ArticleGenome biology2006
Comparative genomics of Drosophila and human core promoters.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed, 158 citations in OpenAlex.
- 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
- 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
- Analysis of Transcript Expression and Core Promoter DNA Sequences of Brain, Adipose Tissues and Testis in Human and Fruit Fly.International journal of molecular sciences · 2025Article
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues.G3 (Bethesda, Md.) · 2024Article
- OVO positively regulates essential maternal pathways by binding near the transcriptional start sites in theeLife · 2024Article
- Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation.bioRxiv : the preprint server for biology · 2024Article
- Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues.bioRxiv : the preprint server for biology · 2024Article
- Interpretable online network dictionary learning for inferring long-range chromatin interactions.PLoS computational biology · 2024Article
- OVO Positively Regulates Essential Maternal Pathways by Binding Near the Transcriptional Start Sites in thebioRxiv : the preprint server for biology · 2024Article
- PMHeliyon · 2024Article
- Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.PLoS computational biology · 2023Article
- Review
- Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.The EMBO journal · 2023Article
- Analysis of theGenes & development · 2023Article
- On the Role of TATA Boxes and TATA-Binding Protein inPlants (Basel, Switzerland) · 2023Review
- Investigating the sequence landscape in thePeerJ · 2023Article
- Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers.Molecular cell · 2022Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe core promoter region plays a critical role in the regulation of eukaryotic gene expression. We have determined the non-random distribution of DNA sequences relative to the transcriptional start site in Drosophila melanogaster promoters to identify sequences that may be biologically significant. We compare these results with those obtained for human promoters.
resultsWe determined the distribution of all 65,536 octamer (8-mers) DNA sequences in 10,914 Drosophila promoters and two sets of human promoters aligned relative to the transcriptional start site. In Drosophila, 298 8-mers have highly significant (p < or = 1 x 10(-16)) non-random distributions peaking within 100 base-pairs of the transcriptional start site. These sequences were grouped into 15 DNA motifs. Ten motifs, termed directional motifs, occur only on the positive strand while the remaining five motifs, termed non-directional motifs, occur on both strands. The only directional motifs to localize in human promoters are TATA, INR, and DPE. The directional motifs were further subdivided into those precisely positioned relative to the transcriptional start site and those that are positioned more loosely relative to the transcriptional start site. Similar numbers of non-directional motifs were identified in both species and most are different. The genes associated with all 15 DNA motifs, when they occur in the peak, are enriched in specific Gene Ontology categories and show a distinct mRNA expression pattern, suggesting that there is a core promoter code in Drosophila.
conclusionDrosophila and human promoters use different DNA sequences to regulate gene expression, supporting the idea that evolution occurs by the modulation of gene regulation.
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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.