Construction Of Diurnal Epigenome And 3D Genome Mapand Study Of Rhythmic Gene Transcription Regulation In Rice

The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes and plays an important role in plant growth,development and metabolism.About one-third of the actively expressed genes are regulated by the circadian clock in rice which is a monocot model plant.However,the circadian epigenome/cistrome,circadian 3D genome and their potential functions underlying rhythmic gene expression remain unclear.Thus,the clock circuit represents an ideal system to study how the epigenetic modifications and 3D chromatin architecture regulate gene transcription.In this study,we used RNA-seq,ChIP-seq and ChIA-PET technologies to get transcriptome and epigenome/cistrome of six time points and 3D genome data of two time points(08:00 and 20:00)across a day and constructed the rhythmic reference transcriptome,epigenome/cistrome and 3D genome.In addation,we investigated the effects of dynamics of epigenome/cistrome and 3D genome on circadian control of rhythmic gene transcription through muti-omics integrated analysis.The main findings are as follows:1.Through RNA-seq,ChIP-seq,FAIRE-seq and BS-seq data analysis of the six time points,we found that there were 7594 rhythmic genes;RNAPII and H3K9/27ac show robust circadian rhythm,and H3K4me3 is relatively less;while rhythmic oscillations of H3K4me3,H3K4me1,H3K27me3,H3K9me2,open chromatin regions and DNA methylation are very rare.2.The results of integrated analysis of RNA-seq and ChIP-seq data show the rhythmic gene expression are significantly correlated with circadian RNAPII,H3K9ac and H3K27ac and precede mRNA accumulation by approximately 2 h,whereas have no correlation with non-rhythnic histone modifications(such as H3K4me1).3.Rhythmic RNAPII binding and histone acetylation(H3K9/27ac)are dynamically linked to diurnal 3D genome architecture remodeling and associate with the circadian rhythm of gene expression.4.RNAPII-associated chromatin spatial clusters(CSCs)show high plasticity during the circadian cycle,and rhythmically expressed genes in the morning phase and non-rhythmically expressed genes in the evening phase tend to be enriched in RNAPII-associated CSCs to orchestrate expression.5.Core circadian clock genes related chromatin connectivity networks suggest that they co-localized within the same network and define a distinct nuclear landscape and circadian outputs in the AM(08:00)and PM(20:00).6.We also find high-switch frequency of acetylated regulatory element-associated active interacting domains and RNAPII-associated transcriptional interacting domains,whereas low-switch frequency of heterochromatin-associated interacting domains between the AM and PM circadian windows.This study identified the rhythmic dynamics of transcriptome,epigenome/cistrome and 3D genome,and explored the rhythmic gene transcription based on rhythmic epigenome/cistrome and 3D genome.At the same time,it is expected that the results of this research will have important scientific value,laying the foundation for transcription regulation mechanism of the circadian clock and the molecular mechanism of important agronomic traits(such as heading stage,photosensitivity and regional adaptability of rice)and having certain guiding significance for rice genetic improvement and molecular breeding design.