Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines

Eukaryotic mRNAs consist of two forms of transcripts: poly(A)+ and poly(A)−, based on the presence or absence of poly(A) tails at the 3′ end. Poly(A)+ mRNAs are mainly protein coding mRNAs, whereas the functions of poly(A)− mRNA are largely unknown. Previous studies have shown that a significant proportion of gene transcripts are poly(A)− or bimorphic (containing both poly(A)+ and poly(A)− transcripts). We compared the expression levels of poly(A)− and poly(A)+ RNA mRNAs in normal and cancer cell lines. We also investigated the potential functions of these RNA transcripts using an integrative workflow to explore poly(A)+ and poly(A)− transcriptome sequences between a normal human mammary gland cell line (HMEC) and a breast cancer cell line (MCF-7), as well as between a normal human lung cell line (NHLF) and a lung cancer cell line (A549). The data showed that normal and cancer cell lines differentially express these two forms of mRNA. Gene ontology (GO) annotation analyses hinted at the functions of these two groups of transcripts and grouped the differentially expressed genes according to the form of their transcript. The data showed that cell cycle-, apoptosis-, and cell death-related functions corresponded to most of the differentially expressed genes in these two forms of transcripts, which were also associated with the cancers. Furthermore, translational elongation and translation functions were also found for the poly(A)− protein-coding genes in cancer cell lines. We demonstrate that poly(A)− transcripts play an important role in cancer development.