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Extensive allele‐level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies Plant Journal ( IF 5.775 ) Pub Date : 2018-10-30 , DOI: 10.1111/tpj.14143 Epigenetic mechanism plays a major role in heterosis, partly due to remodeling of epigenetic modifications in the F1 hybrids. Based on ChIP‐Seq analyses, we show that, at allele level, extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F1 hybrids of rice cultivars, Nipponbare and 93‐11, representing the two subspecies, japonica and indica, of rice. Globally, the allele modification‐altered loci in leaf or root of the reciprocal F1 hybrids involved ca. 12% to > 43% of genomic regions embarked by either of two typical histone methylation markers, H3K4me3 (> 21,000 genomic regions) and H3K27me3 (> 11,000 genomic regions). Nevertheless, at total modification level, majority (from ca. 43% to > 90%) of the modification‐altered alleles was within the range of parental additivity in the hybrids due to concerted alteration towards opposite directions, consistent with an overall attenuation of allelic differences in the modifications. Importantly, of the genomic regions that did show nonadditivity in total modification level by either marker in the two tissues of hybrids, > 80% manifested transgressivity, which involved genes enriched in specific functional categories. Extensive allele‐level alteration of only H3K4me3 was positively correlated with genome‐wide changes in allele‐level gene expression, while at total level both H3K4me3 and H3K27me3 remodeling, which albeit affects only small numbers of genes, contributes to the overall nonadditive‐gene expression to variable extents depending on tissue/marker combinations. Our results emphasize the importance of allele‐level analysis in hybrids to assess remodeling of epigenetic modifications and their relation to changes in gene expression. AI译文（仅供参考）：表观遗传机制在杂种优势中起主要作用，部分原因是F1杂种中表观遗传修饰的重塑。 基于ChIP-Seq分析，我们表明，在等位基因水平，水稻品种，日本晴和93-11的互交F1杂种中的基因组基因座的子集发生了广泛的组蛋白甲基化重塑，代表了两个亚种， 粳稻和籼稻 。白饭。 在全球范围内，等位基因修饰改变了倒数F1杂种的叶或根中的基因座。 12％至> 43％的基因组区域由两种典型的组蛋白甲基化标记物H3K4me3（ > 21,000基因组区域）和H3K27me3（> 11,000种基因组区域）中的任一种起始。 然而，在总修饰水平上，由于向相反方向的协同改变，修饰改变的等位基因的大多数（从约 43％至> 90％）在杂交体中的亲本可加性范围内，与等位基因的总体减弱一致。修改的差异。 重要的是，在通过两种杂种组织中的任一标记确实显示总修饰水平不可加性的基因组区域中，> 80％表现出超越性，其涉及富含特定功能类别的基因。 仅H3K4me3的广泛等位基因水平改变与等位基因水平基因表达的全基因组变化正相关，而总体水平H3K4me3和H3K27me3重塑，尽管仅影响少量基因，但有助于整体非加性基因表达。根据组织/标记物组合，可变程度。 我们的结果强调了杂种中等位基因水平分析的重要性，以评估表观遗传修饰的重塑及其与基因表达变化的关系。 欢迎点击「PaperRss」↑关注我们！  |
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