Characterization of long-noncoding RNA in hepatocellular carcinoma cells with fractionation-then-sequencing

Advancements in sequencing technologies greatly improved our understanding of long non-coding RNA (lncRNA), a class of transcript of length >200nt implicated to play significant regulatory roles in various biological processes. Importantly, deregulation of better characterized lncRNAs have been linked to multiple types of cancers including hepatocellular carcinoma (HCC). The patterns of lncRNA subcellular enrichment in either cytoplasmic or nuclear fraction may provide clues to their biological functions. A transcriptome-wide investigation on the subcellular distributions of HCC-associated lncRNAs might thus provide new insights on their roles and function in cancers.In this study, we performed subcellular fractionation of 8 patient-derived HCC cell lines and separately sequenced RNA residing in their nuclear and cytoplasmic compartments. The cell lines were derived from HCC patient tumor tissues, where all patients are of Asian-Chinese ethnicity and were diagnosed with either prior chronic hepatitis B/C or nonalcoholic steatohepatitis (NASH). The dataset enabled us to derive a catalog of HCC-associated lncRNA with ab initio transcriptome assembly, and to evaluate the subcellular enrichment bias for individual lncRNA genes.