ArticleNature plants2022
The landscape of promoter-centred RNA-DNA interactions in rice.
Article in Nature plants, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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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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.
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Who cites it
23 citing papers in PubMed, 32 citations in OpenAlex.
- Decoding chromatin-associated RNA (caRNA) interaction networks: from genome-wide dynamic capture to epigenetic mechanisms in plants and animals.Epigenetics · 2026Review
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- RNA regulation in plants.Science China. Life sciences · 2026Review
- Domestication-Selected Promoter Insertion in WRKY17 Increases Cadmium Sensitivity in Apple.Plant biotechnology journal · 2026Article
- 3D Chromatin Architecture During Early Development: New Methods and New Findings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ChRD-PET: A Method for Mapping RNA-DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- Chromatin-Associated RNAs Regulate Gene Expression and Chromatin Structure.Non-coding RNA · 2025Review
- Simultaneous Capture of Chromatin-Associated RNA and Global RNA-RNA Interactions With Reduced Input Requirements.Bio-protocol · 2025Article
- Generation and characterization of rice OsCENH3 mutants for haploid induction.Plant cell reports · 2025Article
- Comprehensive analysis of RNA-chromatin, RNA-, and DNA-protein interactions.NAR genomics and bioinformatics · 2025Article
- Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq.Nature communications · 2025Article
- IRGL-RRI: interpretable graph representation learning for plant RNA-RNA interaction discovery.Frontiers in plant science · 2025Article
- Article
- Exploring the roles of RNAs in chromatin architecture using deep learning.Nature communications · 2024Article
- Grafting based DNA methylation alteration of snoRNAs in upland cotton (Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning.bioRxiv : the preprint server for biology · 2023Article
- DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis.Science advances · 2023Article
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation.Communications biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin-associated RNAs play key roles in various biological processes. However, both their repository and conjugation genomic loci and potential functions remain largely unclear. Here, we develop an effective method for mapping of chromatin-associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. We present a comprehensive interaction map between RNAs and H3K4me3-marked regions based on H3K4me3 ChRD-PET data, showing three types of RNA-DNA interactions-local, proximal and distal. We further characterize the origin and composition of the RNA strand in R-loop RNA-DNA hybrids and identify that extensive cis and trans RNAs, including trans-non-coding RNAs, are prevalently involved in the R-loop. Integrative analysis of rice epigenome and three-dimensional genome data suggests that both coding and non-coding RNAs engage extensively in the formation of chromatin loops and chromatin-interacting domains. In summary, ChRD-PET is an efficient method for studying the features of RNA-chromatin interactions, and the resulting datasets constitute a valuable resource for the study of RNAs and their biological functions.
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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.