ArticleGenome research2012
High-resolution mapping of open chromatin in the rice genome.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 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
133 citing papers in PubMed, 243 citations in OpenAlex.
- Targeted mutagenesis and base editing using engineeredPlant biotechnology (Tokyo, Japan) · 2026Article
- Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- Genome-wide profiling and functional characterization of N4-acetyldeoxycytosine reveals conserved epigenetic roles in rice and Arabidopsis.BMC genomics · 2026Article
- Analysis of DNA methylation changes following Cfp1 knockout in mouse spermatocytes.Animal bioscience · 2025Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Epitranscriptomic Control of Drought Tolerance in Rice: The Role of RNA Methylation.Plants (Basel, Switzerland) · 2025Review
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper.Genome biology · 2025Article
- Suppressing an auxin efflux transporter enhances rice adaptation to temperate habitats.Nature communications · 2025Article
- Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.Genome biology · 2024Article
- Functional Characterization of Accessible Chromatin in Common Wheat.International journal of molecular sciences · 2024Article
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- Characterization of the DNA accessibility of chloroplast genomes in grasses.Communications biology · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry.Nature communications · 2024Article
- Advances in epigenetic studies of plant cadmium stress.Frontiers in plant science · 2024Review
- Dynamics ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton.BMC biology · 2023Article
73 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
7 authors at 4 institutions in 1 country.
Funding
Abstract
Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in the callus than in the seedling. For DH sites detected in both the seedling and callus, 31% displayed significantly different levels of DNase I sensitivity within the two tissues. Genes that are differentially expressed in the seedling and callus were frequently associated with DH sites in both tissues. The DNA sequences contained within the DH sites were hypomethylated, consistent with what is known about active gene regulatory elements. Interestingly, tissue-specific DH sites located in the promoters showed a higher level of DNA methylation than the average DNA methylation level of all the DH sites located in the promoters. A distinct elevation of H3K27me3 was associated with intergenic DH sites. These results suggest that epigenetic modifications play a role in the dynamic changes of the numbers and DNase I sensitivity of DH sites during development.
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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.