Nanopore sequencing of TACC2 isoforms transcribed from an intronic promoter

Gene expression is controlled at the transcriptional and post-transcriptional levels. The TACC2 gene was known to be associated with tumors but the control of its expression is unclear. We have reported that the intronic promoter p10 of TACC2 is indicative of lymph node metastasis in low-risk endometrial cancer patients. Here, we analyze p10-derived TACC2 isoforms in JHUEM-1 endometrial cancer cells and primary tissues of endometrial cancers and normal endometrium. Full-length cDNA amplicons are produced by long-range PCR and subjected to nanopore sequencing followed by computational error correction. We identify and confirm 16 stable, 4 variable, and 9 rare exons including 3 novel exons. All variable and rare exons reside N-terminally of the TACC domain and contribute to isoform variety. We found 240 isoforms as high-confidence, supported by more than 20 reads. The large number of isoforms produced from one minor promoter indicates the post-transcriptional complexity of the TACC2 locus in cancer and normal cells.