SynthesisBMC genomics2022
Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum.
Synthesis in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 62 citations in OpenAlex.
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Methionine overaccumulation reinforces heterochromatic non-CG hypermethylation and transposon silencing in Arabidopsis.Plant physiology · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- The gene-like promoter and transcription of LTR retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- Integrative chromosome-scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma.The plant genome · 2026Article
- Genetic diversity and evolution of endogenous pararetroviruses acrossFrontiers in plant science · 2026Article
- Genetic mapping reveals QTLs associated with HLB response determined byFrontiers in plant science · 2026Article
- A Pan-TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- DNA methylation contributes to plant acclimation to naturally fluctuating light.The New phytologist · 2025Article
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- Comparative genomic analyses reveal different genetic basis of two types of fruit in Maloideae.Nature communications · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Genomic Analysis Reveals the Fast-Growing Trait and Improvement Potential for Stress Resistance in the Elite Poplar VarietyInternational journal of molecular sciences · 2025Article
- De novo, high-quality assembly and annotation of the halophyte grass Aeluropus littoralis draft genome and identification of A20/AN1 zinc finger protein family.BMC plant biology · 2025Article
- Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family inJournal of fungi (Basel, Switzerland) · 2025Article
- Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.BioData mining · 2024Article
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- Unlocking plant genetics with telomere-to-telomere genome assemblies.Nature genetics · 2024Review
- Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.Horticulture research · 2024Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum.
resultsWe found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato.
conclusionsOverall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
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