Quantitation of GABA transporter 3 (GAT3) mRNA in rat brain by competitive RT-PCR

Gamma-amino butyric acid is the major inhibitory neurotransmitter in the brain. GABA transporters (GATs) remove GABA from the synaptic cleft. Till now, five distinct GABA transporters have been cloned and termed consecutively GAT1 to GAT4 and vGAT. To study the mechanisms by which tolerance and dependence associated with drugs enhancing GABAergic transmission is brought upon we analysed the mRNA expression levels of GATs in various brain regions under different conditions. In this paper, we describe our protocol for measurement of GAT3 mRNA expression, and its validation through control experiments for the various steps. We performed competitive reverse transcription and polymerase chain reaction (RT-PCR) with a competitor cRNA as internal standard. Different amounts of competitor cRNA were added to total RNA prepared from different tissue samples, reverse-transcribed and PCR amplified. The PCR amplification gave two products: the GAT wild type fragment and the competitor fragment. PCR products were separated by gel electrophoresis and band intensities were determined from which the relative and absolute abundance of GAT3 mRNA was calculated by regression analysis. Validation experiments in our laboratory showed a 6% intra-assay and a 15% inter-assay variability of this method.