In Silico Prediction and Validation of Gfap as an miR-3099 Target in Mouse Brain

作     者：Shahidee Zainal Abidin Jia-Wen Leong Marzieh Mahmoudi Norshariza Nordin Syahril Abdullah Pike-See Cheah King-Hwa Ling 

作者机构：Neuro Biology and Genetics GroupUniversiti Putra Malaysia43400 SerdangSelangorMalaysia Genetics and Regenerative Medicine Research CenterUniversiti Putra Malaysia43400 SerdangSelangorMalaysia Medical Genetics UnitDepartment of Biomedical SciencesUniversiti Putra Malaysia43400 SerdangSelangorMalaysia Department of Human AnatomyFaculty of Medicine and Health SciencesUniversiti Putra Malaysia43400 SerdangSelangorMalaysia Institute of Biological SciencesFaculty of ScienceUniversity of Malaya50603 Kuala LumpurMalaysia 

出 版 物：《Neuroscience Bulletin》 (神经科学通报（英文版）)

年 卷 期：2017年第33卷第4期

页      面：373-382页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071006[理学-神经生物学] 

基　　金：supported by the Science Fund(02-01-04-SF2336) the Fundamental Research Grant Scheme,Ministry of Higher Education,Malaysia(FRGS-04-01-15-1663FR) 

主　　题：Target gene Neurogenesis In silico Astrogliogenesis Bioinformatics 

摘      要：MicroRNAs are small non-coding RNAs that play crucial roles in the regulation of gene expression and protein synthesis during brain development. MiR-3099 is highly expressed throughout embryogenesis, especially in the developing central nervous system. Moreover, miR-3099 is also expressed at a higher level in differentiating neurons in vitro, suggesting that it is a potential regulator during neuronal cell development. This study aimed to predict the target genes of miR-3099 via in-silico analysis using four independent prediction algorithms（miRDB,miRanda, Target Scan, and DIANA-micro-T-CDS） with emphasis on target genes related to brain development and function. Based on the analysis, a total of 3,174 miR-3099 target genes were predicted. Those predicted by at least three algorithms（324 genes） were subjected to DAVID bioinformatics analysis to understand their overallfunctional themes and representation. The analysis revealed that nearly 70% of the target genes were expressed in the nervous system and a significant proportion were associated with transcriptional regulation and protein ubiquitination mechanisms. Comparison of in situ hybridization（ISH） expression patterns of miR-3099 in both published and in-house-generated ISH sections with the ISH sections of target genes from the Allen Brain Atlas identified 7 target genes（Dnmt3a, Gabpa, Gfap, Itga4,Lxn, Smad7, and Tbx18） having expression patterns complementary to miR-3099 in the developing and adult mouse brain samples. Of these, we validated Gfap as a direct downstream target of miR-3099 using the luciferase reporter gene system. In conclusion, we report the successful prediction and validation of Gfap as an miR-3099 target gene using a combination of bioinformatics resources with enrichment of annotations based on functional ontologies and a spatio-temporal expression dataset.