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Genomic analysis of the ecdysone steroid signal at metamorphosis onset using ecdysoneless and EcR Drosophila melanogaster mutants.

Davis MB, Li T - Genes Genomics (2013)

Bottom Line: Around 12 % of the genome responds to the ecdysone hormone signal at the onset of metamorphosis and over half of these are independent of the receptor.In addition, a significant portion of receptor regulated genes are differentially regulated by the receptor, depending on its ligand state.Gene ontology enrichment analyses confirm known ecdysone regulated biological functions and also validate implicated pathways that have been indirectly associated with ecdysone signaling.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Coverdell Biomedical Research Center, University of Georgia, 500 DW Brooks Dr S 270C, Athens, GA 30602 USA.

ABSTRACT
Steroid hormone gene regulation is often depicted as a linear transduction of the signal, from molecule release to the gene level, by activation of a receptor protein after being bound by its steroid ligand. Such an action would require that the hormone be present and bound to the receptor in order to have target gene response. Here, we present data that presents a novel perspective of hormone gene regulation, where the hormone molecule and its receptor have exclusive target gene regulation function, in addition to the traditional direct target genes. Our study is the first genome-wide analysis of conditional mutants simultaneously modeling the steroid and steroid receptor gene expression regulation. We have integrated classical genetic mutant experiments with functional genomics techniques in the Drosophila melanogaster model organism, where we interrogate the 20-hydroxyecdysone signaling response at the onset of metamorphosis. Our novel catalog of ecdysone target genes illustrates the separable transcriptional responses among the hormone, the pre-hormone receptor and the post-hormone receptor. We successfully detected traditional ecdysone target genes as common targets and also identified novel sets of target genes which where exclusive to each mutant condition. Around 12 % of the genome responds to the ecdysone hormone signal at the onset of metamorphosis and over half of these are independent of the receptor. In addition, a significant portion of receptor regulated genes are differentially regulated by the receptor, depending on its ligand state. Gene ontology enrichment analyses confirm known ecdysone regulated biological functions and also validate implicated pathways that have been indirectly associated with ecdysone signaling.

No MeSH data available.


Related in: MedlinePlus

Ecdysone response genes overlap with EcR binding sites. Response genes for the three mutant categories were compared to the binding sites of EcR in four cell lines. Each category has a significant number of genes which overlap with EcR binding targets. Binding target genes were defined as having an EcR binding site within 1 Kb of transcription start site. The EcR binding assays were conducted in four different cell lines including two embryonic lines (Kc and S2) as well as two imaginal disc cell lines (D20 and L1) (Davis and White, unpublished). The hypergeometric pvalue for the overlaps of these respective gene lists is shown
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Fig9: Ecdysone response genes overlap with EcR binding sites. Response genes for the three mutant categories were compared to the binding sites of EcR in four cell lines. Each category has a significant number of genes which overlap with EcR binding targets. Binding target genes were defined as having an EcR binding site within 1 Kb of transcription start site. The EcR binding assays were conducted in four different cell lines including two embryonic lines (Kc and S2) as well as two imaginal disc cell lines (D20 and L1) (Davis and White, unpublished). The hypergeometric pvalue for the overlaps of these respective gene lists is shown

Mentions: Of our inclusive gene set, there were nearly 230 genes that are confirmed EcR binding targets; defined as having a true EcR binding site within 4 kb of their transcription startsite detected in the Kc cell line using a DamID procedure (Davis et. al, in prep) (Fig. 9). There was no bias in either particular mutant category with confirmed binding from the binding data used. We do see some arbitrary enrichment in bound targets from the WPP-EcR- category associated with genes that related to signal transduction and transport, while BG-EcR- bound targets are associated with proteasome. There were several known targets confirmed, including Sgs-4, broad, Eip 63E, Eig E1 as well as some suspected targets validated, including Slobo, shaggy, Rab-proteins, nocturin and others. However, there is most likely some other qualitative differences between the regulation potential of pre-hormone target genes and those which only show a response post-hormone pulse. Further investigations which compare the regulatory elements and cofactor interactions of pre-hormone and post-hormone EcR targets would be necessary to address these possibilities and are forthcoming in a genome-wide analysis of dynamic EcR binding sites (M.Davis and K.White, in prep).Fig. 9


Genomic analysis of the ecdysone steroid signal at metamorphosis onset using ecdysoneless and EcR Drosophila melanogaster mutants.

Davis MB, Li T - Genes Genomics (2013)

Ecdysone response genes overlap with EcR binding sites. Response genes for the three mutant categories were compared to the binding sites of EcR in four cell lines. Each category has a significant number of genes which overlap with EcR binding targets. Binding target genes were defined as having an EcR binding site within 1 Kb of transcription start site. The EcR binding assays were conducted in four different cell lines including two embryonic lines (Kc and S2) as well as two imaginal disc cell lines (D20 and L1) (Davis and White, unpublished). The hypergeometric pvalue for the overlaps of these respective gene lists is shown
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Related In: Results  -  Collection

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Fig9: Ecdysone response genes overlap with EcR binding sites. Response genes for the three mutant categories were compared to the binding sites of EcR in four cell lines. Each category has a significant number of genes which overlap with EcR binding targets. Binding target genes were defined as having an EcR binding site within 1 Kb of transcription start site. The EcR binding assays were conducted in four different cell lines including two embryonic lines (Kc and S2) as well as two imaginal disc cell lines (D20 and L1) (Davis and White, unpublished). The hypergeometric pvalue for the overlaps of these respective gene lists is shown
Mentions: Of our inclusive gene set, there were nearly 230 genes that are confirmed EcR binding targets; defined as having a true EcR binding site within 4 kb of their transcription startsite detected in the Kc cell line using a DamID procedure (Davis et. al, in prep) (Fig. 9). There was no bias in either particular mutant category with confirmed binding from the binding data used. We do see some arbitrary enrichment in bound targets from the WPP-EcR- category associated with genes that related to signal transduction and transport, while BG-EcR- bound targets are associated with proteasome. There were several known targets confirmed, including Sgs-4, broad, Eip 63E, Eig E1 as well as some suspected targets validated, including Slobo, shaggy, Rab-proteins, nocturin and others. However, there is most likely some other qualitative differences between the regulation potential of pre-hormone target genes and those which only show a response post-hormone pulse. Further investigations which compare the regulatory elements and cofactor interactions of pre-hormone and post-hormone EcR targets would be necessary to address these possibilities and are forthcoming in a genome-wide analysis of dynamic EcR binding sites (M.Davis and K.White, in prep).Fig. 9

Bottom Line: Around 12 % of the genome responds to the ecdysone hormone signal at the onset of metamorphosis and over half of these are independent of the receptor.In addition, a significant portion of receptor regulated genes are differentially regulated by the receptor, depending on its ligand state.Gene ontology enrichment analyses confirm known ecdysone regulated biological functions and also validate implicated pathways that have been indirectly associated with ecdysone signaling.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Coverdell Biomedical Research Center, University of Georgia, 500 DW Brooks Dr S 270C, Athens, GA 30602 USA.

ABSTRACT
Steroid hormone gene regulation is often depicted as a linear transduction of the signal, from molecule release to the gene level, by activation of a receptor protein after being bound by its steroid ligand. Such an action would require that the hormone be present and bound to the receptor in order to have target gene response. Here, we present data that presents a novel perspective of hormone gene regulation, where the hormone molecule and its receptor have exclusive target gene regulation function, in addition to the traditional direct target genes. Our study is the first genome-wide analysis of conditional mutants simultaneously modeling the steroid and steroid receptor gene expression regulation. We have integrated classical genetic mutant experiments with functional genomics techniques in the Drosophila melanogaster model organism, where we interrogate the 20-hydroxyecdysone signaling response at the onset of metamorphosis. Our novel catalog of ecdysone target genes illustrates the separable transcriptional responses among the hormone, the pre-hormone receptor and the post-hormone receptor. We successfully detected traditional ecdysone target genes as common targets and also identified novel sets of target genes which where exclusive to each mutant condition. Around 12 % of the genome responds to the ecdysone hormone signal at the onset of metamorphosis and over half of these are independent of the receptor. In addition, a significant portion of receptor regulated genes are differentially regulated by the receptor, depending on its ligand state. Gene ontology enrichment analyses confirm known ecdysone regulated biological functions and also validate implicated pathways that have been indirectly associated with ecdysone signaling.

No MeSH data available.


Related in: MedlinePlus