The optimal compound reference genes for qRT-PCR analysis in the developing rat long bones under physiological conditions and prenatal dexamethasone exposure model

Abstract

Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful tool for evaluating gene expression, but its accuracy is affected by the stability of the reference genes used for normalization. The Minimum Information for Publication of Quantitative Real-time PCR Experiments (MIQE) guidelines indicated that it was important to use multiple stable reference genes as compound reference genes for acquiring optimal experimental results. In this study, the expression levels of eight candidate reference genes (SDHA, TBP, GAPDH, etc.) were detected by qRT-PCR in rat long bones at different developmental stages [gestation day (GD) 20, postnatal week (PW) 6 and PW12] under physiological conditions. Software geNorm, NormFinder, and BestKeeper were used to comprehensively evaluate the stability of the eight reference genes for screening out the most stable compound reference genes in each period. Additionally, the pathological model of prenatal dexamethasone exposure (PDE) was used to verify the stability and reliability of the selected compound reference genes. The result showed that two reference genes as compound reference genes for normalization were optimal. In the intrauterine period, SDHA and TBP could be selected as the compound reference genes, while YWHAZ and GAPDH could be selected at PW6 and PW12, and there was no significant gender difference in the selection of reference genes. The above compound reference genes remained stable in the PDE model and could make the statistical significance of the experimental results more remarkable. In conclusion, this study screened out the optimal compound reference genes in rat long bones before and after birth.