Nucleosome Positioning Analysis In Rice

Rice(Oryza sativa L.)is an important higher eukaryotic model plant with great research significance.The basic structural unit of chromatin in eukaryotic is nucleosome,a histone octamer wrapped around by DNA by 1.75 laps.Each histone octamer contains two copies of histone H2A/H2 B and H3/H4 dimers.DNA wrapped around a nucleosome is ~147 bp.Histone protein H1 locks the entry and exit ends of nucleosome DNA to stabilize nucleosomes.Nucleosomes play an important role in the compression of chromatin,formation of high order chromatin structure and gene transcription regulation.Studies have shown that nucleosome localization is correlated with the location of cis-regulatory elements.For example,nucleosomes are found well positioned near the transcription start site(TSSs)of eukaryotic gene.However,there are very limited studies on the dynamic patterns of nucleosome localization and occupancy and their association with transcriptional regulation.In this project,we digested the rice genome with micrococcal nuclease(MNase)to obtain the DNA fragments wrapping around single nucleosomes for Illumina high-throughput sequencing.We carried out bioinformatic analysis and reveal the global occupancy of nucleosomes in three different rice tissues: roots,stems and leaves.The pattern of nucleosome occupancy at TSSs was found different in three tissues.GO analysis was performed on the genes with differential nucleosome occupancy in different tissue and revealed that the differential occupancy of nucleosome is correlated with the gene expression level.By integrating MNase-seq data analysis,we initially revealed the relationship between nucleosome localization patterns and gene structure,function,and expression regulation in rice.