Transcriptome analysis of long non‐coding RNAs of the nucleus accumbens in cocaine‐conditioned mice

Abstract

Cocaine dependence involves in the brain's reward circuit as well as nucleus accumbens (NAc), a key region of the mesolimbic dopamine pathway. Many studies have documented altered expression of genes and identified transcription factor networks and epigenetic processes that are fundamental to cocaine addiction. However, all these investigations have focused on mRNA of encoding genes, which may not always reflect the involvement of long non-coding RNAs (lncRNAs), which has been implied in a broad range of biological processes and complex diseases including brain development and neuropathological process. To explore the potential involvement of lncRNAs in drug addiction, which is viewed as a form of aberrant neuroplasticity, we used a custom-designed microarray to examine the expression profiles of mRNAs and lncRNAs in brain NAc of cocaine-conditioned mice and identified 764 mRNAs, and 603 lncRNAs were differentially expressed. Candidate lncRNAs were identified for further genomic context characterization as sense-overlap, antisense-overlap, intergenic, bidirection, and ultra-conserved region encoding lncRNAs. We found that 410 candidate lncRNAs which have been reported to act in cis or trans to their targeted loci, providing 48 pair mRNA-lncRNAs. These results suggest that the modification of mRNAs expression by cocaine may be associated with the actions of lncRNAs. Taken together, our results show that cocaine can cause the genome-wide alterations of lncRNAs expressed in NAc, and some of these modified RNA transcripts may to play a role in cocaine-induced neural plasticity and addiction.

Identification of a developmentally-regulated and psychostimulant-inducible novel rat gene mrt3 in the neocortex

“…of the protein-ubiquitin ligase complex. This presumption appears to be compatible with the previous data that expression of a group of LncRNAs is affected in the nucleus accumbens of cocaine-conditioned mice (Bu et al, 2012) and that repeated amphetamine-induced alterations in ubiquitination processes controlling the glutamate receptor stability lead to synaptic and behavioral adaptations to amphetamine (Mao et al, 2009). This viewpoint could provide an alternative explanation for the relationship between behavioral sensitization and the lack of mrt3 modulation by a challenge dose of MAP or cocaine after repeated MAP treatment by the idea that inhibitory effects of mrt3 on behavioral responses to MAP or cocaine administration by repressed expression of the target genes for the mrt3 as a LncRNA could be attenuated in the rats repeatedly exposed to MAP.…”

Integrated analysis of long non-coding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in gastric cancer pathogenesis

“…In some conditions, a reversed direction is possible to promote expression in the 3'-UTR region. The predictive algorithms for the cis-acting analysis were performed as previously described (24)(25)(26).…”

“…First, we performed BLAST (e<1E-5) between lncRNA and the known protein-coding genes followed by RNAplex software to further screening the trans-acting target genes (parameters were set as -e -20). The RNAplex program for trans-acting analysis was performed as previously described (22,(25)(26)(27)(28).…”

Twist-related protein 1-mediated regulation of mesenchymal change contributes to the migration and invasion of cervical cancer cells

“…Sequences of primers used in the qPCR analysis are presented in Table I. The qPCR results were calculated using the 2 -ΔΔCT method as described previously (17).…”