ArticleThe Plant cell2014
Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
64 citing papers in PubMed, 107 citations in OpenAlex.
- 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
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- Decoding hybridization barriers: the molecular and genetic orchestration of the triploid block in Arabidopsis thaliana.BMC plant biology · 2025Review
- Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming.Horticulture research · 2025Article
- Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing.Nucleic acids research · 2024Article
- RNA-directed DNA methylation mutants reduce histone methylation at the paramutated maize booster1 enhancer.Plant physiology · 2024Article
- Molecular basis and evolutionary drivers of endosperm-based hybridization barriers.Plant physiology · 2024Review
- Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation.Plant physiology · 2024Article
- 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
- Review
- Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize.Genome biology · 2023Article
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
- The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm.The Plant cell · 2022Article
- You shall not pass! A Chromatin barrier story in plants.Frontiers in plant science · 2022Review
- CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation.Genome biology and evolution · 2021Article
- An epigenetic basis of inbreeding depression in maize.Science advances · 2021Article
- Genome-wide mapping reveals R-loops associated with centromeric repeats in maize.Genome research · 2021Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Direct and Indirect Transcriptional Effects of Abiotic Stress inFrontiers in plant science · 2021Article
- The Genomics of Plant Satellite DNA.Progress in molecular and subcellular biology · 2021Review
4 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.
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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.