数字农科院2.0

3D organization of regulatory elements for transcriptional regulation in Arabidopsis

文献类型： 外文期刊

作者： Li Deng;Qiangwei Zhou;Jie Zhou;Qing Zhang;Zhibo Jia;Guangfeng Zhu;Sheng Cheng;Lulu Cheng;Caijun Yin;Chao Yang;Jinxiong Shen;Junwei Nie;Jian Kang Zhu;Guoliang Li;Lun Zhao

作者机构：

关键词： Arabidopsis;ChIA-PET;Chromatin architecture;Transcriptional regulation

期刊名称： Genome biology

ISSN： 1474-760X

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCIE（2023版）

摘要： BACKGROUND: Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants. RESULTS: Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression. CONCLUSION: The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.

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