Systematic Identification And Characterization Of RNA Editing In Early Mouse Embryonic Development

RNA editing is a biological phenomenon of changing RNA sequence relative to its corresponding DNA template by inserting,deleting or substituting one or a few nucleotides.RNA editing has been found across all kingdoms of life,including viruses.The deamination of adenosines(As)to inosines(Is)by the family of ADAR enzymes acting on double RNA strands is the prominent RNA editing event occurring in humans.RNA editing contributes to diversification of corresponding protein products.Abnormal RNA editing has also been associated with a number of diseases,including several neurological disorders and cancers.Current research has found RNA editing was important in early embryonic development.The advent of high-throughput sequencing technologies has largely improved the computational detection of RNA editing events at genomic scale.With the development of single-cell high-throughput sequencing technology,it is now possible to sequence the cells at various stages of early mouse embryonic development to obtain RNA-seq data.Based on the transcriptome sequencing results of early mouse embryonic development,this study systematically identifies and analyzes RNA editing during early mouse embryonic development.Firstly,this study proposed an integrated identification pipeline of RNA editing site--MMIRES.MMIRES addressed the problems of low depth of sequencing data and low identification results of RNA editing sites in early mouse embryonic development.MMIRES combines different samples to improve the sequencing depth of the data,and integrates the identification results of robust Separate,Pool,and GIREMI algorithms to improve the number of identified RNA editing sites.After applying MMIRES to sequencing data in early mouse embryonic development,we obtained 470,2015,3757,4940,5313,4117,7264,and 1669 A-to-I editing sites for the MII oocyte,Zygote,early 2-cell,2-cell,4-cell,8-cell,ICM,mESC stages,respectively.We found that the number of editing events increased from that observed in terminally differentiated gametes to that observed in totipotent/pluripotent cells.RNA editing sites are stage-specific and accordingly we classified RNA editing sites into N-stage.Compared with RNA editing sites in normal mouse cell,the RNA editing sites at various stages of early mouse embryonic development are mainly distributed in protein-coding genes.The proportion of RNA editing sites in the non-protein coding gene is low.There are numerous similarities in genes related to RNA editing and protein-coding genes related to RNA editing.We further explored the role of RNA editing in early mouse embryonic development.We found the proportion of RNA editing was almost invariant with gene expression when FPKM is greater than 2.Based on this,we found RNA editing plays a key role in the down-regulation of gene expression during early mouse embryonic development.Decreased expression was more common than increased expression for genes related to RNA editing.The reason why RNA editing regulates gene expression is caused by non-synonymous protein changes,which is of great significance in revealing the role played by RNA editing in early mouse embryonic development.Finally,by GO analysis,we found that most functions of genes related to RNA editing are cell division,phosphorylation and DNA replication.The innovations of this study are mainly reflected in three aspects.Firstly,this paper proposes an RNA editing sites recognition algorithm MMIRES for low-sequence depth data.Secondly,this paper first revealed the dynamic changes of RNA editing during early mouse embryonic development,and found the stage specificity of RNA editing.Thirdly,this paper found out the role of RNA editing in the regulation of gene expression during early mouse embryonic development,and proposed a mechanism model for RNA editing regulation of gene expression during early embryonic development.It is significant to know the role of RNA editing in early mouse embryonic development.