ArticleProceedings of the National Academy of Sciences of the United States of America2013
DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
112 citing papers in PubMed.
- The telomere-to-telomere gap-free reference genome and DNA methylome unveil epigenetic regulation of proanthocyanidin biosynthesis during apricot fruit development.The Plant journal : for cell and molecular biology · 2026Article
- DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications.Genes · 2026Review
- SHH1 cooperates with the DNA methylation reader MBD7 to suppress transcriptional silencing of promoter-methylated genes in Arabidopsis.Plant communications · 2026Article
- Transcription factors instruct DNA methylation patterns in plant reproductive tissues.Nature cell biology · 2025Article
- Loss of function of chromatin remodeler OsCLSY4 leads to RdDM-mediated mis-expression of endosperm-specific genes affecting grain qualities.PLoS genetics · 2025Article
- A chromatin-linked CPL2-PHD2/3 module sustains multiple DNA methylation pathways and Polycomb silencing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes.Nature cell biology · 2025Article
- Epigenetics in Plant Response to Climate Change.Biology · 2025Review
- Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants.Annual review of plant biology · 2025Review
- Review
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing.Nature communications · 2024Article
- Mathematical model of RNA-directed DNA methylation predicts tuning of negative feedback required for stable maintenance.Open biology · 2024Article
- Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler.Nature communications · 2024Article
- Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats.PLoS genetics · 2024Article
- Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation.Current opinion in genetics & development · 2024Review
- Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development.Current opinion in plant biology · 2023Review
- DNA cytosine methylation dynamics and functional roles in horticultural crops.Horticulture research · 2023Article
- DNA-dependent RNA polymerases in plants.The Plant cell · 2023Article
52 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.
Indexed as
Identifiers
What OpenQuestion holds
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.