Genome-wide profiling has revealed that eukaryotic genomes are transcribed into numerous non-coding RNAs. In particular, long non-coding RNAs (lncRNAs) have been implicated in various human diseases due to their biochemical and functional diversity. Epileptic disorders have been characterized by dysregulation of epigenetic regulatory mechanisms, and recent studies have identified several lncRNAs involved in neural development and network function. However, comprehensive profiling of lncRNAs implicated in chronic epilepsy has been lacking. In this study, microarray analysis was performed to obtain the expression profile of IncRNAs dysregulated in pilocarpine and kainate models, two models of temporal lobe epilepsy commonly used for studying epileptic mechanisms. Total of 4622 lncRNAs were analyzed: 384 IncRNAs were significantly dysregulated in pilocarpine model, and 279 lncRNAs were significantly dysregulated in kainate model compared with control mice (>= 3.0-fold, p < 0.05). Among these, 54 and 14 IncRNAs, respectively, had adjacent protein-coding genes whose expressions were also significantly dysregulated (>= 2.0-fold, p < 0.05). Majority of these pairs of IncRNAs and adjacent genes shared the same direction of dysregulation. For the selected adjacent gene-IncRNA pairs, significant Gene Ontology terms were embryonic appendage morphogenesis and neuron differentiation. This was the first study to comprehensively identify dysregulated IncRNAs in two different models of chronic epilepsy and will likely provide a novel insight into developing IncRNA therapeutics. (C) 2015 Elsevier Inc. All rights reserved.