Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development.

TitleIntegrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development.
Publication TypeJournal Article
Year of Publication2018
AuthorsYeung, K, Wang, F, Li, Y, Wang, K, Mardon, G, Chen, R
JournalNucleic Acids Res
Date Published2018 Dec 14
KeywordsAnimals, Body Patterning, Cell Lineage, Compound Eye, Arthropod, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Genomics, Photoreceptor Cells, Invertebrate, Promoter Regions, Genetic, RNA, Untranslated

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.

Alternate JournalNucleic Acids Res
PubMed ID30295802
PubMed Central IDPMC6294497
Grant ListR01 EY016853 / EY / NEI NIH HHS / United States
S10 OD023469 / OD / NIH HHS / United States
R01 EY011232 / EY / NEI NIH HHS / United States

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