ArticleGenome biology2017
The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation.Nucleic acids research · 2025Article
- Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes.Research square · 2025Article
- Genome-wide association study of pre-harvest sprouting resistance and grain color in common wheat (Triticum aestivum L.).BMC plant biology · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024Review
- Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats.PLoS genetics · 2024Article
- Molecular basis and evolutionary drivers of endosperm-based hybridization barriers.Plant physiology · 2024Review
- SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway.Frontiers in plant science · 2024Article
- The Chromatin Remodeling FactorPlants (Basel, Switzerland) · 2023Article
- The transcriptional repressors VAL1 and VAL2 mediate genome-wide recruitment of the CHD3 chromatin remodeler PICKLE in Arabidopsis.The Plant cell · 2022Article
- Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system.Genome biology · 2022Article
- Epigenetic control of abiotic stress signaling in plants.Genes & genomics · 2022Review
- Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Biological role and mechanism of chromatin readers in plants.Current opinion in plant biology · 2021Review
- Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function.PLoS genetics · 2020Article
- Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses.International journal of molecular sciences · 2020Review
- Abnormal Homocysteine Metabolism: An Insight of Alzheimer's Disease from DNA Methylation.Behavioural neurology · 2020Review
- A Chloroplast COR413 Protein FromFrontiers in plant science · 2020Article
- A Role for PICKLE in the Regulation of Cold and Salt Stress Tolerance in Arabidopsis.Frontiers in plant science · 2019Article
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana.
resultsThrough forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant.
conclusionsPKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences non-coding RNA production, DNA methylation, and transcriptional silencing.
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