Dissecting the transcriptional regulation during the transition from proliferation to terminal differentiation during fly spermatogenesis

To investigate how the cell-type-specific gene expression program for spermatocyte differentiation turns on in male flies, we used RNA-seq to map transcript levels, CAGE to map transcription start sites (TSS), and ATAC-seq to map chromatin accessibility as proliferating spermatogonia transition to differentiating spermatocytes. Combining these data, we showed that the promoters that turn on when germ cells become spermatocytes lack most of the canonical core promoter motifs. Instead these promoters require tMAC function to become open and accessible, and are enriched for the tMAC ChIP motif and putative Achi/Vis binding motif. Within the local open region that tMAC creates, a good match to the Inr at +1 and ACA and CNAAATT motifs at specific positions downstream correlates with efficiency of individual TSS usage. Our results reveal a robust cell-type-specific and gene-selective developmental transcription program orchestrated by promoter-proximal elements and protein complexes that interact with them. Overall design: Each sequencing assay included spermagonia-enriched and spermatocyte-enriched samples, with 2 or 3 replicates for each condition