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Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice

文献类型： 外文期刊

作者： Wang, Fei 1 ; Xi, Zengde 1 ; Wang, Mengyao 1 ; Wang, Linyou 2 ; Wang, Jianbo 1 ;

作者机构： 1.Wuhan Univ, Coll Life Sci, State Key Lab Hybrid Rice, Wuhan 430072, Peoples R China

2.Zhejiang Acad Agr Sci, Inst Crop & Nucl Technol Utilizat, Hangzhou 310021, Peoples R China

关键词： inter-subspecific hybrid rice; chromatin accessibility; heterosis; transcriptional regulation; DNA methylation; allele-specific expression

期刊名称：PLANT JOURNAL （ 影响因子：6.2； 五年影响因子：7.1 ）

ISSN： 0960-7412

年卷期： 2024 年

页码：

收录情况： SCI

摘要： The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice. The utilization of rice heterosis is an essential avenue to overcome the yield bottleneck; however, the underlying molecular mechanism remains unclear. We characterized the more actively accessible chromatin state in the inter-subspecific hybrid compared to that in its parents, revealing the regulation of chromatin accessibility and DNA methylation. This study offers a novel perspective on ACR as an embodiment of the regulation of hybrid rice.

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