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

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 can...

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Autores principales:	Yosuke Ito, Yasuhisa Terao, Shohei Noma, Michihira Tagami, Emiko Yoshida, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8983f69eea30409f845b82e690ae80f8
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spelling	oai:doaj.org-article:8983f69eea30409f845b82e690ae80f82021-12-02T17:15:16ZNanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter10.1038/s41598-021-88018-92045-2322https://doaj.org/article/8983f69eea30409f845b82e690ae80f82021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88018-9https://doaj.org/toc/2045-2322Abstract 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.Yosuke ItoYasuhisa TeraoShohei NomaMichihira TagamiEmiko YoshidaYoshihide HayashizakiMasayoshi ItohHideya KawajiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yosuke Ito Yasuhisa Terao Shohei Noma Michihira Tagami Emiko Yoshida Yoshihide Hayashizaki Masayoshi Itoh Hideya Kawaji Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
description	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.
format	article
author	Yosuke Ito Yasuhisa Terao Shohei Noma Michihira Tagami Emiko Yoshida Yoshihide Hayashizaki Masayoshi Itoh Hideya Kawaji
author_facet	Yosuke Ito Yasuhisa Terao Shohei Noma Michihira Tagami Emiko Yoshida Yoshihide Hayashizaki Masayoshi Itoh Hideya Kawaji
author_sort	Yosuke Ito
title	Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
title_short	Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
title_full	Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
title_fullStr	Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
title_full_unstemmed	Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter
title_sort	nanopore sequencing reveals tacc2 locus complexity and diversity of isoforms transcribed from an intronic promoter
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8983f69eea30409f845b82e690ae80f8
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Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter

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