ArticleBMC genomics2022
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data.BMC genomics · 2023Pooled it
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Smoking exposure alters splicing of the nicotinic acetylcholine receptor subunit CHRNA5.Human genomics · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- Long-read sequencing and proteomics reveal blood transcriptome and protein expression profiles in multiple primary lung cancers.BMC cancer · 2026Article
- Applications of omics in deciphering the unique traits of durian, the king of fruits.Plant molecular biology · 2026Review
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- G-quadruplex structures as modulators of alternative promoter usage.NAR genomics and bioinformatics · 2025Article
- Long-read sequencing-based analyses of the adult Drosophila brain transcriptome in physiological and pathological settings.BMC genomics · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Chronic arsenic exposure and hsa-miR-186 overexpression causes transcriptome-wide differential alternative splicing contributing to skin carcinogenesis in human HaCaT cell line.Archives of toxicology · 2025Article
- Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk.Nature communications · 2025Article
- Hybridization and gene expression: Beyond differentially expressed genes.Molecular ecology · 2025Review
- Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons.Open biology · 2025Article
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Human introns contain conserved tissue-specific cryptic poison exons.NAR genomics and bioinformatics · 2024Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Direct RNA sequencing in plants: Practical applications and future perspectives.Plant communications · 2024Review
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
Abstract
backgroundAlternative 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.
resultsWe 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.
conclusionsOur work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.