Gene Expression Regulation Of Alternative Polyadenylation In Arabidopsis Thaliana And Eutrema Salsugineum Under Salt Stress Condition

Soil salinization is one of the worsening environmental problems in the world,with nearly 20%of the farmland being affected.It can affect crop growth,reduce crop productions and economic benefits.To adapt to salinity environment,some plants can tolerante salinity condition through gene expression regulation.Alternative polyadenylation(APA)is emerging as a way used to control gene expression and plays important roles in adaptation to the environment.It can increase the diversity of transcripts,control mRNA stability and influence translation process.However,the role of APA during plant salt stress has not been systematically studied.In this study,glycophyte Arabidopsis thaliana and halophyte Eutrema salsugineum were compared by using poly(A)-tag sequence(PAT-seq)and bioinformatics analysis.We treated plants of these two species with 200 mM NaCl for 3 hours and portrayed poly(A)clusters(PACs)at a whole genome level,analysed differentially expressed PACs(DE-PACs)and differential expressed genes(DE genes)using functional clustering and metabolic pathways,and finally revealed the regulatory mechanism of APA during salt stress in A.thaliana and E.salsugineum.The results will help to understand plants adaptation mechanism to salt stress and potentially pave the way for breeding salt-tolerant crop varieties.The main results are as follows:(1)APA widely occurred in A.thaliana and E.salsugineum.In this research,plants of these two species were treated with 200 mM NaCl for 3 hours.A total of 12 PAT-seq libraries were prepared for Illumina high-throughput sequencing.Results indicate that A.thaliana possessed 44395 PACs,which fell into 20208 annotated genes,and 54.4%genes had more than one PAC.Salt treatment can significantly increase the proportion of APA genes;E.salsugineum had 30226 PACs,which belong to 17939 annotated genes,and 47.1%genes possessed more than one PAC.(2)Gene expression patterns of A.thaliana and E.salsugineum were different from control groups in response to salt stress.By clustering analysis and principal component analysis,salt treatment samples were far away from the control groups,which conferred the different expression patterns of A.thaliana and E.salsugineum.Arabidopsis had 3037 DE-PACs,while E.salsugineum had 998 DE-PACs.They both enriched in biological process such as hyperosmotic salinity reactions,hormone mediated signal pathways,response to wounding,and cellular components such as vacuole,plasma membrane,and chloroplast.For those upregulated PACs in A.thaliana,they are significantly enriched in KEGG pathways such as plant hormone signal transduction,starch and sucrose metabolism,fatty acid elongation.For those upregulated PACs in E.salsugineum,they were enriched in the plant hormone signal transduction,stilbenoid,diarylheptanoid and gingerol biosynthesis,arginine and proline metabolism;The down regulated PACs are mainly enriched in protein processing in endoplasmic reticulum.(3)Polyadenylation or alternative polyadenylation is co-transcriptional in A.thaliana and E.salsugineum under salt stress.In A.thaliana,DE genes overlap 68.1%with DE-PAC genes and 42.2%with DE-APA genes;In E.salsugineum,DE genes overlap 53.8%with DE-PAC genes and 29.3%with DE-APA genes.This suggested that polyadenylation or alternative polyadenylation and gene expression are co-regulated in response to salt stress.(4)A.thaliana and E.salsugineum both tend to use distal poly(A)sites under salt stress condition,while E.salsugineum is less being regulated by APA.The number of 3'UTR(3' untranslated region)lengthening genes are larger than 3'UTR shortening genes both in A.thaliana and E.salsugineum.The significantly lengthening genes or shortening genes have the same tendency.Interesting to find that some mRNA processing components including cleavage factors and polyadenylation factors show APA switching or expression level changes,which may affect the poly(A)site selection according to previous reports.(5)Alternative polyadenylation of A.thaliana show common and different regulation with E.salsugineum under salt stress.Exclusively expressed PAC genes of A.thaliana has 26 genes overlap with exclusively expressed PAC genes of E.salsugineum.Those genes can be significantly enriched to biological process such as ABA response,water deprivation and transcription factor activity;However exclusively expressed PAC genes in A.thaliana is larger than E.salsugineum which suggest a big difference between these two species.