A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression [RNA-seq]

Differential gene transcription enables development and homeostasis in all animals and is regulated by two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers. While enhancers have been thoroughly characterized, the properties and mechansisms of silencers remain largely unknown. By an unbiased genome-wide functional screen in Drosophila melanogaster S2 cells, we discover a novel class of silencers that bind one of three transcription factors (TFs) and are generally not included in chromatin-defined CRE catalogs, as they mostly lack detectable DNA accessibility. The silencer-binding TF CG11247, which we term Saft, safeguards cell fate decisions in vivo and functions via a novel highly-conserved domain ZAC and the corepressor G9a, independently of G9a’s H3K9-methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanisms has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes. To investigate the gene-regulatory functions of the CG11247/Saft transcription factor, we profiled gene expression by RNA-seq in the Drosophila melanogaster brain, ovary and Schneider S2 cells in wt or CG11247/Saft knockout/depletion conditions. Fly tissue experiments were performed in two indepedent Saft frame-shift knockout strains or the parent wt strain. Schneider S2 cell experiments were performed in a CG11247/Saft-FLAG-AID-tagged cell line under 24h and 48h auxin-induced CG11247/Saft depletion or no auxin treatment. Two (brain and Schneider S2 cells) or three (ovary) biological replicates were sequenced in single-read mode.