Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes

Wright, David J., Hall, Nicola A. L., Irish, Naomi, Man, Angela L., Glynn, Will, Mould, Arne, De Los Angeles, Alejandro, Angiolini, Emily, Swarbreck, David, Gharbi, Karim, Tunbridge, Elizabeth M. and Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X (2022) Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. BMC Genomics, 23 (1). ISSN 1471-2164

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Abstract

Background: Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or expressed and how this affects cellular differentiation remains unclear. Long read sequencing allows full-length transcript recovery and quantification, enabling transcript-level analysis of alternative splicing processes and how these change with cell state. Here, we utilise Oxford Nanopore Technologies sequencing to produce a custom annotation of a well-studied human neuroblastoma cell line SH-SY5Y, and to characterise isoform expression and usage across differentiation. Results: We identify many previously unannotated features, including a novel transcript of the voltage-gated calcium channel subunit gene, CACNA2D2. We show differential expression and usage of transcripts during differentiation identifying candidates for future research into state change regulation. Conclusions: Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.

Item Type: Article
Additional Information: Funding Information: The authors acknowledge the support of the UK Medical Research Council and of the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation. The authors also acknowledge the support and work delivered at the Earlham Institute by members of the EI Biofoundry and the technical assistance of the Norwich Research Park CiS team. The authors would like to also thank the editor and reviewers for insightful peer review that greatly improved the manuscript. This study makes grateful use of Genotype-Tissue Expression (GTEx) Project v.8 data which is supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR or the Department of Health. Funding Information: The authors acknowledge the support of the UK Medical Research Council and of the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation. The authors also acknowledge the support and work delivered at the Earlham Institute by members of the EI Biofoundry and the technical assistance of the Norwich Research Park CiS team. The authors would like to also thank the editor and reviewers for insightful peer review that greatly improved the manuscript. This study makes grateful use of Genotype-Tissue Expression (GTEx) Project v.8 data which is supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The views expressed are those of the authors and not necessarily those of the National Health Service, NIHR or the Department of Health. Funding Information: The work was funded by a UK Medical Research Council [MR/P026028/1] award to EMT and WH, supported by the Oxford Health NIHR Biomedical Research Centre. This research was also funded by the Biotechnology and Biological Sciences Research Council (BBSRC) Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work packages - BBS/E/T/000PR9818 (WP1 Signatures of Domestication and Adaptation) and Core Capability Grant BB/CCG1720/1 and the National Capability BBS/E/T/000PR9816 (Supporting EI’s ISPs and the UK Community with Genomics and Single Cell Analysis) and BBS/E/T/000PR9811 (NC4 Enabling and Advancing Life Scientists in data-driven research through Advanced Genomics and Computational Training) and the BBSRC National Capability in Synthetic Biology (BBS/E/T/000PR9815). Publisher Copyright: © 2022, The Author(s).
Uncontrolled Keywords: biotechnology,genetics ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School: Faculty of Science > School of Pharmacy
Faculty of Science > School of Biological Sciences
Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Medicine and Health Sciences > School of Health Sciences
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Depositing User: LivePure Connector
Date Deposited: 16 Sep 2022 13:36
Last Modified: 05 Oct 2022 00:21
URI: https://ueaeprints.uea.ac.uk/id/eprint/88391
DOI: 10.1186/s12864-021-08261-2

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