ArticleNature plants2025
The regulatory potential of transposable elements in maize.
Article in Nature plants, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Hybrid origin and phenotype evolution of the modern maize.Journal of integrative plant biology · 2026Review
- The gene-like promoter and transcription of LTR retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic regulation of mycorrhizal symbioses: from plastic responses to transgenerational legacies.The New phytologist · 2026Review
- A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily.Molecular biology and evolution · 2026Article
- Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression.Nature biotechnology · 2026Article
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- 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
- MaizeGDB Phylostrata Tool: exploring evolutionary origins of maize proteins.Bioinformatics advances · 2026Article
- Role of chromosome ends in meiotic stability, recombination and wheat evolution in the context of breeding.BMC plant biology · 2025Article
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A haplotype-resolved view of human gene regulation.bioRxiv : the preprint server for biology · 2025Article
- Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes.BMC genomic data · 2025Article
- Conservation of dichromatin organization along regional centromeres.Cell genomics · 2025Article
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14 authors.
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Abstract
The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read sequencing have hindered our understanding of their regulatory potential. Here we show that long-read chromatin fibre sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature-hypo-5mCpG methylation and diffuse chromatin accessibility-directing TEs to specific loci, including the loci that sparked McClintock's discovery of TEs.
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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.