Characterization of the TCT motif reveals a crucial role of the core promoter micro-environment in gene regulation. Drosophila melanogaster

The signals initiating gene expression are eventually integrated at the core promoter where diverse core promoter motifs interact with the basal transcription machinery to recruit the RNA polymerase. The diversityThe signals initiating gene expression are eventually integrated at the core promoter where diverse core promoter motifs interact with the basal transcription machinery to recruit the RNA polymerase. The diversity in core promoter motif poises their composition as a means to regulate gene expression. We utilized genome-wide (5’GRO-seq) and biochemical methods to characterize the TCT motif in humans and Drosophila and show that it is a functionally conserved RNA polymerase II core promoter element. Human TCT-containing promoters are ~3-fold enriched for the TATA box motif while Drosophila promoters are depleted. The downstream core promoter element (DPE) is underrepresented. Combinatorial analysis revealed the TCT motif to cooperatively facilitate transcription with the TATA box in some instances, but not others implying a role for the core promoter micro-environment in gene regulation. The interaction among core promoter elements is therefore not as straightforward as previously thought. TCT-containing promoters predominantly regulate the expression of genes involved in translation, thereby providing an example how core promoter motifs facilitate regulatory specialization. This may explain why diverse translation-related genes are observed as commonly altered in some cancers. Overall design: Nascent transcript initiation profiles in S2 cells using 5'GRO-Seq