Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

作     者：Pengfei Dong Xiaoyu Tu Haoxuan Li Jianhua Zhang Donald Grierson Pinghua Li Silin Zhong Pengfei Dong;Xiaoyu Tu;Haoxuan Li;Jianhua Zhang;Donald Grierson;Pinghua Li;Silin Zhong

作者机构：State Key Laboratory of AgrobiotechnologySchool of Life SciencesThe Chinese University of Hong KongHong KongChina Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyZhejiang UniversityHangzhou 310058China State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai’an 271018China 

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

年 卷 期：2020年第62卷第2期

页      面：201-217页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071007[理学-遗传学] 0901[农学-作物学] 0703[理学-化学] 0902[农学-园艺学] 

基　　金：supported by National Key Research and Development Program of China 2016YFD0101003 NSFC 91435108 Hong Kong UGC GRF 14104515 and 14108117 Area of Excellence Scheme(AoE/M-403/16) the Taishan Pandeng program. 

主　　题：plant chromatin domains Tissue-specific Hi-C analyses rice 

摘      要：Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation,which is best studied in the mammalian models.Using in situ Hi-C,we have compared the 3D chromatin architectures of rice mesophyll and endosperm,foxtail millet bundle sheath and mesophyll,and maize bundle sheath,mesophyll and endosperm tissues.We found that their global A/B compartment partitions are stable across tissues,while local A/B compartment has tissue-specific dynamic associated with differential gene expression.Plant domains are largely stable across tissues,while new domain border formations are often associated with transcriptional activation in the region.Genes inside plant domains are not conserved across species,and lack significant co-expression behavior unlike those in mammalian TADs.Although we only observed chromatin loops between gene islands in the large genomes,the maize loop gene pairs’syntenic orthologs have shorter physical distances in small genome monocots,suggesting that loops instead of domains might have conserved biological function.Our study showed that plants’chromatin features might not have conserved biological functions as the mammalian ones.