PDF(Pubmed)
Abstract：
BACKGROUND: Inter-subspecific hybrid rice represents a significant breakthrough in agricultural genetics, offering higher yields and better resilience to various environmental stresses. While the utilization of these hybrids has shed light on the genetic processes underlying hybridization, understanding the molecular mechanisms driving heterosis remains a complex and ongoing challenge. Here, chromatin immunoprecipitation-sequencing (ChIP-seq) was used to analyze genome-wide profiles of H3K4me3 and H3K27me3 modifications in the inter-subspecific hybrid rice ZY19 and its parents, Z04A and ZHF1015, then combined them with the transcriptome and DNA methylation data to uncover the effects of histone modifications on gene expression and the contribution of epigenetic modifications to heterosis.
RESULTS: In the hybrid, there were 8,126 and 1,610 different peaks for H3K4me3 and H3K27me3 modifications when compared to its parents, respectively, with the majority of them originating from the parental lines. The different modifications between the hybrid and its parents were more frequently observed as higher levels in the hybrid than in the parents. In ZY19, there were 476 and 84 allele-specific genes with H3K4me3 and H3K27me3 modifications identified, representing 7.9% and 12% of the total analyzed genes, respectively. Only a small portion of genes that showed differences in parental H3K4me3 and H3K27me3 modifications which demonstrated allele-specific histone modifications (ASHM) in the hybrid. The H3K4me3 modification level in the hybrid was significantly lower compared to the parents. In the hybrid, DNA methylation occurs more frequently among histone modification target genes. Additionally, over 62.58% of differentially expressed genes (DEGs) were affected by epigenetic variations. Notably, there was a strong correlation observed between variations in H3K4me3 modifications and gene expression levels in the hybrid and its parents.
CONCLUSIONS: These findings highlight the substantial impact of histone modifications and DNA methylation on gene expression during hybridization. Epigenetic variations play a crucial role in controlling the differential expression of genes, with potential implications for heterosis.
RESULTS: In the hybrid, there were 8,126 and 1,610 different peaks for H3K4me3 and H3K27me3 modifications when compared to its parents, respectively, with the majority of them originating from the parental lines. The different modifications between the hybrid and its parents were more frequently observed as higher levels in the hybrid than in the parents. In ZY19, there were 476 and 84 allele-specific genes with H3K4me3 and H3K27me3 modifications identified, representing 7.9% and 12% of the total analyzed genes, respectively. Only a small portion of genes that showed differences in parental H3K4me3 and H3K27me3 modifications which demonstrated allele-specific histone modifications (ASHM) in the hybrid. The H3K4me3 modification level in the hybrid was significantly lower compared to the parents. In the hybrid, DNA methylation occurs more frequently among histone modification target genes. Additionally, over 62.58% of differentially expressed genes (DEGs) were affected by epigenetic variations. Notably, there was a strong correlation observed between variations in H3K4me3 modifications and gene expression levels in the hybrid and its parents.
CONCLUSIONS: These findings highlight the substantial impact of histone modifications and DNA methylation on gene expression during hybridization. Epigenetic variations play a crucial role in controlling the differential expression of genes, with potential implications for heterosis.
摘要：
背景：亚种间杂交水稻代表了农业遗传学的重大突破，提供更高的产量和更好的抵御各种环境压力的能力。虽然这些杂种的利用揭示了杂交的遗传过程，了解驱动杂种优势的分子机制仍然是一个复杂而持续的挑战。这里,染色质免疫沉淀测序（ChIP-seq）用于分析亚种间杂交水稻ZY19及其亲本中H3K4me3和H3K27me3修饰的全基因组图谱，Z04A和ZHF1015，然后将它们与转录组和DNA甲基化数据相结合，以揭示组蛋白修饰对基因表达的影响以及表观遗传修饰对杂种优势的贡献。
结果：在混合动力车中，与它的亲本相比，H3K4me3和H3K27me3修饰有8,126和1,610个不同的峰，分别,其中大多数来自父母系。杂种与其亲本之间的不同修饰更频繁地观察到，杂种中的水平高于亲本中的水平。在ZY19中，有476和84个等位基因特异性基因与H3K4me3和H3K27me3修饰鉴定，占总分析基因的7.9%和12%，分别。只有一小部分在亲本H3K4me3和H3K27me3修饰中显示差异的基因在杂种中表现出等位基因特异性组蛋白修饰（ASHM）。杂种中的H3K4me3修饰水平显著低于亲本。在混合动力车中，DNA甲基化在组蛋白修饰靶基因中更频繁地发生。此外,超过62.58％的差异表达基因（DEGs）受到表观遗传变异的影响。值得注意的是,在杂种及其亲本中，H3K4me3修饰的变异与基因表达水平之间存在很强的相关性。
结论：这些发现强调了组蛋白修饰和DNA甲基化对杂交过程中基因表达的实质性影响。表观遗传变异在控制基因的差异表达中起着至关重要的作用,对杂种优势有潜在的影响。
结果：在混合动力车中，与它的亲本相比，H3K4me3和H3K27me3修饰有8,126和1,610个不同的峰，分别,其中大多数来自父母系。杂种与其亲本之间的不同修饰更频繁地观察到，杂种中的水平高于亲本中的水平。在ZY19中，有476和84个等位基因特异性基因与H3K4me3和H3K27me3修饰鉴定，占总分析基因的7.9%和12%，分别。只有一小部分在亲本H3K4me3和H3K27me3修饰中显示差异的基因在杂种中表现出等位基因特异性组蛋白修饰（ASHM）。杂种中的H3K4me3修饰水平显著低于亲本。在混合动力车中，DNA甲基化在组蛋白修饰靶基因中更频繁地发生。此外,超过62.58％的差异表达基因（DEGs）受到表观遗传变异的影响。值得注意的是,在杂种及其亲本中，H3K4me3修饰的变异与基因表达水平之间存在很强的相关性。
结论：这些发现强调了组蛋白修饰和DNA甲基化对杂交过程中基因表达的实质性影响。表观遗传变异在控制基因的差异表达中起着至关重要的作用,对杂种优势有潜在的影响。
