Repetitive elements in the mouse brain: expression and regulation

Retrotransposons are expressed in a cell type-specific manner contributing to cellular differentiation and physiological activities. In brain they are expressed as independent transcriptional units or embedded in transcripts regulating RNA splicing, dendritic localization and translation. They can also mobilize to a different genomic position changing the DNA landscape of neurons. The contribution of repetitive elements to the structure of the transcriptome of an adult neuron is still unclear. To this purpose, I have analyzed the expression and regulation of the two families of retrotransposons: SINEs (Short INterspersed Element) and LINEs (Long INterspersed Element) transposable elements. In the first part, I describe the expression of SINE.IDs, belong to a repetitive family evolutionary derived from retrotransposition of their master gene BC1. By taking advantage of nanoCAGE, we have described the transcriptional landscape of dopaminergic neurons in the Substantia Nigra of the mouse mesencephalon, a major neuronal cell group implicated in Parkinson’s Disease (PD). Together with a definition of the repertory of repetitive elements expressed in these adult neurons, I have identified a large number of different SINE.IDs that are independently expressed in the wild-type mouse brain and in the BC1 KO mice. In particular, I have shown that single SINE.IDs are differentially expressed in mouse brain regions as independent transcriptional units and are regulated during neuronal cell differentiation in a dopaminergic cell line model. The precise temporal and spatial expression of ncRNAs appears to be exceptionally important for mediating CNS form and function. In this case, our data support the hypothesis that repetitive sequences, such as SINE.IDs, are regulated and selectively targeted to specific cellular domains in subsets of neurons of the rodent nervous system. In the second part, I study potential effects of dietary regimens on the genomic landscape of the brain. Nutritional and metabolic factors are associated with onset and progression of neurodegenerative disorders. In particular, B vitamin deprivation and hyperhomocysteinemia is associated with Alzheimer’s disease, by inhibiting DNA methylation of related genes, such as PSEN1. Supporting a strong link between dietary and DNA methylation status, I have hypothesized that retrotranspositional events may be regulated by the B vitamin content of food intake. To this propose, a TaqMan qPCR assay has been developed in mouse for studying LINE1 copy number variation of different repetitive element families. By taking advantage of this new tool, I have unveiled that brain cells present an higher LINE1 content than non-brain tissues. Furthermore, I have accumulated preliminary data suggesting copy number variations triggered by dietary regimens.