Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids

作     者：Zhaoxu Gao Yanning Su Le Chang Guanzhong Jiao Yang Ou Mei Yang Chao Xu Pengtao Liu Zejia Wang Zewen Qi Wenwen Liu Linhua Sun Guangming He Xing Wang Deng Hang He Zhaoxu Gao;Yanning Su;Le Chang;Guanzhong Jiao;Yang Ou;Mei Yang;Chao Xu;Pengtao Liu;Zejia Wang;Zewen Qi;Wenwen Liu;Linhua Sun;Guangming He;Xing Wang Deng;Hang He

作者机构：School of Advanced Agriculture Sciences and School of Life SciencesState Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China College of Grassland ScienceBeijing Forestry UniversityBeijing 100083China Peking University Institute of Advanced Agricultural SciencesShandong Laboratory of Advanced Agricultural Sciences in WeifangWeifang 261325China 

出 版 物：《Journal of Integrative Plant Biology》 (植物学报（英文版）)

年 卷 期：2024年第66卷第2期

页      面：208-227页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071007[理学-遗传学] 

基　　金：supported by the Key Program of National Natural Science Foundation of China(32230006 to D.X.W.) the Shandong Development Fund of Science&Technology the Award of Natural Science Foundation of Shandong Province(ZR2021ZD30) China Postdoctoral Science Foundation(8206300443) Boya Postdoctoral Program of Peking University。 

主　　题：3D chromatin organization H3K27me3 homo-trans hybrids long-distanceinteractions 

摘      要：In plants,the genome structure of hybrids changes compared with their parents,but the effects of these changes in hybrids remain elusive.Comparing reciprocal crosses between Col×C24 and C24×Col in Arabidopsis using high-throughput chromosome conformation capture assay(Hi-C)analysis,we found that hybrid three-dimensional(3D)chromatin organization had more long-distance interactions relative to parents,and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways.The interactions between euchromatin and heterochromatin were increased,and the compartment strength decreased in hybrids.In compartment domain(CD)boundaries,the distal interactions were more in hybrids than their parents.In the hybrids of CURLY LEAF(clf)mutants clfCol×clfC24and clfC24×clfCol,the heterosis phenotype was damaged,and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3.ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type(WT)hybrids,which may have led to more long-distance interactions.In addition,the differentially expressed genes(DEGs)located in the boundaries of CDs and loop regions changed obviously in WT,and the functional enrichment for DEGs was different between WT and clf in the longdistance interactions and loop regions.Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.