ArticleNature communications2022
Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 56 citations in OpenAlex.
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- Regulatory divergence of homoeologs underlies network optimization for fiber improvement in domesticated cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transposable elements and their epigenetic modifications mediate gene expression and subgenome dominance in Brassica carinata.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Genomic and genetic dissection of drought tolerance in a resilient wheat germplasm JIN50.Nature genetics · 2026Article
- Article
- Insights into glandular trichome biology from analysis of organ-specific gene expression programmes in cannabis, hop and tomato.The Plant journal : for cell and molecular biology · 2026Article
- The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation.Nucleic acids research · 2025Article
- Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.Genomics, proteomics & bioinformatics · 2025Article
- Review
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- deepTFBS: Improving within- and Cross-Species Prediction of Transcription Factor Binding Using Deep Multi-Task and Transfer Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- HebQTLs reveal intra-subgenome regulation inducing unbalanced expression and function among bread wheat homoeologs.Genome biology · 2025Article
- TaFT-D1 positively regulates grain weight by acting as a coactivator of TaFDL2 in wheat.Plant biotechnology journal · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Genome-Wide Identification and Functional Analysis ofInternational journal of molecular sciences · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Widespread impact of transposable elements on the evolution of post-transcriptional regulation in the cotton genus Gossypium.Genome biology · 2025Article
- Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14.International journal of molecular sciences · 2025Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
19 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid.
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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.