title: Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis.
abstract: BACKGROUND
  Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.
  
  
  RESULTS
  To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.
  
  
  CONCLUSIONS
  Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Peng
authors.initials: P
authors.lastname: Cui
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Wang
authors.forename: Shoudong
authors.initials: S
authors.lastname: Zhang
authors.forename: Shahjahan
authors.initials: S
authors.lastname: Ali
authors.affiliation: Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. liming.xiong@kaust.edu.sa.
authors.forename: Liming
authors.initials: L
authors.lastname: Xiong
mesh_terms: D017398:Alternative Splicing / Q000187:drug effects; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D005091:Exons; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D012322:RNA Precursors / Q000235:genetics*; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant; D012492:Salts; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000235:genetics*; D015533:Transcriptional Activation / Q000187:drug effects
chemical_list: D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D018749:RNA, Plant; D012492:Salts; D012965:Sodium Chloride