Transcriptome analyses reveal enrichment of specific lncRNAs in specific brain regions and neuronal populations

Despite the availability of large-scale transcriptomics data, specific long noncoding RNAs (lncRNAs) expressed in specific brain regions and populations of neurons are poorly understood. Here we report analysis of expression of lncRNAs and mRNAs expressed in hippocampus and prefrontal cortex (PFC), two regions of brain that are involved in memory storage and neuropsychiatric disorders. Our unbiased analyses have identified specific lncRNAs and mRNAs that are enriched in hippocampus and PFC. We have identified several regions in the chromosomes characterized by clustered lncRNA expression suggesting the transcriptional hotspots of lncRNA in the genome. We find that, a subset of lncRNAs and protein coding genes in their vicinity are uniquely co-expressed in specific brain regions and thus presumably co-regulated. Furthermore, specific brain regions and neuronal populations have characteristic lncRNA expression profile. These studies reveal unexpected complexity in the expression profiles of lncRNAs in the mammalian brain. Overall design: Examination of mRNAs and long noncoding RNAs in mouse hippocampus and prefrontal cortex of 8 adult mice.

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Kadakkuzha BM, Liu XA, McCrate J, Shankar G, Rizzo V, Afinogenova A, Young B, Fallahi M, Carvalloza AC, Raveendra B, Puthanveettil SV