Identification And Analysis Of RNA Editing Events In Arabidopsis Nuclear Genome And Barley Chloroplast Genome

RNA editing,a phenomenon base substitution mutation occurring during DNA transcription to form RNA,takes place either during the transcription process or during the post-transcriptional process of precursor RNA,which of RNA editing occurs more frequently.The re-modification of transcripts made by RNA editing obviously varies the gene expression pattern so that the gene expression level can be adjust directly and indirectly.Therefore,RNA editing is considered as an essential way to rich genetic information and take apart in life activities.Rapid development of RNA-seq technique based on high-throughput sequencing and considerable innovation of bioinformatic tools make it possible that massive identification of RNA editing events in genome.However,the amount of studies in the plant is far less than the amount of studies focusing on human and pattern animal.Therefore,focusing on Arabidopsis nuclear genome and barley chloroplast genome,this study based on large quantity of RNA-seq data identified and analyzed the RNA editing events quickly and exactly by using RES-Scanner softwar to prliminary understand the composition and characteristics of plant nuclear and organelle genomic RNA editing and lay the foundation for further research on biological functions of plant RNA editing.Here are the mainly achieved results:(1)26,231 RNA editing sites were identified from 84 transcriptomes in the reproductive growth stage of Arabidopsis thaliana by using the Arabidopsis genome as a reference.1,886 unique RNA editing sites were remained after redundancy and annotation.And the length of the chromosome and the number of transcripts on that chromosome are substantially proportional to the number of RNA editing events occurring on that chromosome.In Arabidopsis thaliana nuclear genome,most of RNA editing events occur in the CDS region(1468;77.84%),and the intron region(178;9.44%);3'UTR(123;6.52%)and 5'UTR(105;5.57%);ncRNA region(12;0.64%)also occur some editing sites.However,occurrence frequencies of RNA editing taking place in CDS region and exon region can be differ from different growth stages,and the frequency of RNA editing events in the coding region of the gene would increase in the phases or samples with high organizational activity.(2)The analysis of characteristic of RNA editing in Arabidopsis thaliana nuclear genome revealed there were 12 types of base mutation models.Among these types,4 types,including G->A?C->T?T->C and A->G,are advantage type.Base preference analysis of 10 nt bases upstream and downstream in sites of four dominant editing types discovered that base preference for editing of purine was not as same as the editing of pyrimidine.The RNA editing events occurring in CDS region of Arabidopsis thaliana caused the changes of 1,514 codons.759 of them are synonymous editing events;733 of them are non-synonymous editing events,and 22 of them are stop-gain editing events.After the analysis of protein structure changes caused by editing,it is obviously that non-synonymous editing events less impact on amino acid hydrophobicity,but more impact on protein sequence information.The GO enrichment of gene related with stop-gain editing events and non-synonymous editing events discovered that these genes always related with effecting transportation of materials and energy as well as taking apart in glycometabolism.(3)According to the preliminary analysis of the biological functions of sequence changes caused by editing,the original miRNA-mRNA changed because of the RNA editing events occurring in the 3'UTR region of Arabidopsis thaliana.5 RNA editing events happening in the microRNA binding region made 3 microRNA binding region invalid.RNA editing events out of the microRNA binding region caused 9 new miRNA-mRNA,effecting expression of ACA1?HPR?UBP24?CUE1?AT1G02150,which means RNA editing regulate the level of gene expression indirectly by affecting the bind of miRNA and mRNA.In addition,there are 6 editing sites taking in the Kozak sequence in the 5'UTR region of Arabidopsis thaliana.Among these,5 editing sites are negative to translation for corresponding transcript expression levels decreasing.(4)In the barley leaf genome,according the analysis of RNA editing of the chloroplast genome,422 chloroplast RNA editing event based on chloroplast genome and 16 transcriptomes were identified by taking the same procedure.Among the 106 unique RNA editing sites remained after redundancy and annotation,101 sites were new identified sites.77 of 106 are located in the CDS region;3 are located in the intron region;26 are located in the intergenic region,and 80 editing sites located in the gene region are distributed among 37 genes.For the 9 types of RNA editing events,C->T type absolutely has quantity advantage.