Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [BiSulfite-seq]

Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. Core circadian clock genes related chromatin connectivity networks suggested they co-localized within the same “transcriptional factory” and define a distinct nuclear landscape and circadian outputs in the AM and PM. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation. Here, we generated genome-wide occupancy of RNA polymerase II (RNAPII) and histone modifications (H3K4me3, H3K9me2, H3K27ac, H3K27me3, H3K4me1 and H3K9ac) by ChIP-seq, whole-transcriptome by RNA-seq, chromatin accessibility by FAIRE-seq and DNA methylation by Bisulfite-seq throughout the six-time course. We also performed RNAPII long-read ChIA-PET from the same tissues used for ChIP-seq, RNA-seq, FAIRE-seq and Bissulfite-seq at 8:00 and 20:00. Together, we constructed comprehensive high-resolution dynamic chromatin architecture, and disected its effects on diurnal gene expression.