ArticlePLoS genetics2013
Transposon variants and their effects on gene expression in Arabidopsis.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 145 citations in OpenAlex.
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- DNA methylation remodeling reveals epigenetic regulation of early embryogenesis in Arabidopsis hybrid.Communications biology · 2026Article
- A retrotransposon insertion upstream of Arabidopsis thaliana CRK8 receptor-like kinase modulates a trade-off between pathogen defense and salt tolerance.The Plant journal : for cell and molecular biology · 2025Article
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- Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi.Molecular horticulture · 2025Article
- INCREASED DNA METHYLATION 3 forms a potential chromatin remodelling complex with HAIRPLUS to regulate DNA methylation and trichome development in tomato.The Plant journal : for cell and molecular biology · 2025Article
- TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data.Molecular biology and evolution · 2025Article
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- The evolution of transposable elements ineLife · 2024Article
- Chromosome-level genome assembly of Murraya paniculata sheds light on biosynthesis of floral volatiles.BMC biology · 2023Article
- Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion.PLoS genetics · 2023Article
- Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs inFrontiers in genetics · 2023Article
- DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.Journal of advanced research · 2022Article
- Megakaryopoiesis impairment through acute innate immune signaling activation by azacitidine.The Journal of experimental medicine · 2022Article
- Transposable Elements in the Revealing of Polymorphism-Based Differences in the Seeds of Flax Varieties Grown in Remediated Chernobyl Area.Plants (Basel, Switzerland) · 2022Article
- The evolutionary history of small RNAs in Solanaceae.Plant physiology · 2022Article
- Article
- DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava.Frontiers in plant science · 2022Article
- The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation.International journal of molecular sciences · 2021Review
- Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs.Nucleic acids research · 2021Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA-mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA-targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.
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Registered trials
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.