A cell type-specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage

Regulators of chromatin accessibility play key roles in cell fate transitions, triggering the onset of novel transcription programs as cells differentiate. In the Drosophila male germline stem cell lineage, tMAC, a master regulator of spermatocyte differentiation that binds thousands of loci, is required for local opening of chromatin, allowing activation of spermatocyte-specific promoters. Here we show that a cell type-specific surveillance system involving the multiple zinc finger protein Kmg and the pipsqueak domain protein Dany dampens transcriptional output from weak tMAC-dependent promoters and counteracts tMAC binding at thousands of additional cryptic promoters, thus preventing massive expression of aberrant protein-coding transcripts. ChIP-seq showed Kmg enriched at the tMAC-bound promoters that it repressed, consistent with direct action. In contrast, Kmg and Dany did not repress highly expressed tMAC-dependent genes, where they colocalized with their binding partner, the chromatin remodeler Mi-2 (NuRD), along the transcribed regions rather than at the promoter. We discuss a model where Kmg, together with Dany and Mi-2, dampens expression from weak or ectopic promoters while allowing robust transcription from highly expressed Aly-dependent genes.