Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play prevalent roles in transcriptional regulation. We have reported that promoter-associated ncRNAs (pancRNAs) activate the partner gene expression via local epigenetic changes. Here, we identify thousands of genes under the pancRNA-mediated transcriptional regulation in five mammalian species in common. In the mouse, 1) pancRNA-partnered genes show tissue-specific expression pattern, 2) expression of pancRNAs significantly enriched H3K4me3 and H3K27ac marks towards the partner gene expression, 3) H3K4me1 marks the pancRNA-partnered genes regardless of their expression level, and 4) C- or G-skewed motifs were exclusively overrepresented between -200 and -1 bp relative to the transcription start sites of pancRNA-partnered genes. More importantly, the comparative transcriptome analysis among five different mammalian species using a total of 25 counterpart tissues showed that overall pancRNA expression profile exhibited extremely high species-specificity compared to that of mRNA, suggesting that a significant number of pancRNAs contributed to the enhancement of a set of partner genes' expression in a sequence-specific manner. We conclude that the gain and/or loss of gene-activation-associated pancRNA repertories, caused by formation or disorganization of the genomic GC-skewed structure, finely shapes tissue-specific pattern of gene expression according to a given species.