Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter

Sci Rep. 2021 Apr 30;11(1):9355. doi: 10.1038/s41598-021-88018-9.

Abstract

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 activity of the intronic promoter p10 of TACC2 in primary lesion of endometrial cancer is indicative of lymph node metastasis among a low-risk patient group. Here, we analyze the intronic promoter derived 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 16 stable, 4 variable, and 9 rare exons including 3 novel exons validated independently. 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 coupled with transcription at the TACC2 locus in cancer and normal cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Carrier Proteins / genetics*
  • Endometrial Neoplasms / genetics
  • Endometrial Neoplasms / metabolism
  • Endometrial Neoplasms / pathology*
  • Exons*
  • Female
  • Humans
  • Introns*
  • Promoter Regions, Genetic*
  • Protein Isoforms
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Tumor Cells, Cultured
  • Tumor Suppressor Proteins / genetics*

Substances

  • Carrier Proteins
  • Protein Isoforms
  • RNA, Messenger
  • TACC2 protein, human
  • Tumor Suppressor Proteins