Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila (RNA-seq)

The Polycomb group (PcG) proteins are fundamental epigenetic regulators that control the repressive state of target genes in multicellular organisms. One of the open questions is defining the mechanisms of PcG recruitment to chromatin. In Drosophila, the crucial role in PcG recruitment is thought to belong to DNA-binding proteins associated with Polycomb response elements (PREs). However, current data suggests that not all PRE-binding factors have been identified. Here, we report the identification of the transcription factor Crooked legs (Crol) as a novel PcG recruiter. Crol is a C2H2-type Zinc Finger protein that directly binds to poly(G)-rich DNA sequences. Mutation of Crol binding sites as well as crol CRISPR/Cas9 knockout diminish the repressive activity of PREs in transgenes. Like other PRE-DNA binding proteins, Crol co-localizes with PcG proteins inside and outside of H2K27me3 domains. Crol knockout impairs the recruitment of the PRC1 subunit Polyhomeotic and the PRE-binding protein Combgap at a subset of sites. The decreased binding of PcG proteins is accompanied by dysregulated transcription of target genes. Overall, our study identified Crol as a new important player in PcG recruitment and epigenetic regulation. Overall design: We generated ChIP-Seq and RNA-Seq data in this study. ChIP-Seq data are for Crol, Cbp, Fsl, H3K27ac, H3K27me3, Psq, Trx, E(z), Pc and Ph in 3rd instar whole larvae and/or 3rd instar larval imaginal discs and brains. For some proteins, matched ChIP-Seq data for wild-type and Crol-KO Drosophila are both generated. RNA-Seq data are for wild-type and Crol-KO 3rd instar whole larvae.