ArticleThe Plant cell2022
Modeling temporal and hormonal regulation of plant transcriptional response to wounding.
Article in The Plant cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 51 citations in OpenAlex.
- Evaluation of the genes CYPEnvironmental science and pollution research international · 2026Article
- Pretreatment with Silver Thiosulfate Increases the Auxin-Inductive Effect for Rooting Mature Chestnut Shoots.Plants (Basel, Switzerland) · 2025Article
- Strigolactones modulate jasmonate-dependent transcriptional reprogramming during wound signalling in Arabidopsis.Journal of applied genetics · 2025Article
- Predicting Gene Expression Responses to Cold inGenes · 2025Article
- Temporal Dynamics With and Without a Nervous System: Plant Physiology, Communication, and Movement.Cognitive science · 2025Review
- Impact of Lepidopteran Oral Secretions on the Transcriptome ofPlant direct · 2025Article
- Ethylene Action Inhibition Improves Adventitious Root Induction in Adult Chestnut Tissues.Plants (Basel, Switzerland) · 2024Article
- Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression.Quantitative plant biology · 2024Article
- Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research.The Plant journal : for cell and molecular biology · 2023Review
- Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton.BMC biology · 2023Article
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- A hybrid multifunctional physicochemical sensor suite for continuous monitoring of crop health.Scientific reports · 2023Article
- Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice.Frontiers in plant science · 2023Article
- Transcriptomics Analysis Reveals a Putative Role for Hormone Signaling and MADS-Box Genes in Mature Chestnut Shoots Rooting Recalcitrance.Plants (Basel, Switzerland) · 2022Article
- Extracellular ATP plays an important role in systemic wound response activation.Plant physiology · 2022Article
- Decoding the cis-regulation of tomato fruit development with deep learning.The Plant cell · 2022Article
- Machine learning models reveal the importance of time-point specific cis-regulatory elements in Arabidopsis thaliana wounding response.The Plant cell · 2022Article
- Temporal regulation of cold transcriptional response in switchgrass.Frontiers in plant science · 2022Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.