ArticleNature2013
Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 221 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
221 citing papers in PubMed, 403 citations in OpenAlex.
- Dynamic regulation of H3K9 modifications in cancer: pathogenesis and targeted therapies.Biomarker research · 2026Review
- Loss of DET1 in High Pigment 2 Tomato Prevents High Temperature Repression of Anthocyanin Biosynthesis in Fruit Through HY5 Stabilization.Plant, cell & environment · 2026Article
- siRNA-guided DNA-methylation at a sucrose transporter gene potentially contributes to climatic plant adaptation.PLoS biology · 2026Article
- 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
- Dynamic regulatory mechanisms of histone methylation in plant development and environmental adaptation.Horticulture research · 2026Article
- A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium.Genome biology · 2026Article
- DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications.Genes · 2026Review
- Ecological Memory in Plants: Epigenetic Integration of Abiotic Stress and Climate Change.Plants (Basel, Switzerland) · 2026Review
- Long-distance transport of siRNAs with functional roles in pollen development.Nature plants · 2026Article
- Gene Inactivation in Transgenic Plants-A Unique Model for Studying Epigenetic Regulation of Gene Expression.Plants (Basel, Switzerland) · 2026Review
- SHH1 cooperates with the DNA methylation reader MBD7 to suppress transcriptional silencing of promoter-methylated genes in Arabidopsis.Plant communications · 2026Article
- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- Transcription factor-mediated recruitment of small interfering RNA production.Nature plants · 2025Article
- Transcription factors instruct DNA methylation patterns in plant reproductive tissues.Nature cell biology · 2025Article
- The H3K27me3 reader UAD-2 recruits a TAF-12-containing transcription machinery to initiate piRNA expression within heterochromatic clusters.Nature communications · 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
- mop1 affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin.Nature communications · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Molecular mechanisms and biological functions of active DNA demethylation in plants.Epigenetics & chromatin · 2025Review
161 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
9 authors at 5 institutions in 1 country.
Funding
Abstract
DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.
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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.