ArticlePLoS genetics2012
Spreading of heterochromatin is limited to specific families of maize retrotransposons.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed, 175 citations in OpenAlex.
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing in Drosophila.Genome biology · 2025Article
- Suppressing an auxin efflux transporter enhances rice adaptation to temperate habitats.Nature communications · 2025Article
- The brown fiber phenotype in cotton line SA-40 is linked to a missing Ty3-like retrotransposon upstream of theFrontiers in plant science · 2025Article
- Epiallelic variation of non-coding RNA genes and their phenotypic consequences.Nature communications · 2024Article
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion.PLoS genetics · 2023Article
- Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Methylation Inhibitor 5-Aza-2'-Deoxycytidine Induces Genome-Wide Hypomethylation in Rice.Rice (New York, N.Y.) · 2022Article
- Article
- You shall not pass! A Chromatin barrier story in plants.Frontiers in plant science · 2022Review
- Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Assessment of natural DNA methylation variation and its association with economically important traits in dolichos bean (Lablab purpureus L. Var. Lignosus) using AMP-PCR assay.Journal of applied genetics · 2021Article
- Drought induces variation in the DNA methylation status of the barley HvDME promoter.Journal of plant research · 2021Article
- Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse.Epigenetics & chromatin · 2021Article
- The genomic ecosystem of transposable elements in maize.PLoS genetics · 2021Article
- Whole-genome variation of transposable element insertions in a maize diversity panel.G3 (Bethesda, Md.) · 2021Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
Abstract
Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some retrotransposon families exhibit enrichment of heterochromatic marks within 800-1,200 base pairs of insertion sites, while other families exhibit very little evidence for the spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the heterochromatin in low-copy DNA flanking retrotransposons often results from the spreading of silencing marks rather than insertion-site preferences. Genes located near TEs that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of retrotransposon families may act as controlling elements influencing neighboring sequences, while the majority of retrotransposons have little effect on flanking sequences.
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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.