ArticlePloS one2013
Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 67 citations in OpenAlex.
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- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
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- Toward a monocot SynBio toolkit: assessing regulatory element performance and eudicot compatibility.Plant cell reports · 2025Article
- Foundation models in plant molecular biology: advances, challenges, and future directions.Frontiers in plant science · 2025Review
- Widespread position-dependent transcriptional regulatory sequences in plants.Nature genetics · 2024Article
- A foundational large language model for edible plant genomes.Communications biology · 2024Article
- Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies.BMC genomics · 2024Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- Predmoter-cross-species prediction of plant promoter and enhancer regions.Bioinformatics advances · 2024Article
- On the Role of TATA Boxes and TATA-Binding Protein inPlants (Basel, Switzerland) · 2023Review
- Transcriptional and post-transcriptional controls for tuning gene expression in plants.Current opinion in plant biology · 2023Review
- Plant Promoters and Terminators for High-Precision Bioengineering.Biodesign research · 2023Review
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.Briefings in bioinformatics · 2021Article
- The durum wheat annexin, TdAnn6, improves salt and osmotic stress tolerance in Arabidopsis via modulation of antioxidant machinery.Protoplasma · 2021Article
- Article
- Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters.Nature plants · 2021Article
- In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes inInternational journal of molecular sciences · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription initiation, essential to gene expression regulation, involves recruitment of basal transcription factors to the core promoter elements (CPEs). The distribution of currently known CPEs across plant genomes is largely unknown. This is the first large scale genome-wide report on the computational prediction of CPEs across eight plant genomes to help better understand the transcription initiation complex assembly. The distribution of thirteen known CPEs across four monocots (Brachypodium distachyon, Oryza sativa ssp. japonica, Sorghum bicolor, Zea mays) and four dicots (Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera, Glycine max) reveals the structural organization of the core promoter in relation to the TATA-box as well as with respect to other CPEs. The distribution of known CPE motifs with respect to transcription start site (TSS) exhibited positional conservation within monocots and dicots with slight differences across all eight genomes. Further, a more refined subset of annotated genes based on orthologs of the model monocot (O. sativa ssp. japonica) and dicot (A. thaliana) genomes supported the positional distribution of these thirteen known CPEs. DNA free energy profiles provided evidence that the structural properties of promoter regions are distinctly different from that of the non-regulatory genome sequence. It also showed that monocot core promoters have lower DNA free energy than dicot core promoters. The comparison of monocot and dicot promoter sequences highlights both the similarities and differences in the core promoter architecture irrespective of the species-specific nucleotide bias. This study will be useful for future work related to genome annotation projects and can inspire research efforts aimed to better understand regulatory mechanisms of transcription.
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