In our previous studies, we demonstrated that the Drosophila zinc finger protein Aef1 interacts with the SAGA DUB module. The Aef1 binding sites colocalize with the SAGA histone acetyltransferase complex and the dSWI/SNF chromatin remodeling complex, as well as the origin recognition complex (ORC). Aef1 predominantly localizes with the promoters of active genes (55% of all sites) and can be involved in transcriptional regulation. In this study, we showed that Aef1 binding sites in Drosophila S2 cells, located outside gene promoters, are nucleosome-depleted regions and colocalize with the SAGA, dSWI/SNF, and ORC complexes. Aef1 binding sites colocalize with the CBP protein and the H3K27Ac histone tag, which is considered to be an active enhancer mark. An RNA-Seq experiment was conducted in Drosophila S2 cells, both normal and with RNA interference targeting the Aef1 protein, to study the role played by the Aef1 protein in transcriptional regulation. The Aef1 protein was shown to affect the transcription of 342 genes, more than half of those (178 genes) containing Aef1 at their promoters or enhancers. Hence, we infer that the Aef1 protein is recruited to both promoters and enhancers and is involved, both directly and indirectly, in the regulation of the transcription of the respective genes.