Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP]

Silencers active in the Drosophila embryonic mesoderm were identified by reporter assays in dissociated embryonic cells. We find that, despite the presence of ChIP peaks for known transcriptional corepressors and marks of repressed chromatin, the only significantly enriched source of mesodermal silencers is non-mesodermal enhancers. We present evidence that a subset of silencers acts by looping to target promoters. Overall design: We generated a population of Drosophila embryos in which GFP is driven by a strong, ubiquitous enhancer modified by the activity of a library of candidate silencers. We FACS-sorted embryonic mesodermal cells with reduced GFP expression and recovered mesodermal silencers by PCR and Illumina high-throughput sequencing.