ArticleScientific reports2022
Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 10 citations in OpenAlex.
- PLETHORA-autophagy axis activates organ regeneration through ROS modulation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Comparative TSS-seq analysis among natural variations ofNAR genomics and bioinformatics · 2025Article
- ABC1K2 is involved in stress response and secondary metabolism during seed development in Arabidopsis thaliana.Plant cell reports · 2025Article
- Combining the CowPEAsy Web Application With in Planta Agroinfiltration for Native Promoter Validation in Vigna unguiculata.Plant, cell & environment · 2025Article
- Species-specific design of artificial promoters by transfer-learning based generative deep-learning model.Nucleic acids research · 2024Article
- The landscape of transcription factor promoter activity during vegetative development in Marchantia.The Plant cell · 2024Article
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis.Nucleic acids research · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes are transcribed from transcription start sites (TSSs), and their position in a genome is strictly controlled to avoid mis-expression of undesired regions. In this study, we designed and developed a methodology for the evaluation of promoter context, which detects proximal promoter regions from - 200 to - 60 bp relative to a TSS, in Arabidopsis and rice genomes. The method positively evaluates spacer sequences and Regulatory Element Groups, but not core promoter elements like TATA boxes, and is able to predict the position of a TSS within a width of 200 bp. An important feature of the evaluation/prediction method is its independence of the core promoter elements, which was demonstrated by successful prediction of all the TATA, GA, and coreless types of promoters without notable differences in the accuracy of prediction. The positive relationship identified between the evaluation scores and gene expression levels suggests that this method is useful for the evaluation of promoter maturity.
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