1/13/2024 0 Comments Promoter consensus sequence![]() Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Core promoter sequence in yeast is a major determinant of expression level. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. ![]() The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Three key subregions contribute to the function of the downstream RNA polymerase II core promoter. The MTE, a new core promoter element for transcription by RNA polymerase II. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. EPD in 2020: enhanced data visualization and extension to ncRNA promoters. Meylan, P., Dreos, R., Ambrosini, G., Groux, R. Eukaryotic core promoters and the functional basis of transcription initiation. The punctilious RNA polymerase II core promoter. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. More broadly, these findings show that functional DNA motifs can be identified by machine learning analysis of a comprehensive set of sequence variants. Notably, there appears to be a duality between the DPR and the TATA box, as many promoters contain one or the other element. These results show that the DPR is a functionally important core promoter element that is widely used in human promoters. We then analysed the HARPE data by support vector regression (SVR) to provide comprehensive models for the sequence motifs, and found that the SVR-based approach is more effective than a consensus-based method for predicting transcriptional activity. We developed a method termed HARPE (high-throughput analysis of randomized promoter elements) to create hundreds of thousands of DPR (or TATA box) variants, each with known transcriptional strength. Here we analyse the human Pol II core promoter and use machine learning to generate predictive models for the downstream core promoter region (DPR) and the TATA box. The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription 1, 2, 3, 4, 5, but the downstream core promoter in humans has been difficult to understand 1, 2, 3.
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