ArticlePLoS genetics2019
Monitoring the interplay between transposable element families and DNA methylation in maize.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 74 citations in OpenAlex.
- Constitutive and tissue-specific target site preferences of the maize Mutator transposon.bioRxiv : the preprint server for biology · 2026Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- Precise engineering of gene expression by editing plasticity.Genome biology · 2025Article
- Emerging trends in genome integration tools for precision engineering of diverse bacterial species.Synthetic biology (Oxford, England) · 2025Review
- Influence of aging and maternal protein restriction on PIWI-interacting RNA expression in the offspring rat ventral prostate.Scientific reports · 2024Article
- Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm.The Plant journal : for cell and molecular biology · 2024Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.G3 (Bethesda, Md.) · 2024Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- Epiallelic variation of non-coding RNA genes and their phenotypic consequences.Nature communications · 2024Article
- Establishing an optimized ATAC-seq protocol for the maize.Frontiers in plant science · 2024Article
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- Article
- Review
- DNA demethylation affects imprinted gene expression in maize endosperm.Genome biology · 2022Article
- DNA methylation dynamics during stress response in woodland strawberry (Horticulture research · 2022Article
- You shall not pass! A Chromatin barrier story in plants.Frontiers in plant science · 2022Review
- Epigenome plasticity in plants.Nature reviews. Genetics · 2022Review
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) in many eukaryotic genomes. A majority of the maize genome is derived from TEs that can be classified into different orders and families based on their mechanism of transposition and sequence similarity, respectively. TEs themselves are highly methylated and it can be tempting to view them as a single uniform group. However, the analysis of DNA methylation profiles in flanking regions provides evidence for distinct groups of chromatin properties at different TE families. These differences among TE families are reproducible in different tissues and different inbred lines. TE families with varying levels of DNA methylation in flanking regions also show distinct patterns of chromatin accessibility and modifications within the TEs. The differences in the patterns of DNA methylation flanking TE families arise from a combination of non-random insertion preferences of TE families, changes in DNA methylation triggered by the insertion of the TE and subsequent selection pressure. A set of nearly 70,000 TE polymorphisms among four assembled maize genomes were used to monitor the level of DNA methylation at haplotypes with and without the TE insertions. In many cases, TE families with high levels of DNA methylation in flanking sequence are enriched for insertions into highly methylated regions. The majority of the >2,500 TE insertions into unmethylated regions result in changes in DNA methylation in haplotypes with the TE, suggesting the widespread potential for TE insertions to condition altered methylation in conserved regions of the genome. This study highlights the interplay between TEs and the methylome of a major crop species.
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