ArticleMolecular systems biology2021
A genome-scale TF-DNA interaction network of transcriptional regulation of Arabidopsis primary and specialized metabolism.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Unraveling the metabolic regulation of Eleutherococcus senticosus leaves by Penicillium oxalicum: insights from targeted and non-targeted metabolomics.BMC plant biology · 2026Article
- Transcription factor-promoter interactions forbioRxiv : the preprint server for biology · 2025Article
- Transcription Factors in Plant Gene Expression Regulation.International journal of molecular sciences · 2025Article
- A functional and applied perspective of Vitreoscilla hemoglobin: from oxygen carriage to biotechnological innovation.Biotechnology letters · 2025Review
- Article
- Novel Regulators and Their Epistatic Networks in Arabidopsis' Defence Responses to Alternaria alternata Infection.Molecular plant pathology · 2025Article
- Recent advances in paclitaxel biosynthesis and regulation.Journal of experimental botany · 2025Review
- Transcriptional activation ofFrontiers in plant science · 2025Article
- Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Evolution of the biochemistry underpinning purine alkaloid metabolism in plants.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- The landscape of transcription factor promoter activity during vegetative development in Marchantia.The Plant cell · 2024Article
- The RNA-Binding Protein BoRHON1 Positively Regulates the Accumulation of Aliphatic Glucosinolates in Cabbage.International journal of molecular sciences · 2024Article
- The Putative GATA Transcription FactorLife (Basel, Switzerland) · 2024Article
- Plant biochemical genetics in the multiomics era.Journal of experimental botany · 2023Review
- Non-canonical and developmental roles of the TCA cycle in plants.Current opinion in plant biology · 2023Review
- Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.Molecular systems biology · 2023Article
- Chemical imaging reveals diverse functions of tricarboxylic acid metabolites in root growth and development.Nature communications · 2023Article
- The SmMYB36-SmERF6/SmERF115 module regulates the biosynthesis of tanshinones and phenolic acids inHorticulture research · 2023Article
- Feature importance network reveals novel functional relationships between biological features inFrontiers in plant science · 2022Article
- A genome-scale TF-DNA interaction network of transcriptional regulation of Arabidopsis primary and specialized metabolism.Molecular systems biology · 2021Article
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Authors and funding
11 authors.
Funding
Abstract
Plant metabolism is more complex relative to individual microbes. In single-celled microbes, transcriptional regulation by single transcription factors (TFs) is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Plant primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber, and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana TFs and gene promoters in primary and specialized metabolic pathways were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the tricarboxylic acid (TCA) cycle. The resulting network suggests that plant metabolic design principles are distinct from those of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.
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