An integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis.

Human endogenous retroviruses (HERVs) occupy a large portion of the human genome. Most HERVs are transcriptionally silent, but can be reactivated during pathological states such as viral infection and certain cancers. The HERV-K HML-2 clade includes elements that recently have integrated in the human germ line and often contain intact open reading frames (ORFs) that possibly support peptide and protein expression. Understanding HERV-K-host interactions and their potential as biomarkers is problematic due to the high similarity among different elements. Previously we described a long-read single molecule real-time sequencing (PacBio) strategy to analyze HERV-K RNA expression profiles in different cell types. However, identifying HERV-K HML-2 proteins accurately is difficult without robust and reliable methods and reagents. Here we present a new approach to characterize the HML-2 elements that (a) are being translated and (b) produce enough protein to be detected and identified by mass spectrometry. Our data reveal that RNA expression profiling alone cannot accurately predict which HML-2 elements are responsible for protein production, as we observe several differences between the highest expressed RNAs and the elements that are the predominant source of HERV-K HML-2 protein synthesis. These studies represent an important advance towards untangling the complexity of HERV-K-host interactions. RNA-seq profiling of untreated NCCIT cells with respect to endogenous retrovirus expression in 3 biological replicates.