ArticlePlant physiology2022
Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription.
Article in Plant physiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 34 citations in OpenAlex.
- The DNA G-Quadruplex-Stabilizing Ligand TMPyP4 Inhibits Maize Radicle Growth by Modulating Reactive Oxygen Species Homeostasis.Life (Basel, Switzerland) · 2026Article
- TOP1α-mediated stabilization of CYP82C4 G-quadruplex DNA represses lateral root primordium initiation in Arabidopsis.Nature plants · 2026Article
- Role of chromosome ends in meiotic stability, recombination and wheat evolution in the context of breeding.BMC plant biology · 2025Article
- Decoding G-Quadruplexes Sequence inPlants (Basel, Switzerland) · 2025Article
- Global identification and functional characterization of Z-DNA in rice.Plant biotechnology journal · 2025Article
- Protocol for cellular RNA G-quadruplex profiling using G4RP.v2.STAR protocols · 2024Article
- The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress.International journal of molecular sciences · 2024Article
- 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
- CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis inInternational journal of molecular sciences · 2023Article
- The multivalent G-quadruplex (G4)-ligands MultiTASQs allow for versatile click chemistry-based investigations.RSC chemical biology · 2023Article
- Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs.iScience · 2023Article
- Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds inLife (Basel, Switzerland) · 2023Article
- Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Mitochondria and G-quadruplex evolution: an intertwined relationship.Trends in genetics : TIG · 2023Review
- Interactions of small molecules with DNA junctions.Nucleic acids research · 2022Review
- The Newly Sequenced Genome ofInternational journal of molecular sciences · 2022Article
- Epigenomic Features and Potential Functions of KInternational journal of molecular sciences · 2022Article
- Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice.Nucleic acids research · 2022Article
- Unraveling the role of DNA G-quadruplexes in transcription in the rice.Plant physiology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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.