The Drosophila Zinc Finger Protein Aef1 Colocalizes with Enhancers and Is Involved in the Transcriptional Regulation of Numerous Genes

TL;DR

This study shows that the Drosophila protein Aef1 is involved in regulating gene transcription by binding to enhancers and promoters.

Contribution

The study reveals that Aef1 is involved in transcriptional regulation at both promoters and enhancers in Drosophila.

Findings

Aef1 binding sites colocalize with SAGA, dSWI/SNF, and ORC complexes and are found in nucleosome-depleted regions.

Aef1 is associated with the H3K27Ac histone mark and CBP protein, indicating a role in enhancer activity.

RNA interference targeting Aef1 affects transcription of 342 genes, with 178 having Aef1 at their regulatory regions.

Abstract

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.

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