Neural Development

Recently, a universal class of endogenous noncoding circular RNAs (circRNAs) has piqued the interest of multiple areas of research. In eukaryotes, these particularly stable single-stranded circular RNA molecules are generated by an alternative splicing mechanism that covalently links the 5’ end of one exon with the 3’ end of another exon. These highly conserved circRNAs are characterized by tissue- and developmental stage-specific expression patterns. More specifically, it was recently shown that circRNAs are particularly enriched in the brain with expression dynamics independent of the linear mRNA transcripts derived from the same gene. Although abundantly expressed in the nervous system, their function remains largely unknown. In addition, evidence has emerged for circRNA involvement in various diseases, including cancer, possibly by regulating gene expression levels through interaction with other molecules. The accurate detection and localization of circRNAs is pivotal to elucidate their biological functions especially given the fact that they could serve as putative clinical biomarkers.

In this study, we evaluated the expression of various circRNAs and their linear mRNA counterparts in P1, P10 and P30 C57Bl/6J developmental mouse brains using the novel in situ hybridization BaseScope™ technology. This assay allows for the visualization of specific splice junctions in a highly specific and sensitive manner within the morphological tissue context.

Here, we highlight the anatomical localization and corresponding quantification of the linear mRNA and circRNA splice variants for the brain plasticity-related target Dlgap1 in the hippocampus by detecting the mRNA-specific and circRNA-specific (head-to-tail junction) exon junction, respectively.

yellow=circular RNA specific probe; blue=mRNA specific probe; green=common RNA probe

The BaseScope™ assay can be used to visualize circRNAs in tissue - please download our scientific poster “Highly sensitive and specific in situ detection of circular RNAs in C57Bl/6J developing mouse brain using BaseScope™ technology” to read more