National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China.
Nucleic Acids Res. 2023 Sep 22;51(17):9001-9018. doi: 10.1093/nar/gkad658.
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.
光周期与生物钟整合，协调基因表达节律，从而确保植物适应环境。在不同光照条件下对节律基因进行全基因组鉴定和比较，揭示了水稻在持续黑暗（DD）下相位延迟和持续光照（LL）下振幅降低。有趣的是，节律基因的 ChIP-seq 和 RNA-seq 分析显示，在其基因座处的 H3K9ac 修饰和近端基因座处的长非编码 RNA（lncRNA）表达具有同步的生物钟振荡。为了研究水稻中基因表达节律是如何调控的，我们通过时间序列 ATAC-seq 分析了开放染色质区域和转录因子（TF）足迹。尽管开放染色质区域没有表现出生物钟变化，但大量 TF 被鉴定为以时间依赖性方式与染色质同步关联，并驱动基因表达。进一步的转录调控网络映射揭示了核心生物钟基因与参与光/温度信号转导的转录因子之间存在显著相关性。ZT8 特异性表达基因的原位 Hi-C 显示在同一时间具有高度连接的染色质关联，而这个 ZT8 染色质连接网络在 ZT20 时解离，这表明基因表达的生物钟控制是通过动态空间染色质构象实现的。这些发现共同表明，生物钟 H3K9ac 修饰、TF 与基因表达的染色质关联以及与基因表达节律相关的空间染色质构象的生物钟动态之间存在同步机制。
