ArticleProceedings of the National Academy of Sciences of the United States of America2015
RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
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128 citing papers in PubMed, 235 citations in OpenAlex.
- Presence and function of small RNAs during plant reproduction.RNA biology · 2026Review
- 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
- Genome-Wide DNA Methylation Analysis of the Toxicological Responses to Foliar Cerium Application in Soybean.Toxics · 2026Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- Reconfiguration of DNA methylation at growth resumption after winter dormancy in Kiwifruit.Scientific reports · 2025Article
- Decades' progress and prospects on maize functional genomics and molecular breeding.Science China. Life sciences · 2025Review
- Transcription factor-mediated recruitment of small interfering RNA production.Nature plants · 2025Article
- mop1 affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin.Nature communications · 2025Article
- The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation.Nucleic acids research · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Molecular mechanisms and biological functions of active DNA demethylation in plants.Epigenetics & chromatin · 2025Review
- Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper.Genome biology · 2025Article
- Article
- Transposable Element Landscape in the Monotypic SpeciesBiomolecules · 2025Article
- A maize architect: An epiallele of a PfkB-type carbohydrate kinase affects plant growth and development.The Plant cell · 2025Article
- Genome-wide identification and characterization of DNA methyltransferases and demethylases inFrontiers in plant science · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- An epiallele of a gene encoding a PfkB-type carbohydrate kinase affects plant architecture in maize.The Plant cell · 2024Article
68 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The maize genome is relatively large (∼ 2.3 Gb) and has a complex organization of interspersed genes and transposable elements, which necessitates frequent boundaries between different types of chromatin. The examination of maize genes and conserved noncoding sequences revealed that many of these are flanked by regions of elevated asymmetric CHH (where H is A, C, or T) methylation (termed mCHH islands). These mCHH islands are quite short (∼ 100 bp), are enriched near active genes, and often occur at the edge of the transposon that is located nearest to genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications revealed that mCHH islands mark the transition from heterochromatin-associated modifications to euchromatin-associated modifications. The presence of an mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of insertion/deletions in promoters often influences the presence and position of an mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities and are lost in mop1 and mop3 mutants, but the nearby genes rarely exhibit altered expression levels. Instead, loss of an mCHH island is often accompanied by additional loss of DNA methylation in CG and CHG contexts associated with heterochromatin in nearby transposons. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of nearby genes.
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