ArticleNucleic acids research2023
Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Efficient co-transcriptional splicing enforces rapid microexon definition and inclusion by SRRM4.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic and RNA Modification Landscape of Severe Fever with Thrombocytopenia Syndrome Virus Revealed by Nanopore Direct RNA Sequencing.Microorganisms · 2026Article
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas.Cell reports · 2025Article
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- Steering research on mRNA splicing in cancer towards clinical translation.Nature reviews. Cancer · 2024Review
- Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States.Molecular systems biology · 2024Review
- Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small exons are pervasive in transcriptomes across organisms, and their quantification in RNA isoforms is crucial for understanding gene functions. Although long-read RNA-seq based on Oxford Nanopore Technologies (ONT) offers the advantage of covering transcripts in full length, its lower base accuracy poses challenges for identifying individual exons, particularly microexons (≤ 30 nucleotides). Here, we systematically assess small exons quantification in synthetic and human ONT RNA-seq datasets. We demonstrate that reads containing small exons are often not properly aligned, affecting the quantification of relevant transcripts. Thus, we develop a local-realignment method for misaligned exons (MisER), which remaps reads with misaligned exons to the transcript references. Using synthetic and simulated datasets, we demonstrate the high sensitivity and specificity of MisER for the quantification of transcripts containing small exons. Moreover, MisER enabled us to identify small exons with a higher percent spliced-in index (PSI) in neural, particularly neural-regulated microexons, when comparing 14 neural to 16 non-neural tissues in humans. Our work introduces an improved quantification method for long-read RNA-seq and especially facilitates studies using ONT long-reads to elucidate the regulation of genes involving small exons.
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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.