SRA

Plants are extremely sensitive to and can re-output rhythm by light signals during photoperiod cues. The circadian transcriptome and epigenetically modified rice genome exhibited distinct circadian behavioural outputs under three light signals during the photoperiod.By comparing and analysing the output circadian genes under different light signals, we detected that constant light (LL) shortens the day-night cycle, while constant night (DD) suppresses the oscillation amplitude. The circadian changing lncRNAs at the genome-wide level that were temporally correlated with oscillating genes at proximal loci and accompanied by synchronised circadian oscillations of H3K9ac modifications. We used the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to profile the open chromatin regions and transcription factor (TF) footprints in rice at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20). The regulation of circadian gene expression occurs, not through temporal regulation of chromatin opening but through time-dependent binding of transcription factors in cis-regulatory elements. We mapped the 4D genome architecture of rice by employing BL-Hi-C, to capture oscillating chromatin interactions at ZT8 and ZT20. Circadian genes within the same peak phases of expression were preferentially coordinated transcription with non-circadian genes. Circadian genes at the ZT8 circadian phase tended to be enriched in ZT8-speific spatial clusters to orchestrate gene expression. Our findings contribute significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways in rice. Overall design: Circadian gene expression analysis of RNA-seq data at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20) under LL, LD, and DD conditions.