Integrative Genomic Analyses Reveal Putative Cell Type-specific Targets of the Drosophila Ets Transcription Factor Pointed

The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is required for several aspects of eye development and regulates cell cycle progression, specification, and differentiation. Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Integrating ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) reveals genes that may be putative cell type-specific genes regulated by Pnt. Finally, our ChIP-seq data predict cell type-specific functional enhancers that were not reported previously. Our study provides a greatly expanded list of putative Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Pnt.