Identification And Characterization Of DNase Ⅰ Hypersensitive Site Based On High-throughput Sequence In Cotton

Cotton is the most indispensable enconomic crops,and the fiber of cotton is also one of the important raw materials in textile industry.The whole genome sequencing sketches have been completed in different cotton species.However,the research combined to functional genomics of cotton is tremendously limited,that is,there are some limitations and lagging behind the research of transcriptional regulatory elements.DNase-seq technology is a new method for exploring genomic regulatory elements and reveal gene expression regulation mechanisms.In this study,we selected Gossypium hirsutum and its two ancestral species,Gossypium raimondii and Gossypium arboreum as the materials to study the regulatory element.Through researching DNase Ⅰ hypersensitive sites that depend on high-throughput sequencing and further bioinformatics analysis.Meanwhile,we combine with the data of RNA-seq and ChIP-seq of three different epigenetic modification histones,like H3K27me1,H3K27me3 and H3K27ac to deeply mine the character of those elements.The number and distribution of DNase Ⅰ hypersensitive sites identified at the whole genome represent the number and distribution of some regulatory elements.The experimental results are as follows.(1)Numbers of DNase Ⅰ hypersensitive site are counted 61351,47242 and 54740 in Gossypium raimondii,Gossypium arboreum and Gossypium hirsutum,respectively.(2)Comparative Analysis on the distribution of DNase Ⅰhypersensitive sites in chromosomes and genes of three Cotton species.It has been found that the distribution characteristics of regulatory elements are concentrated on the chromosome arm.The trend of those elements distribution on chromosomes is parallel to the gene distribution.(3)Statistical analysis of regulatory elements length in different positions of genes shows that the region of intergenic,also 1000bp upstream and 100bp downstream of TSS much longer than other regions.In addition to,the GC content of regulatory elements has been found to be higher than that of average level of genome sequence.(4)Analysis combined with data of RNA-seq,which we could explore the DNase I hypersensitive sites mostly connect with high expression level gene.It is also found that high expression gene shows fairly high sensitivity of DNase I enzyme cleavage,which reflects the looser chromatin status of highly expressed genes.All of those conditions improve the efficiency of gene expression.(5)Coupling the ChIP-seq data of three different epigenetic modification histones to analyse the epigenomics.The results show that H3K27ac enrichment a lot in different gene position.The histone modification of H3K27me3 is enriched in the intergenic region.The H3K27mel shows different distribution trends in various position of gene.Through studying the correlation between the distribution of these histone and DNase I hypersensitive sites,which the effect of epigenetic analysis on the regulation of gene expression can be further analyzed.