The Genome-wide Prediction Of Chicken Micrornas And Studies Of Their Mutation In Blue-shelled Chicken And White Leghorn

MicroRNAs are families of non-coding RNAs molecules,which come from the genome of plants and animals with a length of 21-25 nt.They are derived from 70-110 nt microRNAs precursor by Dicer.Mature microRNAs involve in posttranscriptional regulation by targeting m RNAs for expression inhibition.So far,most studies have focused on microRNAs in Drosophila melanogaster,mouse and human,yet,few of them paid attention to Gallus,especially in genome-wide.As bioinformatics predictions are not limited by tissue specificity and time restrictions,they have been widely used in the prediction of microRNAs.However,most of these predictions just remained as pre-microRNAs prediction studies.Therefore,it is worth that study for prediction of Gallus microRNAs in genome-wide to mature microRNAs level.Meanwhile,few studies have been reported to explore Blue-shelled chicken and White leghorn from the standpoint of microRNAs mutation.The paper will perform these studies:(1).Built chicken genome-wide premicroRNAs filter for pre-microRNAs prediction and predicted these premicroRNAs into mature microRNAs level;(2).Utilized microRNAs mutations to research downstream pathways between Blue-shelled chicken and White leghorn.The methods and the results may provide references for further studies.1.Genome-wide prediction of chicken mature microRNAs: We built the support-vector-machine(SVM)-based machine learning classifier to make a genome-wide scan on the pre-microRNAs of chicken with a sensitivity of 90.00%,a specificity of 91.10%,and a total prediction accuracy of 91.06% respectively,in which we found 3,935 novel premicroRNA candidates.Then,we adopted mi Rdup as a tool for mature microRNAs prediction.Based on all-species-model,3,781 microRNAsmicroRNAs* duplex were generated from both 3’-end and 5’-end of the3,935 predicted pre-microRNAs.When based on Gallus-specific-model,the number was 3,067.2.Study of Blue-shelled chicken and White leghorn in microRNAs mutation:Blue-shelled Chicken is a Chinese traditional breed,which has different characters from the introduced-breed White Leghorn,especially in growth and laying.This study utilized microRNAs to explore these potential differences.Global genome microRNAs was combined by the identified microRNAs and complementary lab-predicted microRNAs.Then the two breed chicken’s GGRS SNP data were mapped to the microRNAs and focused on SNP that deliberately located in mature-microRNAs.Bioinformatics methods was adopted for target prediction on microRNAs which had SNPs.By further gene enrichment analysis,the study found these genes significantly enriched in 22 GO terms,10 KEGG pathways,and 3 IPA important networks.