ArticleGenome research2019
Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Dbp7 interacts with RNA exosome component Dis3 to mediate CENP-A loading to centromeres.Genome biology · 2026Article
- The DNA G-Quadruplex-Stabilizing Ligand TMPyP4 Inhibits Maize Radicle Growth by Modulating Reactive Oxygen Species Homeostasis.Life (Basel, Switzerland) · 2026Article
- TMS5-mediated R-loop dynamics regulate thermosensitive fertility conversion in rice.Nature communications · 2026Article
- Epitranscriptomic Control of Drought Tolerance in Rice: The Role of RNA Methylation.Plants (Basel, Switzerland) · 2025Review
- Circular RNAs derived from MIR156D promote rice heading by repressing transcription elongation of pri-miR156d through R-loop formation.Nature plants · 2025Article
- Global identification and functional characterization of Z-DNA in rice.Plant biotechnology journal · 2025Article
- Unveiling the distinctive traits of functional rye centromeres: minisatellites, retrotransposons, and R-loop formation.Science China. Life sciences · 2024Article
- Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat.Science China. Life sciences · 2024Article
- Approaches for Mapping and Analysis of R-loops.Current protocols · 2024Review
- The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.Nucleic acids research · 2024Article
- The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice.International journal of molecular sciences · 2024Article
- Ribonucleotide and R-Loop Damage in Plastid DNA and Mitochondrial DNA during Maize Development.Plants (Basel, Switzerland) · 2023Article
- Centromeric and pericentric transcription and transcripts: their intricate relationships, regulation, and functions.Chromosoma · 2023Review
- A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature.Genome biology · 2023Article
- The expanding role of RNA modifications in plant RNA polymerase II transcripts: highlights and perspectives.Journal of experimental botany · 2023Review
- Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs.iScience · 2023Article
- Non-B-form DNA tends to form in centromeric regions and has undergone changes in polyploid oat subgenomes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis.The New phytologist · 2022Review
- Epigenomic Features and Potential Functions of KInternational journal of molecular sciences · 2022Article
- R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures.Journal of molecular biology · 2022Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expression and epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-loop peak levels was dependent on the positions of R-loops within gene structures (hereafter named "genic position"). Both antisense only (ASO)-R-loops and sense/antisense (S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peak levels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generally spread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. In addition, integrative analyses of R-loop data with existing RNA-seq, chromatin immunoprecipitation sequencing (ChIP-seq), DNase I hypersensitive sites sequencing (DNase-seq), and whole-genome bisulfite sequencing (WGBS or BS-seq) data revealed interrelationships and intricate connections among R-loops, gene expression, and epigenetic signatures. Experimental validation provided evidence that the demethylation of both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants that reveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptional regulation.
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