Bioinformatics Analysis Of MiRNA Editing And Mutation In Huntington’s Disease Based On High-throughput Sequencing

Huntington’s disease(HD)is caused by repeated amplification of the triplet code(CAG)in exon 1 of the Huntington Gene(HTT).It is a neurodegenerative disease inherited by autosomal dominant.HD is lethal,but there is currently no cure at home and abroad.Micro RNA(mi RNA)is a small endogenous non-coding RNA that plays an important role in post-transcriptional gene regulation.Mi RNA editing may affect the stability of mi RNA structure and the specificity of target.Analysis of mi RNA editing events in HD can improve our understanding of mi RNA editing or mutation in the disease,and can also facilitate the design of new therapeutic approaches based on mi RNA targeting.We collected 111 published s RNA-seq data from human brain tissue for the bioinformatics analysis of mi RNA editing or mutation.Among them,28 are sample data of patients with Huntington’s disease,and 83 are sample data of healthy people.111 s RNA-seq data are of good quality and meet the requirements of bioinformatics analysis.Mi RME algorithm is a novel,accurate and fast detection method for discovering mi RNA editing or mutation site(M/E site)in s RNA-seq data which has three main features.First,Mi RME has three progressive rounds of sequence alignment steps to reach a high sensitivity without loosing speed.Second,reads mapped to multiple loci in the genome are normalized using the cross-mapping correction method to reduce the number of false positive predictions.Third,Mi RME can identify and visualize all types of M/E sites at one system.We used the Mi RME algorithm to identify a total of 1890 M/E sites with statistically significant differences in editing level.According to the position of nucleotide sequence in mature mi RNA and the types of mi RNA editing found in previous studies,1890 M/E sites are divided into 9 categories including 592 3’-A,439 3’-U,401 Other,225 3’-Other,89 5’,69 SNP,41 A-to-I(G),26C-to-U and 8 Pseudo(false positive events).In this study,a total of four nucleotide deletion events occur in mi RNA of human brain tissue,and no nucleotide insertion events are found.The number of pre-mi RNA which has only one M/E site is the largest,and the M/E site is most concentrated in the central region of mi RNA.The number of pre-mi RNA which has multiple M/E sites is relatively small,and the M/E sites are most concentrated in the 3’ end of mi RNA.There is a small difference between the editing level of mi RNA in prefrontal cortex(PC)tissue of HD brains and the editing level of mi RNA in PC tissue of healthy individual brains.Compared with the editing level of mi RNA in other tissues of healthy individual brains,there is a large difference in PC tissue of HD brains.The difference of editing level in A-to-I(G)between HD and healthy individual brains is small.A total of 23 A-to-I(G)editing sites occur in the seed sequence of mi RNA and samples of the most significant editing level are from the healthy individual brains.Compared with RADAR database and DARNED database,we found 10 unreported A-to-I(G)editing sites.A-to-I(G)has a strong preference for the nucleotide U on the 5’ side and the nucleotide G on the 3’ side of the editing site.The difference of C-to-U editing level between HD and healthy individual brains is small.Four SNP events occur in the seed sequence of mi RNA.There are 164 M/E sites with statistically significant difference between HD and healthy individual brains,of which 4 M/E sites occur in the seed sequence of mi RNA,namely hsa-mir-376a-1＿49＿A＿g,hsa-mir-376a-2＿55＿A＿g,hsa-mir-1301＿52＿A＿g and hsa-mir-4454＿4＿G＿u.It is PAR-CLIP(Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation)that is an effective method to identify animal mi RNA targets.The MICPAR algorithm uses corrected PAR-CLIP sequencing profiles to predict the targets of mi RNA.In addition to hsa-mir-4454＿4＿G＿u,we used the MICPAR algorithm to predict the targets of the remaining 3 M/E sites.The edited mi RNA targets more genes than original mi RNA and the targets are almost different between the original and edited mi RNA.We compared the targets of the three edited mi RNAs to the genes with dysregulated expression in HD reported by two published studies.hsa-mir-376a-1＿49＿A＿g has 34 targets that are the same as the genes reported to be dysregulated in the two studies.The gene PAK1 is shared and is considered to be a potential therapeutic target of neurological diseases.hsa-mir-376a-2＿55＿A＿g has 42 targets which are reported to be dysregulated in one study but are not overlapped with the other study.hsa-mir-1301＿52＿A＿g has 51 targets that are the same as the genes reported to be dysregulated in the two studies,but there are no common genes.We performed GO and KEGG analysis on the targets of three M/E sites,namely hsa-mir-376a-1＿49＿A＿g,hsamir-376a-2＿55＿A＿g,and hsa-mir-1301＿52＿A＿g.It is found that mi RNA editing events obviously change the targets of mi RNA and the functions of the targets between original and edited mi RNA also change greatly,indicating that mi RNA editing events may result in targeting another set of targets with different functions.