ArticleBMC genomics2010
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 98 citations in OpenAlex.
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- 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
- Deciphering the Contribution of TATA Box and 5'UTR to Defense Signaling in Rice Under Blast Infection.Biology · 2025Review
- Harnessing promoter elements to enhance gene editing in plants: perspectives and advances.Plant biotechnology journal · 2025Review
- Comparative Proteome and Weighted Gene Co-Expression Network Analyses Uncover the Mechanism of Wheat Grain Protein Accumulation in Response to Nitrogen Fertilizer Application.Foods (Basel, Switzerland) · 2025Article
- GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte.The Plant journal : for cell and molecular biology · 2025Article
- Core promoterome of barley embryo.Computational and structural biotechnology journal · 2024Article
- Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17.International journal of molecular sciences · 2023Article
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi.BMC plant biology · 2023Article
- Comprehensive Analysis of the NF-YB Gene Family and Expression under Abiotic Stress and Hormone Treatment inInternational journal of molecular sciences · 2023Article
- 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 analysis of the3 Biotech · 2022Article
- Identification of the yield traits related haplotype combinations of transcription factor genesMolecular breeding : new strategies in plant improvement · 2022Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model organisms studied so far have been found to contain either one of these elements. Indeed different core-promoter elements are involved in the recruitment of the TATA-box-binding protein. Here we assessed the possibility of identifying novel functional motifs in plant genes, sharing the TATA-box topological constraints.
resultsWe developed an ab-initio approach considering the preferential location of motifs relative to the TSS. We identified motifs observed at the TATA-box expected location and conserved in both Arabidopsis thaliana and Oryza sativa promoters. We identified TC-elements within non-TA-rich promoters 30 bases upstream of the TSS. As with the TATA-box and TATA-variant sequences, it was possible to construct a unique distance graph with the TC-element sequences. The structural and functional features of TC-element-containing genes were distinct from those of TATA-box- or TATA-variant-containing genes. Arabidopsis thaliana transcriptome analysis revealed that TATA-box-containing genes were generally those showing relatively high levels of expression and that TC-element-containing genes were generally those expressed in specific conditions.
conclusionsOur observations suggest that the TC-elements might constitute a class of novel regulatory elements participating towards the complex modulation of gene expression in plants.
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