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


Alternative splicing (AS) 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 AS 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 and to characterise isoform expression and usage across differentiation. 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, and identify a putative molecular regulator underlying this state change.

Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.

Authors: David J Wright, Nicola Hall, Naomi Irish, Angela L Man, Will Glynn, Arne Mould, Alejandro De Los Angeles, Emily Angiolini, David J Swarbreck, Karim Gharbi, Elizabeth M Tunbridge, Wilfried Haerty

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