Studies On Effects Of Salt Stress On Gene Expression And Chromatin Dynamic Changes In Rice

As one of the main sources providing starches for human being,rice is one of the most important food crops in the world,which plays an important role in agricultural production.The demand of rice keeps increasing with the global population keeps growing,However,abiotic stresses such as drought,salt and heavy metals etc.have seriously affected the yield of rice,and showed a significant upward trend.With the spreading of saline lands,the trend of rice yield reduction caused by salt stress is even more severe.Therefore,studies on molecular mechanisms for salt responses will improve our understanding and of molecular mechanisms for salt-tolerance in rice,and will ultimately be good for molecular breeding of salt-tolerant rice species.In this study,RNA-seq based transcriptomic analysis was used to investigate the effects of salt stress on the transcription of genes from leaf and root tissues before and after salt treatment,respectively,at the genome-wide level,which will further help to screen and utilize salt-tolerance marks for rice breeding.Moreover,it will pave the way for the identification of salt responsive functional DNA elements such as promoters and enhancers etc.in the future.On the other hand,to further investigate how chromatin dynamic changes associated with salt stress affect the differential expression of salt-responsive genes above,histone marks based ChIP-seq,using six commercial antibodies against H3K4/27/36me3,H3K9/27ac and H4K12ac,were conducted with the same tissues as RNA-seq mentioned above.This analysis will help to elucidate how salt stress cause chromatin dynamic changes between leaf and root tissues,and will help to reveal the relationship between changes in histone marks and gene differential expression during salt treatment,thereby helping to explain the chromatin-based epigenetic mechanisms for salt-tolerance in rice.The main results are as follows:1.There are the total of 3,652 and 4,112 differentially expressed genes(DEGs)corresponding to rice leaf and root tissues before and after salt treatment,of which,1,852 and 2,327 genes were up-regulated and 1,800 and 1,785 genes were down-regulated in leaf and root tissues,and 62.36%and 54.47%of DEGs are related to stress between leaf and root tissues,respectively..2.Salt stress could lead to the global changes in histone modifications,and some of changes are tissue-dependent.For example,chromatin dynamic changes in leaf tissue mainly occurs in exons,introns and intergenic regions.The histone marks,H3K4/36me3,display dynamics within exons and introns,while dynamics of the histone marks,H3K27me3 and H3K9/27ac mainly occur within the exons and the intergenic regions.In contrast,salt-related chromatin dynamics in root tissue mainly occur in the promoter,exon and intergenic regions.3.The expression of H3K27ac,H4K12ac,H3K4ac and H3K9ac in the second group is the effect of partial differential gene expression,such as histone Modified H3K4me3,H3K36me3.4.Considering chromatin states consisting of combined action of six histone marks tested between leaf and root tissues,we found that a certain specific chromatin state and function in up and down-regulation of salt-responsive genes.Most importantly,salt-related DEGs are possibly differentially regulated by the chromatin states with distinct distribution across the corresponding genes.