ArticleBMC genomics2015
Global epigenomic analysis indicates that epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 43 citations in OpenAlex.
- Haplotype-resolved 3D genome maps reveal RNAPII-mediated allelic regulation in hybrid rice.aBIOTECH · 2026Article
- Comparative transcriptomics among peach, almond and their interspecific F1 hybrid reveal key common and species-specific regulatory pathways involved in fruit development.BMC plant biology · 2026Article
- Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs.Nature communications · 2025Article
- Sequence and parent-of-origin dependent mThe EMBO journal · 2025Article
- Suppressing an auxin efflux transporter enhances rice adaptation to temperate habitats.Nature communications · 2025Article
- Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit.International journal of molecular sciences · 2025Article
- Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives.International journal of molecular sciences · 2024Review
- Insights into heterosis from histone modifications in the flag leaf of inter-subspecific hybrid rice.BMC plant biology · 2024Article
- Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato.BMC plant biology · 2024Article
- Epigenetic Regulation in Heterosis and Environmental Stress: The Challenge of Producing Hybrid Epigenomes to Face Climate Change.Epigenomes · 2023Review
- Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation.Plant communications · 2021Article
- Advances in Research on the Mechanism of Heterosis in Plants.Frontiers in plant science · 2021Review
- Article
- Understanding epigenomics based on the rice model.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.Frontiers in genetics · 2020Review
- Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection.BMC genomics · 2019Article
- Exploiting induced and natural epigenetic variation for crop improvement.Nature reviews. Genetics · 2017Review
- Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs.Rice (New York, N.Y.) · 2016Article
- Cooperation between the H3K27me3 Chromatin Mark and Non-CG Methylation in Epigenetic Regulation.Plant physiology · 2016Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFor heterozygous genes, alleles on the chromatin from two different parents exhibit histone modification variations known as allele-specific histone modifications (ASHMs). The regulation of allele-specific gene expression (ASE) by ASHMs has been reported in animals. However, to date, the regulation of ASE by ASHM genes remains poorly understood in higher plants.
resultsWe used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL × 93-11 and GL × TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study.
conclusionsOur results demonstrate that epialleles from parents can be inherited by the F1 to produce ASHMs in the F1 hybrid. Our findings indicate that ASHM-H3K36me3, rather than H3K27me3, mainly regulates ASE in hybrid rice.
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