ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2011
Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 60 citations in OpenAlex.
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Comparative TSS-seq analysis among natural variations ofNAR genomics and bioinformatics · 2025Article
- SEQSIM: A novel bioinformatics tool for comparisons of promoter regions-a case study of calcium binding protein spermatid associated 1 (CABS1).BMC bioinformatics · 2025Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.G3 (Bethesda, Md.) · 2023Article
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.bioRxiv : the preprint server for biology · 2023Article
- Building a pipeline to identify and engineer constitutive and repressible promoters.Quantitative plant biology · 2023Article
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- The Epigenetic Regulation in Plant Specialized Metabolism: DNA Methylation Limits PaclitaxelFrontiers in plant science · 2022Article
- Article
- A Fruitful Decade Using Synthetic Promoters in the Improvement of Transgenic Plants.Frontiers in plant science · 2019Review
- Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.The Plant cell · 2016Review
- SENSITIVE TO PROTON RHIZOTOXICITY1, CALMODULIN BINDING TRANSCRIPTION ACTIVATOR2, and other transcription factors are involved in ALUMINUM-ACTIVATED MALATE TRANSPORTER1 expression.Plant physiology · 2015Article
- Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.The Plant cell · 2014Article
- Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters.BMC genomics · 2013Article
- Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice.Rice (New York, N.Y.) · 2013Article
- Gene promoters show chromosome-specificity and reveal chromosome territories in humans.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is now well known that vertebrates use multiple types of core promoter to accomplish differentiated tasks in Pol II-dependent transcription. Several transcriptional characteristics are known to be associated with core types, including distribution patterns of transcription start sites (TSSs) and selection between tissue-specific and constitutive expression profiles. However, their relationship to gene structure is poorly understood. In this report, we carried a comparative analysis of three Arabidopsis core types, TATA, GA, and Coreless, with regard to gene structure. Our genome-wide investigation was based on the peak TSS positions in promoters that had been identified in a large-scale experimental analysis. This analysis revealed that the types of core promoter are related with the room for promoters that is measured as the distance from the TSS to the end of the upstream gene, the distance from the TSS to the start position of the coding sequence (CDS), and the number and species of the cis-regulatory elements. Of these, it was found that the distance from the TSS to the CDS has a tight, inverse correlation to the expression level, and thus the observed relationship to the core type appears to be indirect. However, promoter length and preference of cis-elements are thought to be a direct reflection of core type-specific transcriptional initiation mechanisms.
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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.