ArticleNucleic acids research2007
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Generation and Characterization of Novel Low-Amylose Rice Germplasm via Prime Editing of theInternational journal of molecular sciences · 2026Article
- Fruit-Specific Promoters in Plants: Advances, Regulatory Mechanisms and Applications in Plant Biotechnology.Plants (Basel, Switzerland) · 2026Review
- The gene-like promoter and transcription of LTR retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- Research progress on the regulatory mechanisms of the PSY promoter.Transgenic research · 2026Review
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- A transcription factor ensemble orchestrates bundle sheath expression in rice.Nature communications · 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
- Characterization, Evolution, Expression and Functional Divergence of theInternational journal of molecular sciences · 2024Article
- A foundational large language model for edible plant genomes.Communications biology · 2024Article
- Drought stress-inducible synthetic promoters designed for poplar are functional in rice.Plant cell reports · 2024Article
- Review
- 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 characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response.Frontiers in plant science · 2023Article
- Genome-wide analysis of the3 Biotech · 2022Article
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also found in plant promoters, it is not known if CpG-type promoters exist in plants. Plant promoters contain Y Patches (pyrimidine patches) in the core promoter region, and the ubiquity of these beyond higher plants is not understood as well. Sets of promoter sequences were utilized for the analysis of local distribution of short sequences (LDSS), and approximately one thousand octamer sequences have been identified as promoter constituents from Arabidopsis, rice, human and mouse, respectively. Based on their localization profiles, the identified octamer sequences were classified into several major groups, REG (Regulatory Element Group), TATA box, Inr (Initiator), Kozak, CpG and Y Patch. Comparison of the four species has revealed three categories: (i) shared groups found in both plants and mammals (TATA box), (ii) common groups found in both kingdoms but the utilized sequence is differentiated (REG, Inr and Kozak) and (iii) specific groups found in either plants or mammals (CpG and Y Patch). Our comparative LDSS analysis has identified conservation and differentiation of promoter architectures between higher plants and mammals.
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