HERV-K HML-2 transcriptional profiling and splicing pattern unveiled by direct single-molecule long-read RNA sequencing

The evolution of human genome has been inextricably linked to germ cell infectivity and retrotransposition activity of endogenous retroviruses (ERVs). In result, 8% of the modern human DNA is occupied by human ERVs (HERVs), which although non-infectious and replication incompetent, are transcriptionally active in several cases (such as viral infections and cancer), and are able to produce functional mRNAs, non-coding RNAs and proteins, which on one hand are utilized for cell processes and on the other hand have been reported to be implicated in various pathologies. We used Nanopore Direct RNA Sequencing (DRS) technology to study the transcriptome of the transcriptionally active HERV family, HERV-K HML-2 (HK2) in a teratocarcinoma cell line. We developed a unique pipeline of HK2 DRS data analysis, which along with DRS itself, enabled us to investigate the true HK2 transcriptional profile on a single-molecule basis, unveiling alternative and non-canonical splicing patterns, length variants distribution and polyadenine tail length estimation. We uncovered a plethora of non-annotated HK2 transcriptional isoforms and read-through transcripts that utilized HK2 splicing sites, promoters and polyadenylation signals to assemble copies of the surrounding genes. This finding supports the observation that HERVs are involved in regulation of cellular transcription.