ArticleGenome biology2002
Computational analysis of core promoters in the Drosophila genome.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 252 papers.
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Who cites it
252 citing papers in PubMed, 457 citations in OpenAlex.
- Toward transgenic multicellular parasites: CRISPR-Cas12a germline editing ofScience advances · 2026Article
- Naturally Occurring Variability in the Regulatory Region of theInternational journal of molecular sciences · 2026Article
- Machine learning analysis of the human initiator region reveals key features of different types of core promoters.Genes & development · 2026Article
- Decoding promoter activity from DNA sequence using pre-trained language models.Scientific reports · 2026Article
- NovelbioRxiv : the preprint server for biology · 2026Article
- Embedded CRISPRi Enhances Gene-Silencing Efficiency in Drosophila.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Combinatorial histone modifications direct ATP-dependent chromatin remodeling by NURF to promoter-proximal nucleosomes.Nucleic acids research · 2026Article
- Machine Learning Analysis of the Human Initiator Region Reveals Key Features of Different Types of Core Promoters.bioRxiv : the preprint server for biology · 2026Article
- Article
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- Increasing pathogenic germline variant diagnosis rates in precision medicine: current best practices and future opportunities.Human genomics · 2025Review
- Drosophila architectural proteins M1BP and Opbp cooperatively form the active promoter of a ribosomal protein gene.Epigenetics & chromatin · 2025Article
- Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states.Briefings in bioinformatics · 2024Article
- Dissecting thebioRxiv : the preprint server for biology · 2024Article
- OVO positively regulates essential maternal pathways by binding near the transcriptional start sites in theeLife · 2024Article
- From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function in vivo.Development (Cambridge, England) · 2024Article
- Arthropod promoters for genetic control of disease vectors.Trends in parasitology · 2024Review
- OVO Positively Regulates Essential Maternal Pathways by Binding Near the Transcriptional Start Sites in thebioRxiv : the preprint server for biology · 2024Article
- Developmental and Housekeeping Genes: Two Types of Genetic Organization in theInternational journal of molecular sciences · 2024Review
- ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements.Bioinformatics (Oxford, England) · 2024Article
192 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundThe core promoter, a region of about 100 base-pairs flanking the transcription start site (TSS), serves as the recognition site for the basal transcription apparatus. Drosophila TSSs have generally been mapped by individual experiments; the low number of accurately mapped TSSs has limited analysis of promoter sequence motifs and the training of computational prediction tools.
resultsWe identified TSS candidates for about 2,000 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome, while applying stringent criteria concerning coverage and 5'-end distribution. Examination of the sequences flanking these TSSs revealed the presence of well-known core promoter motifs such as the TATA box, the initiator and the downstream promoter element (DPE). We also define, and assess the distribution of, several new motifs prevalent in core promoters, including what appears to be a variant DPE motif. Among the prevalent motifs is the DNA-replication-related element DRE, recently shown to be part of the recognition site for the TBP-related factor TRF2. Our TSS set was then used to retrain the computational promoter predictor McPromoter, allowing us to improve the recognition performance to over 50% sensitivity and 40% specificity. We compare these computational results to promoter prediction in vertebrates.
conclusionsThere are relatively few recognizable binding sites for previously known general transcription factors in Drosophila core promoters. However, we identified several new motifs enriched in promoter regions. We were also able to significantly improve the performance of computational TSS prediction in Drosophila.
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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.