Eyeless (ey) is one of the most critical transcription factors for initiating 
the entire eye development in Drosophila. However, the molecular mechanisms 
through which Ey regulates target genes and pathways have not been characterized 
at the genomic level. Using ChIP-Seq, we generated an endogenous Ey-binding 
profile in Drosophila developing eyes. We found that Ey binding occurred more 
frequently at promoter compared to non-promoter regions. Ey promoter binding was 
correlated with the active transcription of genes involved in development and 
transcription regulation. An integrative analysis revealed that Ey directly 
regulated a broad and highly connected genetic network, including many essential 
patterning pathways, and known and novel eye genes. Interestingly, we observed 
that Ey could target multiple components of the same pathway, which might 
enhance its control of these pathways during eye development. In addition to 
protein-coding genes, we discovered Ey also targeted non-coding RNAs, which 
represents a new regulatory mechanism employed by Ey. These findings suggest 
that Ey could use multiple molecular mechanisms to regulate target gene 
expression and pathway function, which might enable Ey to exhibit a greater 
flexibility in controlling different processes during eye development.