MicroRNAs are widely referred to as gene expression regulators for different diseases. The integration between single nucleotide polymorphisms (Snps) and miRnAs has been associated with both human and animal diseases. In order to gain new insights on the effects of SNPs on miRNA and their related sequences, we steadily characterized a whole mouse genome miRNA related SNPs, analyzed their effects on the miRNA structural stability and target alteration. In this study, we collected 73643859 SNPs across the mouse genome, analyzed 1187 pre-miRNAs and 2027 mature miRNAs. Upon mapping the SNPs, 1700 of them were identified in 702 pre-miRNAs and 609 SNPs in mature miRNAs. We also discovered that Snp densities of the pre-miRnA and mature miRnAs are lower than the adjacent flanking regions. Also the flanking regions far away from miRNAs appeared to have higher SNP density. In addition, we also found that transitions were more frequent than transversions in miRNAs. Notably, 841 SNPs could change their corresponding miRNA's secondary structure from stable to unstable. We also performed target gain and loss analysis of 163 miRNAs and our results showed that few miRNAs remained unchanged and many miRNAs from wild mice gained target site. These results outline the first case of SNP variations in the mouse whole genome scale. Those miRNAs with changes in structure or target could be of interest for further studies.
Puberty onset is a milestone in sexual development. A tumor suppress gene (TSG) network had been reported to be involved in the regulation of female puberty onset. The observations in rodents and primates showed a potential link between microRNAs and puberty onset. To figure out what miRNAs play roles in this important biological process, profilings of microRNAs in the hypothalamus of female mice from three different pubertal stages, juvenile [postnatal day (P10)], early pubertal (P25) and pubertal (P30) were performed on the Affymetrix GeneChip miRNA 3.0 Arrays, the cerebral cortex (CTX) was used as a control tissue. 20 miRNAs were shown to be differentially expressed in hypothalamus (fold change > 1.5, P < 0.05), but not in CTX during the transition from juvenile to pubertal. Four of them were validated by real-time quantitative RT-PCR (qRT-PCR) method. 1018 genes were predicted as the targets of these miRNAs. Further bioinformatics analysis suggested that these target genes were involved in many important signaling pathways, especially in the cancer related pathways. We also found that about 90% of these target genes were expressed in the hypothalamus, as well as in the immortalized GnRH-producing GT1-7 cells, which provided additional evidence that these miRNAs could be female puberty onset related. Here we present a novel comprehensive data set of miRNA gene expression during the puberty onset; and it provides an important recourse for the future functional characterization of individual miRNAs and their targets in mouse hypothalamus and in GT1-7 cells.
Puberty is a transition period where a child transforms to an adult. Puberty can be affected by various genetic factors and environmental influences. In mammals, the regulation of puberty is enhanced by the hypothalamic-pituitary-gonadal axis (HPG axis). A number of genes such as GnRH, Kiss1, and GPR54 have been reported as key regulators of puberty onset. In this study, we have conducted an association study of puberty-related candidate genes in Chinese female population. Gene variations reported to be related with some traits in a population may not exist in others due to different genetic and ethnic backgrounds, hence the need for this kind of study. The genotyping of SNPs was based on multiplex PCR and the next-generation sequencing (NGS) platform of Illumina. We finally performed association study using PLINK software. Our results confirmed that SNPs rs34787247 in LIN28, rs74795793 and rs9347389 in OCT-1, and rs379202 and rs10491080 in ZEB1 genes showed a significant association with puberty. With the result, it is reasonable to conclude that these genes affect the process of puberty in Shanghai Chinese female population, yet the mechanism remains to be investigated by further study.
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