Transcriptome analyses of adult mouse brain reveal enrichment of IncRNAs in specific brain regions and neuronal populations

Despite the importance of the long non-coding RNAs (IncRNAs) in regulating biological functions, the expression profiles of IncRNAs in the sub-regions of the mammalian brain and neuronal populations remain largely uncharacterized. By analyzing RNASeq datasets, we demonstrate region specific enrichment of populations of IncRNAs and mRNAs in the mouse hippocampus and pre-frontal cortex (PFC), the two major regions of the brain involved in memory storage and neuropsychiatric disorders. We identified 2759 IncRNAs and 17,859 mRNAs in the hippocampus and 2561 IncRNAs and 17,464 mRNAs expressed in the PFC. The IncRNAs identified correspond to 14% of the transcriptome of the hippocampus and PFC and 70% of the IncRNAs annotated in the mouse genome (NCBIM37) and are localized along the chromosomes as varying numbers of clusters. Importantly, we also found that a few of the tested IncRNA-mRNA pairs that share a genomic locus display specific co-expression in a region-specific manner. Furthermore, we find that sub-regions of the brain and specific neuronal populations have characteristic IncRNA expression signatures. These results reveal an unexpected complexity of the IncRNA expression in the mouse brain.