Systemic Analysis Of The Distribution Feature Of H2A.Z And The Association Of H2A.Z With Gene Expression In Rice

Histone variant H2A.Z is highly conserved among eukaryotes and functionally involved in diverse genomic processes,such as transcriptional regulation,meiotic recombination,DNA repair and chromatin dynamic changes.In comparison with yeast and mammals,how H2A.Z nucleosome occupancy mediates gene activity in plants is still poorly understood,especially in rice which is a worldwide crop species and a model organism for monocotyledons.Hence,I explored the distribution pattern of histone variant H2A.Z in rice genome and the relationship between H2A.Z and gene expression by the combination of epigenomics and bioinformatics.In this study,the effectiveness of the antibody against H2A.Z was demonstrated in rice and then I performed genome-wide profiling of H2A.Z using chromatin immunoprecipitation combined with high-throughput sequencing.It was found that H2A.Z was significantly enriched at the 5' UTR and exon regions.To explore the relationship between the gene expression levels and H2A.Z deposition in rice,genes with different expression levels in rice seedling tissue were identified by RNA-seq data.Highly expressed genes were associated with a marked enrichment of H2A.Z at the 5' end,whereas inactive genes with low expression levels were covered by H2A.Z.To investigate the concurrence of H2A.Z,H3K4me3,H3K27me3 and DHSs in rice seedling and callus tissues,it was found that H2A.Z was significantly correlated with H3K27me3,H3K4me3 and DHSs,compared with random genomic regions.H2A.Z showed a negative correlation relationship with DNA methylation.Furthermore,I identified the differentially expressed genes between the callus and seedling by comparing the transcriptomics data sets generated from both tissues,and found that H2A.Z deposition negatively correlated with the expression of these genes,which suggested that H2A.Z probably participates in rice tissue development.In addition,I also analyzed the H2A.Z deposition in the tissues of seedlings that were harvested at 10:00 am and 10:00 pm.Our results indicated that H2A.Z might play an important role in diurnal oscillation process.Except development and environmental response,the putative function of H2A.Z in the process of transport or signal transmission was also explored.In Arabidopsis,H2A.Z deposition was negatively correlated with phosphate starvation response gene AtSPXl.OsSPXl which was the ortholog of AtSPX1 and had diurnal expression pattern was identified as phosphate starvation response genes in rice.Therefore,I tentatively explored the relationship between H2A.Z deposition and gene expression in OsSPX1-antisense transgenic lines.The result showed that the degree of H2A.Z enrichment was not only positively correlated with gene expression but also had a negative correlation relationship.Using the GO enrichment analysis,it was found that the highly expressed genes which had differential deposition of H2A.Z in OsSPX1-antisense transgenic lines played an important role in phosphate signaling transduction and phosphorus metabolism.Meanwhile,lowly expressed genes which had different deposition of H2A.Z in OsSPX1-antisense transgenic lines may be involved in energy metabolism,redox reaction and transport.All of these results revealed that H2A.Z might have dual function in transcriptional activity.To study the function of H2A.Z from multiple levels,I integrated rice epigenomic datasets,such as DHSs,histone modification,DNA methylation etc.,and tried to define chromatin states associated with distinct functions,and then explored the distribution of H2A.Z from the chromatin level.The Hidden Markov Model was applied to aggregate or collapse the multi-dimensional matrices into a small number of chromatin states.13 chromatin states included 452,202 segments were identified across the whole genome.After chromatin states partition,self-organization mapping was employed to integrate,visualize,and mine diverse epigenomic datasets,including 1,350 units which contained different chromatin signatures.In the SOM maps from different epigenomic datasets,I observed that units with high deposition of H2A.Z had overlapped with H3K4me3 and H3K27me3,respectively.In addition,I constructed a functional analysis platform based on chromatin states for rice epigenomic data named RiceEpi through chromatin states analysis,self-organization mapping analysis,SOM map comparison,as well as advanced search and visualization,then will help scientists to interpret the complex epigenomic data and discover some causal functions hidden in chromatin.Finally,I used RiceEpi platform to analysis the SOM maps of H2A.Z datasets which were harvested at 10:00 am and 10:00 pm and found that H2A.Z might be important to diurnal oscillation process.This study uses epigenomics,transcriptomics and bioinformatics to explore the distribution pattern of H2A.Z and the correlation between H2A.Z deposition and transcriptional activity,and will provide a theoretical basis for gene regulation from the epigenetic perspective.