller, Dorota Skowronska-Krawczyk, Herwig Baier, Jean-Marc Matter, Ewan Birney, Joachim Wittbrodt |
MARC
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| 245 | 1 | 0 | |a In vivo validation of a computationally predicted conserved Ath5 Target Gene Set |c Filippo Del Bene, Laurence Ettwiller, Dorota Skowronska-Krawczyk, Herwig Baier, Jean-Marc Matter, Ewan Birney, Joachim Wittbrodt |
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| 520 | |a Author SummaryTo establish regulatory gene networks that drive key biological processes is of crucial importance to identify the genes that are directly controlled by transcriptional regulators. Ideally, this can be accomplished by identifying the direct transcription factor binding site in the cis-regulatory regions of the respective target genes. However, problems related to the fact that the motifs recognized and bound by transcription factors are short (6-20 bp) and consequently found very frequently and spread all over the genome, have limited this approach. The transcription factor Ath5 is involved in the specification and differentiation of retinal ganglion cells in the developing vertebrate eye. We show that Ath5 directly regulates its own expression by binding to a small region of its proximal promoter that contains two identical motifs. Using this motif description, together with conservation across large evolutionary distances, we then searched in the genome for other target genes of Ath5 and predicted 166 direct target genes. We then validated a subset of these predictions both in vitro and in vivo. Our analysis therefore provides an example of computation prediction of transcriptional target genes. At the same time, the genes identified represent the most comprehensive list of effectors mediating the role of Ath5 during eye development. | ||
| 650 | 4 | |a Comparative genomics | |
| 650 | 4 | |a Embryos | |
| 650 | 4 | |a Gene prediction | |
| 650 | 4 | |a Gene regulation | |
| 650 | 4 | |a Genome evolution | |
| 650 | 4 | |a Sequence alignment | |
| 650 | 4 | |a Sequence motif analysis | |
| 650 | 4 | |a Transcription factors | |
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