PMID:21963537

Citation	Chung, S, Chavez, C and Andrew, DJ (2011) Trachealess (Trh) regulates all tracheal genes during Drosophila embryogenesis. Dev. Biol. 360:160-72
Abstract	The Drosophila trachea is a branched tubular epithelia that transports oxygen and other gases. trachealess (trh), which encodes a bHLH-PAS transcription factor, is among the first genes to be expressed in the cells that will form the trachea. In the absence of trh, tracheal cells fail to invaginate to form tubes and remain on the embryo surface. Expression of many tracheal-specific genes depends on trh, but all of the known targets have relatively minor phenotypes compared to loss of trh, suggesting that there are additional targets. To identify uncharacterized transcriptional targets of Trh and to further understand the role of Trh in embryonic tracheal formation, we performed an in situ hybridization screen using a library of ~100 tracheal-expressed genes identified by the Berkeley Drosophila Genome Project (BDGP). Surprisingly, expression of every tracheal gene we tested was dependent on Trh, suggesting a major role for Trh in activation and maintenance of tracheal gene expression. A re-examination of the interdependence of the known early-expressed transcription factors, including trh, ventral veinless (vvl) and knirps/knirps-related (kni/knrl), suggests a new model for how gene expression is controlled in the trachea, with trh regulating expression of vvl and kni, but not vice versa. A pilot screen for the targets of Vvl and Kni/Knrl revealed that Vvl and Kni have only minor roles compared to Trh. Finally, genome-wide microarray experiments identified additional Trh targets and revealed that a variety of biological processes are affected by the loss of trh.
Links	PubMed PMC3215829 Online version:10.1016/j.ydbio.2011.09.014
Keywords	Alternative Splicing; Amino Acid Sequence; Animals; Drosophila Proteins/genetics; Drosophila Proteins/metabolism; Drosophila melanogaster/embryology; Drosophila melanogaster/genetics; Drosophila melanogaster/metabolism; Gene Expression Regulation, Developmental; Gene Knockout Techniques; Genes, Insect; Genome-Wide Association Study; Homeostasis; In Situ Hybridization, Fluorescence; Molecular Sequence Data; POU Domain Factors/genetics; POU Domain Factors/metabolism; RNA, Messenger/genetics; RNA, Messenger/metabolism; Repressor Proteins/genetics; Repressor Proteins/metabolism; Sequence Homology, Amino Acid; Tissue Distribution; Trachea/embryology; Trachea/metabolism; Transcription Factors/genetics; Transcription Factors/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
DROME:TRH		GO:0007424: open tracheal system development	ECO:0000315:		P		Fig 2 shows tracheal gene expression is absent in trh mutants.	complete CACAO 6744
DROME:TRH	involved_in	GO:0007424: open tracheal system development	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete

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