ArticlePLoS genetics2020
Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 31 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
- Histone variant H2A.X represses deposition of active H3K4me3 marks and restricts H2A.W incorporation.Nucleic acids research · 2026Article
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology (ONT).Molecular ecology resources · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide.Nature plants · 2024Article
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
- Remodeling of H3K9me3 during the pluripotent to totipotent-like state transition.Stem cell reports · 2023Article
- Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Review
- Satellite DNAs in Health and Disease.Genes · 2022Review
- The Role of DNA Methylation in Genome Defense in Cnidaria and Other Invertebrates.Molecular biology and evolution · 2022Article
- The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements.Mobile DNA · 2022Article
- Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice.The New phytologist · 2021Article
- Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication.Progress in molecular and subcellular biology · 2021Article
- Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis.International journal of molecular sciences · 2020Article
- First Come, First Served: Sui Generis Features of the First Intron.Plants (Basel, Switzerland) · 2020Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intronic regions of eukaryotic genomes accumulate many Transposable Elements (TEs). Intronic TEs often trigger the formation of transcriptionally repressive heterochromatin, even within transcription-permissive chromatin environments. Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of rice genes contain intronic heterochromatin, most of which are associated with TEs and repetitive sequences. These heterochromatic introns are longer and highly enriched in promoter-proximal positions. On the other hand, introns also accumulate hypomethylated short TEs. Genes with heterochromatic introns are implicated in various biological functions. Transcription of genes bearing intronic heterochromatin is regulated by an epigenetic mechanism involving the conserved factor OsIBM2, mutation of which results in severe developmental and reproductive defects. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study demonstrates that heterochromatin is a common epigenetic feature associated with actively transcribed genes in the rice genome.
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