ArticleNature communications2020
Integrative analysis of reference epigenomes in 20 rice varieties.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed, 222 citations in OpenAlex.
- Haplotype-resolved 3D genome maps reveal RNAPII-mediated allelic regulation in hybrid rice.aBIOTECH · 2026Article
- Targeted anthocyanin biofortification in black rice: a review of spatial metabolic control, growth-defence trade-offs and genotype-environment-management design.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RPT2a-mediated degradation of WDR5a regulates flowering time in Arabidopsis.Plant cell reports · 2026Article
- DNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesis.Nature communications · 2026Article
- Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis.Nature communications · 2026Article
- Premeiotic chromatin states orchestrate gene expression during male gametogenesis in rice.Genome biology · 2026Article
- The CPK3-mediated cytosolic-nuclear translocation of bHLH107 recruits HY5 to regulate the CuJournal of advanced research · 2026Article
- Histone variant H2A.X represses deposition of active H3K4me3 marks and restricts H2A.W incorporation.Nucleic acids research · 2026Article
- Occupancy-based mechanism is the chief mode of ROS1 function in preventing DNA hypermethylation.Nature plants · 2026Article
- Deciphering Pesticide Stress Responses in Rice Through Integrated Multi-Omic Assessment.Toxics · 2026Review
- Genome-wide profiling and functional characterization of N4-acetyldeoxycytosine reveals conserved epigenetic roles in rice and Arabidopsis.BMC genomics · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice.Genome biology · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- ChRD-PET: A Method for Mapping RNA-DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genomic and epigenomic coordination maintains subgenome transcriptional balance in allotetraploidHorticulture research · 2026Article
- H3K4me2 orchestrates H2A.Z and Polycomb repressive marks in Arabidopsis.Nature communications · 2025Article
- ricePSP: a database of rice phase separation-associated proteins.Genome biology · 2025Article
- Epigenetic Regulation of Salt Stress Responses in Rice: Mechanisms and Prospects for Enhancing Tolerance.Epigenomes · 2025Review
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.
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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.