IN SILICO Analysis of SOX9 Deletion
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https://doi.org/10.5281/zenodo.8404309Keywords:
miRNA, miRWalk, SOX9Abstract
SOX9 gene is a transcription factor that plays a key role in sex determination, chondrocyte differentiation and skeletal development in embryonic development. Decreased SOX9 expression often leads to campomelic dysplasia, a skeletal malformation syndrome observed with disorders of sex development. With their full or partial complementarity, miRNAs are important mediators that regulate the expression of their target transcripts. Deletion of SOX9 gene may result in increased expression levels of miRNAs targeting this gene and thus decreased expression levels of other target genes. This study aimed to identify miRNAs that deletion of SOX9 could potentially affect and their target genes in silico. For this, miRNAs targeting SOX9 gene were searched from the data stored with the machine learning algorithm using miRWalk database. Four miRNAs with scores greater than 0.95 and at least matching in the other two miRNA target databases (miRTarBase, miRDB, TargetScan) were identified from the results. The possible conformation of these miRNAs with SOX9 transcript was generated using the algorithms of STarMir and miRanda databases. The genes targeted by all four miRNAs were identified as RLIM, MBNL3, ZNF516 and FZD4 using miRDB. Using the GeneMANIA prediction server, 20 other genes with which these target genes interact were determined using association data, including protein and genetic interactions, pathways, co-expression and localization, and protein domain similarities. The expression in protein and RNA levels, molecular functions and roles in biological processes of these four target genes were investigated with human proteome data and experimental studies. The results of this study suggest the possibility that SOX9 gene deletion may cause expression changes in potential target genes via miRNA.
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