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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...alternative splicing across multiple exons, and are high priority for review in the context of variant pathogenicity assessment.DiscussionWe present SeqSplice, a high-throughput minigene splicing assay using a barcode approach that enabled simultaneous quantitative characterization of 1269 samples...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...of neurobiology.One mechanism well described to generally contribute to signal-regulated alternative splicing is alterations in expression or function of RBPs that directly bind pre-mRNAs and direct the recognition or skipping of exons by the splicing machinery (Heyd and Lynch 2011; Fu and Ares 2014...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...to produce multiple distinct mRNA transcripts, increasing protein diversity (Nilsen and Graveley 2010). In humans, >90% of multiexon genes undergo alternative splicing, generating roughly seven mRNA isoforms per gene on average, although only a fraction of these yield functionally distinct proteins (Pan et...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
....Most human genes consist of multiple exons and introns that are transcribed into precursor mRNAs (pre-mRNAs). The process of pre-mRNA splicing that removes introns and joins exons is required to produce mature mRNAs ready for protein translation (Black 2003; Chen and Manley 2009). In addition, alternative...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
..., and translation efficiency. In contrast, ALE-APA results from multiple PASs located in alternative terminal exons, which could lead to the production of truncated protein isoforms (Mariella et al. 2019; Goering et al. 2021). These alternatively polyadenylated mRNAs greatly expand the diversity of transcripts...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...divided the poplar seedlings into roots and shoots due to the difference in the mRNA expression levels of the response genes in these two parts. Approximately 50,000 post-transcriptional events were identified in each sample. Among these, alternative polyadenylation (APA) and alternative transcription...
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Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
- Netanya Keil,
- Carolina Monzó,
- Lauren McIntyre,
- and Ana Conesa
Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
...detection without the need for an assembly step. As with any technology, lrRNA-seq is not without errors, and factors such as mRNA degradation, library preparation failures, and sequencing inaccuracies can result in bias in the data.A database tracking bioinformatic tools for LRS (Amarasinghe et al. 2021...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
..., is part of a couple of alternatively spliced pseudorepeats (Fig. 5B). Although we found conserved tissue-regulation patterns for 11_3, the other s-exon in the couple, it was not reported in Merkin et al. (2012). This example highlights the difficulty of assessing the tissue-specific expression of several...
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Method: Identifying cell state–associated alternative splicing events and their coregulation
- Carlos F. Buen Abad Najar,
- Prakruthi Burra,
- Nir Yosef,
- and Liana F. Lareau
Genome Res. July 2022 32: 1385-1397; Published in Advance July 20, 2022, doi:10.1101/gr.276109.121
...splicing shapes the transcriptome and contributes to each cell's unique identity, but single-cell RNA sequencing (scRNA-seq) has struggled to capture the impact of alternative splicing. We previously showed that low recovery of mRNAs from single cells led to erroneous conclusions about the cell...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...splicing, and 3′ end cleavage and polyadenylation—can be alternatively regulated to create a multitude of mRNA isoforms from a single gene region (Fig. 1A). Importantly, splicing occurs at specific splice sites on an mRNA (delineated by strong sequence motifs), but there is more stochasticity in the choice...
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