Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK.
Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK.
BMC Genomics. 2022 Jan 10;23(1):42. doi: 10.1186/s12864-021-08261-2.
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.
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.
Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.
可变剪接是细胞分化的关键机制，也是哺乳动物神经元组织复杂性的驱动因素。然而，对于哪些异构体被差异使用或表达，以及这如何影响细胞分化，人们的了解仍不清楚。长读测序允许全长转录本的恢复和定量，从而能够对可变剪接过程及其随细胞状态的变化进行转录本水平的分析。在这里，我们利用牛津纳米孔技术测序对一个研究充分的人类神经母细胞瘤细胞系 SH-SY5Y 进行了定制注释，并对分化过程中的异构体表达和使用进行了特征描述。
我们鉴定出了许多以前未注释的特征，包括电压门控钙通道亚基基因 CACNA2D2 的一个新转录本。我们在分化过程中显示了转录本的差异表达和使用，确定了未来研究状态变化调控的候选者。
我们的工作强调了长读测序揭示以前未知的转录本多样性和影响可变剪接的机制的潜力。
Zotero 插件
