Antisense RNAs influence promoter usage of their counterpart sense genes in cancer

Natural antisense transcripts (NATs) are those RNAs transcribed from the same locus, but in the opposite direction to a sense gene transcript. non-coding NATs (ncNATs) have been reported to modulate key biological events such as cell differentiation and carcinogenesis through gene expression regulation; nevertheless, their actual impact on cancer remains largely unknown. Due to their low expression levels and their overlap with sense genes, the study of ncNATs using RNA-seq is challenging. Public databases frequently register incomplete sequences of ncNATs, and mostly in a not tissue-specific manner. In the present study, we aim to better characterize the nature of ncNATs expressed in liver and hepatocellular carcinoma (HCC). For that, we performed strand-specific RNA-seq in 6 pairs of HCC - normal adjacent liver tissues from 6 HCC patients. Knowing the strand origin of the reads, we will be able to determine the actual nature and span of those ncNATs expressed in the liver and in HCC. Overall design: We constructed strand-specific cDNA libraries of 12 total RNA samples, corresponding to six paired sets of HCC and normal adjacent liver tissues.