Both brown adipose tissue and skeletal muscle have abundant mitochondria and energy consumption capacity. They are similar in origin and gain different potential of energy metabolism after differentiation and maturation. The mechanism that cause the difference is not yet fully understood. Long non-coding RNAs (lncRNAs) which comprise the bulk of the human non-coding transcriptome have been proved to play key roles in various biological processes. Whether they will have a function on the differentiation and energy metabolism between BAT and skeletal muscle is still unknown. To identify the cellular long noncoding RNAs (lncRNAs) involved in the progress, we used the next generation transcriptome sequencing and microarray techniques, and investigated 704 up-regulated and 896 down-regulated lncRNAs (fold-change >3.0) in BAT by comparing the expression profile. Furthermore, we reported AK003288 associated with junctophilin 2 (Jph2) gene which may affect energy metabolism. This study show distinct expression profiles of LncRNAs between brown adipose tissue and skeletal muscle which provide information for further research on differentiation of adipocyte and transdifferentiation between BAT and skeletal muscle that will be helpful to find a new therapeutic target for combatting obesity. (C) 2013 Elsevier Inc. All rights reserved.