The features of Drosophila core promoters revealed by statistical analysis

Using Drosophila-specific position-weight matrices, we identified promoters containing TATA box, Initiator, Downstream Promoter Element (DPE), and Motif Ten Element (MTE), as well as core elements discovered in Human (TFIIB Recognition Element (BRE) and Downstream Core Element (DCE)). Promoters utilizing known synergetic combinations of two core elements (TATA_Inr, Inr_MTE, Inr_DPE, and DPE_MTE) were identified. We also establish the existence of promoters with potentially novel synergetic combinations: TATA_DPE and TATA_MTE. Our analysis revealed several motifs with the features of promoter elements, including possible novel core promoter element(s). Comparison of Human and Drosophila showed consistent percentages of promoters with TATA, Inr, DPE, and synergetic combinations thereof, as well as most of the same functional and mutual positions of the core elements. No statistical evidence of MTE utilization in Human was found. Distinct nucleosome positioning in particular promoter classes was revealed.We present lists of promoters that potentially utilize the aforementioned elements/combinations. The number of these promoters is two orders of magnitude larger than the number of promoters in which transcription initiation was experimentally studied. The sequences are ready to be experimentally tested or used for further statistical analysis. The developed approach may be utilized for other species.Research over the past thirty years has revealed the diversity of transcription initiation scenarios in eukaryotes. Only some of the scenarios have been studied in detail and more are likely to be discovered. So far, six core promoter elements have been experimentally identified in eukaryotes. These elements are TATA box, Initiator (Inr), Downstream Promoter Element (DPE), TFIIB recognition element (BRE), Downstream Core Element (DCE), and Motif Ten Element (MTE) [1-3].The basal transcriptional machinery includes Pol II and general transcription factors (TF): TFIIA, B, D, E