Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [HiC]

Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. Target genes and associated cis-binding motifs of transcription factors enrichment points to the existence of subnuclear organization hub enriched around the TFs. RNAPII-associated chromatin interaction domains (CIDs) are under circadian control, and static CIDs with common node genes but changed connecting genes along the circadian cycle, reveal they may function as distinct clock components in the interconnected circuits between morning and evening. Core circadian clock genes related chromatin connectivity networks reveal a compact and highly connected chromatin architecture serving to coordinate gene expression in the morning, whereas a scattered, loose chromatin architecture coordinates PM gene expression. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal the distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation. Overall design: Here, we generated genome-wide occupancy of RNA polymerase II (RNAPII) by ChIP-seq, whole-transcriptome by RNA-seq, and chromatin accessibility by FAIRE-seq throughout the six-time course. We also performed RNAPII long-read ChIA-PET from the same tissues used for ChIP-seq, RNA-seq, and FAIRE-seq at 8:00 and 20:00. Together, we constructed comprehensive high-resolution dynamic chromatin architecture, and dissected its effects on diurnal gene expression.

RNA聚合酶II（RNA polymerase II, RNAPII）的全基因组节律性占据与节律基因的表达呈现高度协同关系。节律性RNAPII结合可动态调控昼夜节律性三维基因组结构重塑，其中91%的染色质互作均发生了改变。在上午8点的昼夜节律时相聚集的节律基因会形成空间互作簇，进而协同调控节律基因的表达；而非节律基因则倾向于相互锚定，并在晚间20点的昼夜节律窗口中促进基因表达。转录因子（transcription factors, TFs）的靶基因及其相关顺式结合基序的富集分析显示，存在围绕TFs富集的亚核组织枢纽。与RNAPII相关的染色质互作结构域（chromatin interaction domains, CIDs）受昼夜节律调控；在昼夜周期中，携带共同节点基因但连接基因发生改变的静态CIDs，表明其可能在昼夜节律的昼夜互联环路中发挥独特的生物钟组件功能。与核心生物钟基因相关的染色质互作网络显示，上午的染色质结构呈现紧凑且高度互联的状态，以协同调控基因表达；而晚间的染色质结构则较为分散松散，用于协调晚间的基因表达。本研究揭示了植物中全新的昼夜节律性基因组折叠基本规律，并阐明了独特的染色体高级组织结构，该结构对于协调转录调控的昼夜动态变化至关重要。总体实验设计：本研究通过染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）获取全基因组范围内的RNAPII占据情况、通过RNA测序（RNA Sequencing, RNA-seq）获取全转录组数据、通过甲醛辅助分离调控元件测序（Formaldehyde-Assisted Isolation of Regulatory Elements sequencing, FAIRE-seq）检测染色质开放状态，覆盖六个时间节点的全周期实验。此外，我们还在上午8点和晚间20点两个时间点，针对与ChIP-seq、RNA-seq及FAIRE-seq同源的组织样本，开展了RNAPII长读长染色质互作分析成对末端标签测序（Chromatin Interaction Analysis by Paired-End Tag sequencing, ChIA-PET）实验。综上，本研究构建了全面的高分辨率动态染色质结构图谱，并解析了其对昼夜节律基因表达的调控作用。