A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression. Hofbauer et al.

Cell type-specific gene transcription is a profoundly regulated process that enables development and homeostasis in all animals. Two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers, activate or repress transcription, respectively. However, while enhancers have been thoroughly characterized, the sequence and chromatin properties of silencers, as well as their mechanisms of distal transcriptional repression, remain largely unknown. We performed an unbiased genome-wide silencer screen in Drosophila melanogaster S2 cells and discover a novel class of silencers, which recruit one of three different zinc finger transcription factors (TFs) through conserved DNA motifs. Surprisingly, these silencers lack detectable DNA accessibility, placing them outside current chromatin-defined catalogs of CREs (e.g. modENCODE). Further we find that the TF CG11247, which we term Saft, binds to one type of silencers via the orphan DLM3 motif and seems to safeguard cell fate decisions by repressing trachea- and cuticle-specific genes in non- trachea/non-cuticle tissues, such as the ovary or brain. Saft contains the previously unknown, highly conserved effector domain ZAC and functions via the corepressor G9a, yet independently of G9a’s H3K9 methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanism of action has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.