Study On The Circadian Rhythm Of Soybean Chromatin Accessibility

Circadian clock has a great influence on the growth and development of plants.Plant scientists have identified many genes involved in the circadian clock.The core genes of the circadian clock are composed of the morning circadian genes CCA1(CIRCADIAN CLOCK ASSOCIATED1),LHY(LATE ELONGATED HYPOCOTYL)and night circadian genes TOC1(TIMING OF CAB EXPRESSION1).CCA1/LHY can inhibit the expression of TOC1,and TOC1 can bind to the CCA1/LHY promoter through the CCT domain to inhibit its transcription.The circadian is also regulated by epigenetics.The rhythmic change of histone modified H3K4me3 is controlled by histone methyltransferase and histone demethylase,and the synergistic effect of histone demethylase and TOC1 positively regulates the expression of CCA1 and LHY.CCA1/LHY inhibits the expression of the demethylase by binding to its promoter.In recent years,there have been a lot of studies on the relationship between epigenetic modifications and circadian clock,but little research has been done on the rhythmic changes of chromatin accessible and its regulation of gene expression.Chromatin accessible is when DNA transcription occurs,nucleosome from tight to loose state,at this time there will be some transcriptional regulatory factors bind to gene promoter regions,thus regulate gene transcription and translation.Soybean is an important economic and oil crop in the world,which provides abundant plant protein and oil for human.In order to study the relationship between chromatin accessible and circadian clock of soybean,this study used a widely used soybean cultivar Williams 82 as the research subject,analyzed the circadian clock changes of chromatin open region by using ATAC-seq and RNA-seq techniques.A 24-hour(12h/12 h light/dark)cycle was taken,and ZT0 was recorded from the beginning of the light.Samples were taken every four hours,including diurnal critical points ZT0 and ZT12,to analyze the changes in chromatin accessible level.Then,combined with RNA-seq data at all time points,the relative between circadian genes and chromatin accessible region were analyzed.Conclusions:1 Successfully built ATAC-seq library in soybean leaves: A total of 10,356 chromatin accessible regions were obtained from ZT0 and 7,000 from ZT12.These open regions of chromatin were mainly distributed in the upstream 2kb of genes,followed by the intergenic region,genes and other sites.The accessible chromatin regions were reduced at ZT12.2 Identification of specific chromatin accessible in soybean during the day and night: By analyzing the difference between two time points chromatin accessible region,there were 1,870 specific open chromatin regions at morning and 284 specific open chromatin regions at night.3 Identification of rhythmic expression genes during the day and night in soybean:A total of 11,697 rhythmically expressed genes were identified from soybean leaf by transcriptome data at seven time points of ZT0,ZT4,ZT8,ZT12,ZT16,ZT20 and ZT24.According to K-means clustering,9,395 of them were highly expressed at night and 2,302 of them were highly expressed during the day.4 The chromatin accessible level of CCA1 significantly decreased at night: The circadian clock core genes CCA1 and TOC1 were expressed rhythmically in soybean Williams 82,and the chromatin accessible level of TOC1 was consistent during the day and night.5 Differential accessible regions of chromatin in soybean are associated with rhythmic expression genes: By identifying specific morning and evening chromatin accessible regions in soybean,227 morning and 19 night related rhythmically expressed genes were found.6 Rhythm changing of chromatin accessible regions enrich light-reactive related genes and participate in circadian clock regulation: The genes associated with morning specific chromatin accessible region were mainly enriched in response to red and far-red light and circadian rhythm pathways.There was no significant enrichment in the evening specific chromatin accessible region.Homer predicts motifs of morning and evening specific chromatin accessible region,morning-specific regions of b ZIP18 and b ZIP28 of the b ZIP transcription factor family,and PIF4 and PIF7 of the b HLH family,which have been shown to be associated with light responses and involved in clock regulation.