Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [ATAC-Seq - INTACT]

TATA box-containing promoters are often associated with tissue-specific effector genes, genes that are important for the structure and function of differentiated tissues. The underlying reason for this promoter preference is unclear, in part because tissue-specific genes have not been studied as widely as genes that drive embryonic development. To fill this gap in knowledge, we performed single-cell RNA-seq on differentiated cells derived from the late Drosophila embryo, identified the various tissues and analyzed the relationship between promoter types and gene expression across tissues. Our analysis confirmed the usage of TATA-containing promoters but revealed that tissue-specific effector genes are induced by two distinct promoter types, which have different mechanisms of regulation by RNA polymerase II (Pol II) and different expression characteristics. TATA-enriched promoters are highly tissue-specific and are only occupied by Pol II in the tissue in which they are active; the other promoter type is depleted in TATA motifs and shows high levels of paused Pol II throughout the embryo, even in tissues where the genes are not expressed. Interestingly, the single-cell RNA-seq data revealed that the paused promoters have more robust expression when expressed, but have higher background expression in tissues where these genes are not expressed. TATA genes, on the other hand, have little background expression, but larger variations in expression among the cells that show expression. To explain this difference, we propose that TATA-containing promoters have a higher activation barrier, but preferentially evolve in tissue-specific genes due to their strong activation potential and higher evolvability. Overall design: ScRNAseq, RNAseq,Tissue Specific ChIP-Seq or Whole embryo ChIP-Seq and ATAC-Seq was performed in Drosphila embryos.