Cloning and Functional Characterization of a Novel Long Non-coding RNA Gene Associated With Hepatocellular Carcinoma

Abstract

Recently, we sequenced the transcriptomes of a hepatocellular carcinoma biopsy and a normal liver tissue using the RNA-Sequencing(RNA-Seq) strategy based on the Next Generation Sequencing(NGS) technique, and identified several adjacent high RNA-Seq signal peaks on chromosome 11q13.1 in the hepatocellular carcinoma biopsy, while not in the normal control tissue. In this chromosome region, there is no characterized genes have been identified, implying that these RNA-Seq peaks may represent one or more novel genes. Further study was confirmed that these RNA-Seq peaks were transcribed by one novel gene. Through cloning the full length of this novel gene, we found that this novel gene transcribed many splicing isoforms, and the longest isoform is 3 562 bp. Then we deposited twelve representative RNA isoforms into the GenBank database of the National Center for Biotechnology Information(NCBI), and created the GenBank IDs from KC136297 to KC136308 for these isoforms. None significant open reading fragment(ORF) was found in any transcripts of this novel gene, implying that this gene may encodes long non-coding RNAs(lncRNAs). To further elucidate the potential transcriptional regulation mechanism of this lncRNA gene, we predicted the promoter from the upstream sequence of the lncRNA gene using bioinformatic tools, and found that there is one potential promoter in-719 to-469 bp from the transcript start site of the lncRNA gene, and there are seven Sp1, one STAT5 and one EGR1 transcription factor binding sites in the promoter region. The molecular mechanisms of the lncRNA gene in carcinogenesis and progression of hepatocellular carcinoma are worthful for further investigation.