Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice

文献类型： 外文期刊

第一作者： Zhang, Ying

作者： Zhang, Ying;Chen, Guoting;Deng, Li;Gao, Baibai;Yang, Jing;Ding, Cheng;Zhang, Qing;Ouyang, Weizhi;Guo, Minrong;Wang, Wenxia;Liu, Beibei;Zhang, Qinghua;Yan, Jiapei;Li, Guoliang;Li, Xingwang;Li, Guoliang;Li, Xingwang;Li, Guoliang;Li, Xingwang;Chen, Guoting;Li, Guoliang;Chen, Guoting;Li, Guoliang

作者机构：

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：14.9； 五年影响因子：16.4 ）

ISSN： 0305-1048

年卷期： 2023 年

页码：

收录情况： SCI

摘要： Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness to the environment. Genome-wide characterization and comparison of rhythmic genes under different light conditions revealed delayed phase under constant darkness (DD) and reduced amplitude under constant light (LL) in rice. Interestingly, ChIP-seq and RNA-seq profiling of rhythmic genes exhibit synchronous circadian oscillation in H3K9ac modifications at their loci and long non-coding RNAs (lncRNAs) expression at proximal loci. To investigate how gene expression rhythm is regulated in rice, we profiled the open chromatin regions and transcription factor (TF) footprints by time-series ATAC-seq. Although open chromatin regions did not show circadian change, a significant number of TFs were identified to rhythmically associate with chromatin and drive gene expression in a time-dependent manner. Further transcriptional regulatory networks mapping uncovered significant correlation between core clock genes and transcription factors involved in light/temperature signaling. In situ Hi-C of ZT8-specific expressed genes displayed highly connected chromatin association at the same time, whereas this ZT8 chromatin connection network dissociates at ZT20, suggesting the circadian control of gene expression by dynamic spatial chromatin conformation. These findings together implicate the existence of a synchronization mechanism between circadian H3K9ac modifications, chromatin association of TF and gene expression, and provides insights into circadian dynamics of spatial chromatin conformation that associate with gene expression rhythms.

分类号：

  • 相关文献
作者其他论文 更多>>

微信小程序