ArticleProceedings of the National Academy of Sciences of the United States of America2011
Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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129 citing papers in PubMed, 218 citations in OpenAlex.
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- Identification, evolution, and expression analysis of the PEBP gene family in tobacco (Nicotiana tabacum) and its role in flowering regulation via interaction with 14-3-3 proteins.BMC plant biology · 2026Article
- Cis-regulatory elements in CAMTA-mediated stress signalling: mechanisms and prospects for CRISPR-based crop improvement.Frontiers in plant science · 2026Review
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- Identification and application of bioparts for plant synthetic biology.Molecules and cells · 2025Review
- Identification of the Q-type ZFP gene family in Triticeaes and drought stress expression analysis in common wheat.Genetica · 2025Article
- Mechanisms of plant acclimation to multiple abiotic stresses.Communications biology · 2025Review
- Genome-wide identification of PEBP gene family inFrontiers in plant science · 2025Article
- Requirement of two simultaneous environmental signals for activation of ArabidopsisPlant signaling & behavior · 2024Article
- Genome-Wide Profiling of the ACTIN Gene Family and Its Implications for Agronomic Traits inInternational journal of molecular sciences · 2024Article
- Genomic identification and expression profiling of DMP genes in oat (Avena sativa) elucidate their responsiveness to seed aging.BMC genomics · 2024Article
- Characterization of theInternational journal of molecular sciences · 2024Article
- Genome-wide characterization of DELLA gene family in blueberry (Vaccinium darrowii) and their expression profiles in development and response to abiotic stress.BMC genomics · 2024Article
- Exploring Evolutionary Pathways and Abiotic Stress Responses through Genome-Wide Identification and Analysis of the Alternative Oxidase (AOX) Gene Family in Common Oat (International journal of molecular sciences · 2024Article
- Molecular characterization and expression patterns of MTP genes under heavy metal stress in mustard (Brassica juncea L.).Scientific reports · 2024Article
- Multiome in the Same Cell Reveals the Impact of Osmotic Stress on Arabidopsis Root Tip Development at Single-Cell Level.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Evidence Supporting a Role of Alternative Splicing Participates in Melon (International journal of molecular sciences · 2024Article
69 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Environmental stress leads to dramatic transcriptional reprogramming, which is central to plant survival. Although substantial knowledge has accumulated on how a few plant cis-regulatory elements (CREs) function in stress regulation, many more CREs remain to be discovered. In addition, the plant stress cis-regulatory code, i.e., how CREs work independently and/or in concert to specify stress-responsive transcription, is mostly unknown. On the basis of gene expression patterns under multiple stresses, we identified a large number of putative CREs (pCREs) in Arabidopsis thaliana with characteristics of authentic cis-elements. Surprisingly, biotic and abiotic responses are mostly mediated by two distinct pCRE superfamilies. In addition, we uncovered cis-regulatory codes specifying how pCRE presence and absence, combinatorial relationships, location, and copy number can be used to predict stress-responsive expression. Expression prediction models based on pCRE combinations perform significantly better than those based on simply pCRE presence and absence, location, and copy number. Furthermore, instead of a few master combinatorial rules for each stress condition, many rules were discovered, and each appears to control only a small subset of stress-responsive genes. Given there are very few documented interactions between plant CREs, the combinatorial rules we have uncovered significantly contribute to a better understanding of the cis-regulatory logic underlying plant stress response and provide prioritized targets for experimentation.
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