UCSF

The initiation of tissue specific genetic programs requires that a signaling pathway must activate a subset of its complete repertoire of targets at the appropriate time and in the correct location. This is an extreme challenge for a pathway that operates in multiple tissues during the same stage of development. To achieve this level of specificity, tissue specific transcription of target genes relies on the activity of local factors that define a zone of activation competence.

The Drosophila Hedgehog (Hh) signaling pathway functions in a variety of tissues, effecting gene activation by modulating the activity of its downstream transcription factor, Cubitus interruptus (Ci). Cells receiving the Hh signal produce a full-length Ci transcriptional activator. Cells that do not receive Hh signal convert full length Ci into a transcriptional repressor. Little concerted effort has been put forth to identify the direct downstream targets of Ci that mediate the effect of Hh signaling. In this work, I use a combination of genomic approaches to identify regions in the genome where Ci binds (DAMID) and to determine the genes that respond to Hh signaling (expression array analysis) in the Drosophila embryo.

I find that DAMID signals for repressor (DamCiRep) and activator (DamCiAct) forms of Ci overlap hundreds of times indicating that repressor and activator forms of Ci recognize the same sequences in vivo. Transcriptional profiling of Hh pathway mutants uncovers genes that respond to all genetic backgrounds as well as sub-clusters of genes that change expression levels in specific mutant backgrounds. High confidence putative Ci targets are found to be largely tissue specific in their expression and function. A validation of putative Ci targets via in situ hybridization reveals a tissue specific response to Ci in three developmental systems: the embryonic visual system, dorsal ectoderm, and the developing tracheal system. Sequence specific binding sites for tissue specific regulators are present in Ci enhancers leading to a model by which Ci functions in synergy with local factors for optimal gene activation.