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The molecular mechanisms underlying epileptogenesis have been widely investigated by differential gene expression approach, especially RT-qPCR methodology. However, controversial findings highlight the occurrence of unpredictable sources of variance in the experimental designs. Here, we investigated if diurnal rhythms of transcript’s levels may impact on differential gene expression analysis in hippocampus of rats with experimental epilepsy. For this, we have selected six core clock genes ( Per1 ,  Per3 ,  Bmal1 ,  Clock ,  Cry1  and  Cry2 ), whose rhythmic expression pattern in hippocampus had been previously reported. Initially, we identified  Tubb2a / Rplp1  and  Tubb2a / Ppia  as suitable normalizers for circadian studies in hippocampus of rats maintained to 12:12 hour light:dark (LD) cycle. Next, we confirmed the temporal profiling of  Per1 ,  Per3 ,  Bmal1 ,  Cry1  and  Cry2  mRNA levels in the hippocampus of naive rats by both Acrophase and CircWave statistical tests for circadian analysis. Finally, we showed that temporal differences of sampling can change experimental results for  Per1 ,  Per3 ,  Bmal1 ,  Cry1  and  Cry2 , but not for  Clock , which was consistently decreased in rats with epilepsy in all comparison to the naive group. In conclusion, our study demonstrates it is mandatory to consider diurnal oscillations, in order to avoid erroneous conclusions in gene expression analysis in hippocampus of rats with epilepsy. Investigators, therefore, should be aware that genes with circadian expression could be out of phase in different animals of experimental and control groups. Moreover, our results indicate that a sub-expression of  Clock  may be involved in epileptogenicity, although the functional significance of this remains to be investigated.

plos one

Diurnal Variation Has Effect on Differential Gene Expression Analysis in the Hippocampus of the Pilocarpine-Induced Model of Mesial Temporal Lobe Epilepsy