ArticleMolecular plant2013
Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.
Article in Molecular plant, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 143 citations in OpenAlex.
- H3K4 Methylation Readers in Plants: Recognition Mechanisms and Biological Functions.International journal of molecular sciences · 2026Review
- Dynamics of H3K4me3 and H3K36me3 histone modifications in response to powdery mildew infection in common wheat.BMC plant biology · 2026Article
- Coordinated epigenomic reprogramming and chromatin-mediated transcriptional regulation during soybean callus development.Frontiers in plant science · 2026Article
- D-limonene inhibits the growth of Fusarium proliferatum by decreasing H3K9ac and H3K27ac modifications.BMC genomics · 2025Article
- Epigenetics in forest trees- key driver to phenotypic plasticity and adaptation under stress.Functional & integrative genomics · 2025Review
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- A chromosome-scale genome assembly and epigenomic profiling reveal temperature-dependent histone methylation in iridoid biosynthesis regulation inHorticulture research · 2025Article
- Genome-wide mapping of main histone modifications and coordination regulation of metabolic genes under salt stress in pea (Horticulture research · 2024Article
- Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat.Nature communications · 2024Article
- Actively Expressed Intergenic Genes Generated by Transposable Element Insertions inPlants (Basel, Switzerland) · 2024Article
- Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato.BMC plant biology · 2024Article
- Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves.Plant molecular biology · 2023Article
- Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model DiatomPlants (Basel, Switzerland) · 2023Article
- Epigenetic Landscape Is Largely Shaped by Diversiform Transposons inInternational journal of molecular sciences · 2023Article
- Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress.BMC genomics · 2022Article
- Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors.International journal of molecular sciences · 2022Review
- Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants.International journal of molecular sciences · 2022Review
- Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat.Nature communications · 2022Article
- Characterization of Histone H3 Gene Family Reveals ThatFrontiers in genetics · 2022Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.
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