ArticleGenome biology2009
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed, 103 citations in OpenAlex.
- Decoding promoter activity from DNA sequence using pre-trained language models.Scientific reports · 2026Article
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches.mSphere · 2024Article
- Developmental and Housekeeping Genes: Two Types of Genetic Organization in theInternational journal of molecular sciences · 2024Review
- Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis inFrontiers in physiology · 2024Article
- Investigating the sequence landscape in thePeerJ · 2023Article
- Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle.Human genomics · 2022Article
- Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction.Nature communications · 2022Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information.BMC genomics · 2022Article
- An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.Genome biology · 2021Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Computational identification and experimental characterization of preferred downstream positions in human core promoters.PLoS computational biology · 2021Article
- Transcription initiation of distant core promoters in a large-sized genome of an insect.BMC biology · 2021Article
- 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
- Transcriptional Enhancers inGenetics · 2020Review
- Predictive features of gene expression variation reveal mechanistic link with differential expression.Molecular systems biology · 2020Article
- Bicoid-Dependent Activation of the Target Gene hunchback Requires a Two-Motif Sequence Code in a Specific Basal Promoter.Molecular cell · 2019Article
- Article
7 more citing papers are in PubMed but not listed here.
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5 authors at 2 institutions in 2 countries.
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Abstract
backgroundTranscription initiation is a key component in the regulation of gene expression. mRNA 5' full-length sequencing techniques have enhanced our understanding of mammalian transcription start sites (TSSs), revealing different initiation patterns on a genomic scale.
resultsTo identify TSSs in Drosophila melanogaster, we applied a hierarchical clustering strategy on available 5' expressed sequence tags (ESTs) and identified a high quality set of 5,665 TSSs for approximately 4,000 genes. We distinguished two initiation patterns: 'peaked' TSSs, and 'broad' TSS cluster groups. Peaked promoters were found to contain location-specific sequence elements; conversely, broad promoters were associated with non-location-specific elements. In alignments across other Drosophila genomes, conservation levels of sequence elements exceeded 90% within the melanogaster subgroup, but dropped considerably for distal species. Elements in broad promoters had lower levels of conservation than those in peaked promoters. When characterizing the distributions of ESTs, 64% of TSSs showed distinct associations to one out of eight different spatiotemporal conditions. Available whole-genome tiling array time series data revealed different temporal patterns of embryonic activity across the majority of genes with distinct alternative promoters. Many genes with maternally inherited transcripts were found to have alternative promoters utilized later in development. Core promoters of maternally inherited transcripts showed differences in motif composition compared to zygotically active promoters.
conclusionsOur study provides a comprehensive map of Drosophila TSSs and the conditions under which they are utilized. Distinct differences in motif associations with initiation pattern and spatiotemporal utilization illustrate the complex regulatory code of transcription initiation.
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