ArticlePLoS genetics2008
Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 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
101 citing papers in PubMed, 181 citations in OpenAlex.
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- Gene regulatory mechanisms downstream of DNA methylation.Nature reviews. Genetics · 2026Review
- A VIM2/4 deletion, and premature truncations of CMT2 and FBX5, drive DNA methylation changes after colonization of a novel habitat.Nature plants · 2026Article
- Genome-wide CG hypomethylation of theProceedings of the National Academy of Sciences of the United States of America · 2026Article
- 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
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Cryo-EM reveals evolutionarily conserved and distinct structural features of plant CG maintenance methyltransferase MET1.Nature communications · 2025Article
- Article
- Using targeted genome methylation for crop improvement.Journal of experimental botany · 2025Review
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Temperature-induced variation in the transcriptome of maritime pine (Pinus pinaster Ait.) embryogenic masses modulates the phenotype of the derived plants.BMC genomics · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Characterization of DNA methylation reader proteins inGenome research · 2024Article
- Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.Nature communications · 2024Article
- GhVIM28, a negative regulator identified from VIM family genes, positively responds to salt stress in cotton.BMC plant biology · 2024Article
- TheMolecules and cells · 2023Article
- Article
- From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution.Functional & integrative genomics · 2023Review
- Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation.bioRxiv : the preprint server for biology · 2023Article
- Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis.Nucleic acids research · 2023Article
41 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
3 authors at 1 institution in 1 country.
Funding
Abstract
Methylcytosine-binding proteins decipher the epigenetic information encoded by DNA methylation and provide a link between DNA methylation, modification of chromatin structure, and gene silencing. VARIANT IN METHYLATION 1 (VIM1) encodes an SRA (SET- and RING-associated) domain methylcytosine-binding protein in Arabidopsis thaliana, and loss of VIM1 function causes centromere DNA hypomethylation and centromeric heterochromatin decondensation in interphase. In the Arabidopsis genome, there are five VIM genes that share very high sequence similarity and encode proteins containing a PHD domain, two RING domains, and an SRA domain. To gain further insight into the function and potential redundancy among the VIM proteins, we investigated strains combining different vim mutations and transgenic vim knock-down lines that down-regulate multiple VIM family genes. The vim1 vim3 double mutant and the transgenic vim knock-down lines showed decreased DNA methylation primarily at CpG sites in genic regions, as well as repeated sequences in heterochromatic regions. In addition, transcriptional silencing was released in these plants at most heterochromatin regions examined. Interestingly, the vim1 vim3 mutant and vim knock-down lines gained ectopic CpHpH methylation in the 5S rRNA genes against a background of CpG hypomethylation. The vim1 vim2 vim3 triple mutant displayed abnormal morphological phenotypes including late flowering, which is associated with DNA hypomethylation of the 5' region of FWA and release of FWA gene silencing. Our findings demonstrate that VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.
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.