ArticleNucleic acids research2018
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 53 citations in OpenAlex.
- Naturally Occurring Variability in the Regulatory Region of theInternational journal of molecular sciences · 2026Article
- Enhancer RNA transcription near segmentation gene enhancers can be analyzed in situ using FISH.G3 (Bethesda, Md.) · 2026Article
- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- Coordinated gene family evolution shapes the genome of dimorphic Mucorales.Nature communications · 2026Article
- Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis.Cell reports · 2025Article
- Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.Nature communications · 2024Article
- Review
- Dynamic interplay between non-coding enhancer transcription and gene activity in development.Nature communications · 2023Article
- mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay.PLoS genetics · 2022Article
- CMTr cap-adjacent 2'-O-ribose mRNA methyltransferases are required for reward learning and mRNA localization to synapses.Nature communications · 2022Article
- Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells.Nucleic acids research · 2022Article
- Epromoters function as a hub to recruit key transcription factors required for the inflammatory response.Nature communications · 2021Article
- An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.Genome biology · 2021Article
- Generation and characterization ofJournal of neurogenetics · 2021Article
- Current Advances on the Important Roles of Enhancer RNAs in Molecular Pathways of Cancer.International journal of molecular sciences · 2021Review
- Review
- Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.Nucleic acids research · 2020Article
- Characterization ofThe Plant cell · 2020Article
- Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements.Genes & development · 2020Article
- Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction.Nature genetics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The seemingly separable layer of regulation by gene promoters with housekeeping enhancer potential is also indicated by chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.