Even though the molecular mechanisms of gene expression in neurons are quite broadly described in the literature, little is known about the relationship between these processes and the architecture of the neuronal cell nucleus. For example, it is firmly established that waves of gene expression occurring after neuronal stimulation comprise plenty of genes playing important roles in cognitive and epileptic phenomena. However, it has never been examined whether these bursts of transcriptional activity involve any regulation at the level of higher-order nuclear structure. Accordingly, we have performed studies on the structure of neuronal nucleus in epileptic animals. Based on the literature we chose the genes for BDNF and TRKB that play key roles in synaptic plasticity in the brain. We have investigated clustering of these genes in the nucleus by means of fluorescent in situ hybridization. We found that in hippocampal neurons the bdnf-trkb distance decreases 2 hours after seizure induction compared to control. Moreover, using bioinformatical approach we selected 2 linear clusters of the genes that are upregulated after seizures. One of them was selected on the chromosome 1 and the other one on chromosome 20. Those linear gene clusters appeared to associate 4 weeks after seizure compared to control. Our results suggest that upon epileptogenesis there is a reorganization of neuronal nucleus involving clustering of the genes in three-dimensional space. The phenomenon could occur also in other forms of synaptic plasticity, and should be a topic to follow up in the future.
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