ArticleBMC genomics2006
The features of Drosophila core promoters revealed by statistical analysis.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility.Nucleic acids research · 2025Article
- Review
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Episodes of Rapid Recovery of the Functional Activity of theFrontiers in genetics · 2021Article
- The Core Promoter Is a Regulatory Hub for Developmental Gene Expression.Frontiers in cell and developmental biology · 2021Review
- Sequence Diversity, Locus Structure, and Evolutionary History of theFrontiers in immunology · 2021Article
- Identification and characterization of stem-bulge RNAs in Drosophila melanogaster.RNA biology · 2019Article
- TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis.BMC genomics · 2015Article
- Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation.The Journal of biological chemistry · 2015Article
- Analysis of the sericin1 promoter and assisted detection of exogenous gene expression efficiency in the silkworm Bombyx mori L.Scientific reports · 2015Article
- TRF2: TRansForming the view of general transcription factors.Transcription · 2015Review
- Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome.Nucleic acids research · 2014Article
- Core promoter functions in the regulation of gene expression of Drosophila dorsal target genes.The Journal of biological chemistry · 2014Article
- Regulation of gene expression in the genomic context.Computational and structural biotechnology journal · 2014Review
- P-value-based regulatory motif discovery using positional weight matrices.Genome research · 2013Article
- Article
- Article
- Functional characterization of the sciarid BhC4-1 core promoter in transgenic Drosophila.BMC molecular biology · 2011Article
- Nucleotide composition-linked divergence of vertebrate core promoter architecture.Genome research · 2011Article
- Regulation of gene expression via the core promoter and the basal transcriptional machinery.Developmental biology · 2010Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExperimental investigation of transcription is still a very labor- and time-consuming process. Only a few transcription initiation scenarios have been studied in detail. The mechanism of interaction between basal machinery and promoter, in particular core promoter elements, is not known for the majority of identified promoters. In this study, we reveal various transcription initiation mechanisms by statistical analysis of 3393 nonredundant Drosophila promoters.
resultsUsing 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.
conclusionWe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.