Age-Related Expression of a Repeat-Rich Intergenic Long Noncoding RNA in the Rat Brain

Genome-wide transcriptome analysis has shown that ∼90 % of the mammalian genome undergoes pervasive transcription into various small and long noncoding RNAs with diverse biological functions and only ∼1.5 % is protein coding. Recent literature suggests that various structurally diverse sense and antisense long noncoding RNAs (lncRNAs) (>200 nt) are expressed from the intronic, intergenic and repeat-rich regions in the mammalian central nervous system (CNS). Till date, many of them have been found to be regulated in developmental, spatio-temporal and cell type-specific manners and are involved in various neurological processes. However, still much is left to be understood regarding their functional relevance in mammalian brain development, maturation and ageing. Furthermore, various signalling factors and metabolites such as all-trans retinoic acid (atRA) have been known to regulate brain functions during development, though their role in adult brain function is much less known. Here, we report differential and age-related expression of a novel repeat sequence-rich, long intergenic nonprotein coding RNA (lincRNA), named as LINC-RSAS (repeat-rich sense-antisense transcript) in different neuroanatomical regions of the rat brain. The LINC-RSAS was found to be moderately conserved and contained regulatory elements of various cell growth- and development-specific transcriptional factors in its up/downstream flanking sequences in the genome. Through RNA expression by reverse transcription polymerase chain reaction (RT-PCR) and localization by in situ RNA hybridization, we found that both sense and antisense transcripts of LINC-RSAS were expressed in the cortex, hippocampus and cerebellum regions of the rat brain in cell type-specific and age-related manner. Furthermore, both the expression level and subcellular localization of the antisense LINC-RSAS transcript were significantly induced in the cultured primary hippocampal neurons after treatment with atRA. Overall, our study provides insights into the possible involvement of an atRA-inducible, intergenic lncRNA in different functional regions of mammalian brain and its association with brain maturation and ageing.