Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene regulated by ectopic expression of Sage in the entire Drosophila embryo

ABSTRACT: FoxA transcription factors play major roles in organ-specific gene expression. How FoxA proteins achieve specificity is unclear, given their broad expression patterns and requirements in multiple cell types. Here, we characterize Sage, a basic helix-loop-helix (bHLH) transcription factor expressed exclusively in the Drosophila salivary gland (SG). We identify Sage targets and show that not only are both Sage and the single Drosophila FoxA protein, Fork head (Fkh), required for expression of these genes, but coexpression of Sage and Fkh is sufficient to drive target gene expression in multiple other cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage/Fkh targets. Importantly, Sage, Fkh and Sens colocalize on salivary gland polytene chromosomes. Thus, Fkh drives cell-type specific gene expression as part of a tissue-specific transcription module that includes Sage and Sens, providing a new paradigm for how mammalian FoxA proteins acheive specificity. Three wild type (reference) samples were obtained from the Oregon R strain, age matched and treated the same as the three experimental samples isolated from Stages 11-16 embryos expressing UAS-Sage controlled by the tub-Gal4 driver.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Deborah Andrew

PROVIDER: E-GEOD-40358 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA.

Fox Rebecca M RM Vaishnavi Aria A Maruyama Rika R Andrew Deborah J DJ

Development (Cambridge, England) 20130411 10

FoxA transcription factors play major roles in organ-specific gene expression, regulating, for example, glucagon expression in the pancreas, GLUT2 expression in the liver, and tyrosine hydroxylase expression in dopaminergic neurons. Organ-specific gene regulation by FoxA proteins is achieved through cooperative regulation with a broad array of transcription factors with more limited expression domains. Fork head (Fkh), the sole Drosophila FoxA family member, is required for the development of mu ...[more]

PMID: 23578928

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Project description:When misexpressed in late Drosophila prepupae, the transcription factor Fork head (Fkh) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Fkh that might mediate the effect of the protein on cell death and other biological processes. Fkh was expressed in the line P[hs-Fkh111] from a heat-inducible transgene that encodes wild-type Fkh protein. Expression of Fkh was induced by incubating prepupae for 30 min in a 37 Â°C water bath, starting at 9.5 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from w1118 animals treated the same way. The microarray analysis identified 55 genes annotated as functioning in apoptosis whose expression was at least 1.5-fold changed by Fkh. These genes include the death genes hid and reaper, which play a central role in the control of salivary gland death. Other groups of significantly enriched genes include genes functioning in autophagy, steroid-signaling pathways, salivary gland secretion, and phospholipid metabolism. In addition, the microarray data identify genes as responsive to Fkh that are known to be controlled by the FOXA counterparts of Fkh in vertebrates, indicating that target genes and biological processes controlled by Fkh are evolutionarily conserved. SUBMITTER_CITATION: Liu and Lehmann, 2008: Genes and biological processes controlled by the Drosophila FOXA orthologue Fork head. Insect Molecular Biology, 17, 91-101; link: http://www.blackwell-synergy.com/toc/imb/17/2) Experiment Overall Design: Experimental RNA samples were obtained in 3 biological replicates from fkh-expressing salivary glands (SG_Fkh_14APF_rep1, SG_Fkh_14APF_rep2, SG_Fkh_14APF_rep3) and compared to control samples obtained in two biological replicates from the salivary glands of w1118 control animals (SG_w1118(3)_14APF_rep1, SG_w1118(3)_14APF_rep2). All samples were compared using dChip and normalized to the same baseline array (median intensity 134).

Project description:When misexpressed in late Drosophila prepupae, the transcription factor Senseless (Sens) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Sens that might mediate the effect of the protein on cell death and other biological processes. The yeast transcription factor GAL4, expressed from a heat-inducible transgene (P{GAL4-Hsp70.PB}89-2-1), was used to drive expression of Sens from a UAS-sens transgene. After crossing the GAL4 and UAS lines, expression of GAL4 was induced by a 30-min heat shock treatment (37 Â°C) of the progeny at 9 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from animals treated the same way carrying one copy of the GAL4 transgene (progeny of a cross between flies of the P{GAL4-Hsp70.PB}89-2-1 and w1118 strains) and w1118 animals. The microarray data identified several genes associated with programmed cell death, including caspase genes, which respond to Sens. In addition, the data show that many Drosophila genes respond to the yeast transcription factor GAL4 in a UAS-independent manner. To identify target genes of Sens that are of biological relevance, gene expression patterns in the presence of Sens were compared to gene expression patterns in both the presence and the absence of GAL4. This comparison revealed that Sens seems to preferentially downregulate targets that are upregulated by GAL4, suggesting that these genes may not necessarily constitute true transcriptional targets of Sens. Experiment Overall Design: Experimental RNA samples were obtained in 3 biological replicates from sens-expressing salivary glands (SG_sens_14APF_rep1, SG_sens_14APF_rep2, SG_sens_14APF_rep3) and compared to control samples obtained from GAL4-expressing salivary glands (SG_1P{hsGAL4}89(S)_14APF_rep1) and non-GAL4-expressing salivary glands (SG_w1118_14APF_rep1, SG_w1118_14APF_rep2). All samples were compared using dChip and normalized to the same baseline array (median intensity 150).

Dataset Information

Gene regulated by ectopic expression of Sage in the entire Drosophila embryo

Publications

Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA.

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