ArticleNucleic acids research2015
Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed, 109 citations in OpenAlex.
- Article
- 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
- The genetic control of rapid genome content divergence inbioRxiv : the preprint server for biology · 2026Article
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2026Article
- A pangenome insight into the genome divergence and flower color diversity among Rhododendron species.BMC genomics · 2026Article
- DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst inInternational journal of molecular sciences · 2025Article
- Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Epigenetic variation in early and late flowering plants of the rubber-producing Russian dandelion Taraxacum koksaghyz provides insights into the regulation of flowering time.Scientific reports · 2024Article
- Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes.Horticulture research · 2024Article
- NLR receptors in plant immunity: making sense of the alphabet soup.EMBO reports · 2023Review
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- The creation of autotetraploid provides insights into critical features of DNA methylome changes after genome doubling in water spinach (Frontiers in plant science · 2023Article
- Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors.International journal of molecular sciences · 2022Review
- Review
- Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.).The Plant journal : for cell and molecular biology · 2022Article
- Article
- The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass,Frontiers in plant science · 2022Article
- Transposable Elements: Distribution, Polymorphism, and Climate Adaptation inFrontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes of higher eukaryotes, including plants, contain numerous transposable elements (TEs), that are often silenced by epigenetic mechanisms, such as histone modifications and DNA methylation. Although TE silencing adversely affects expression of nearby genes, recent studies reveal the presence of intragenic TEs marked by repressive heterochromatic epigenetic marks within transcribed genes. However, even for the well-studied plant model Arabidopsis thaliana, the abundance of intragenic TEs, how they are epigenetically regulated, and their potential impacts on host gene expression, remain unexplored. In this study, we comprehensively analyzed genome-wide distribution and epigenetic regulation of intragenic TEs in A. thaliana. Our analysis revealed that about 3% of TEs are located within gene bodies, dominantly at intronic regions. Most of them are shorter and less methylated than intergenic TEs, but they are still targeted by RNA-directed DNA methylation-dependent and independent pathways. Surprisingly, the heterochromatic epigenetic marks at TEs are maintained within actively transcribed genes. Moreover, the heterochromatic state of intronic TEs is critical for proper transcription of associated genes. Our study provides the first insight into how intragenic TEs affect the transcriptional landscape of the A. thaliana genome, and suggests the importance of epigenetic mechanisms for regulation of TEs within transcriptional gene units.
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