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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
...constructs also incorporated longer flanking intronic sequences, enabling capture of additional splicing signals that could influence splice site recognition.The SeqSplice method was sensitive to detect splice-altering variants irrespective of the produced specific aberrant transcript. Therefore, SeqSplice...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...result most likely from the different cell types expanded during carcinogenesis rather than different mechanisms of action of the mutated SF3B1. These results have important implications for understanding the role of SF3B1 mutations in hematological malignancies and other related diseases.Splicing...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...:197,402,110 T → C), a mutation frequently observed at a subclonal level in CLL patients (Wan and Wu 2013; Landau et al. 2015, 2017). The K700E mutation can interrupt the recruitment of SF3B1 to the correct 3′ end branch site and consequently result in alternative splicing (Zhang et al. 2019). We identified...
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Research: HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo
- Jonathan M. Howard,
- Hai Lin,
- Andrew J. Wallace,
- Garam Kim,
- Jolene M. Draper,
- Maximilian Haeussler,
- Sol Katzman,
- Masoud Toloue,
- Yunlong Liu,
- and Jeremy R. Sanford
Genome Res. May 2018 28: 689-698; Published in Advance April 12, 2018, doi:10.1101/gr.229062.117
...recognition is shared by the two subunits of U2AF (Merendino et al. 1999; Wu et al. 1999; Zorio and Blumenthal 1999). The small and large subunits of U2AF, encoded by U2AF1 and U2AF2, recognize the AG dinucleotide and the upstream polypyrimidine tract, respectively (Merendino et al. 1999; Wu et al. 1999...
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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
...genes. The model architecture enables DeltaSplice to perform “reference-informed prediction” by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...found that G. lamblia assemblage A does not use any known auxiliary element (Bilodeau et al. 2022), highlighting the potential diversity of cleavage site recognition within the eukaryotic tree.View larger version: In this window In a new window Figure 1. Characterization of poly(A) signals in diverse...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...DNA deletion mutation (bottom) s. Different colors denote different electron transport chain complexes or the mitochondrial ribosomal RNAs.Chimeric RNAs in the nucleus are transcripts formed by gene fusion or intergenic splicing events and have been studied extensively in cancer and rare nuclear genetic...
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Research: Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
- Maitri Y. Shah,
- Manuela Ferracin,
- Valentina Pileczki,
- Baoqing Chen,
- Roxana Redis,
- Linda Fabris,
- Xinna Zhang,
- Cristina Ivan,
- Masayoshi Shimizu,
- Cristian Rodriguez-Aguayo,
- Mihnea Dragomir,
- Katrien Van Roosbroeck,
- Maria Ines Almeida,
- Maria Ciccone,
- Daniela Nedelcu,
- Maria Angelica Cortez,
- Taghi Manshouri,
- Steliana Calin,
- Muharrem Muftuoglu,
- Pinaki P. Banerjee,
- Mustafa H. Badiwi,
- Jan Parker-Thornburg,
- Asha Multani,
- James William Welsh,
- Marcos Roberto Estecio,
- Hui Ling,
- Ciprian Tomuleasa,
- Delia Dima,
- Hui Yang,
- Hector Alvarez,
- M. James You,
- Milan Radovich,
- Elizabeth Shpall,
- Muller Fabbri,
- Katy Rezvani,
- Leonard Girnita,
- Ioana Berindan-Neagoe,
- Anirban Maitra,
- Srdan Verstovsek,
- Riccardo Fodde,
- Carlos Bueso-Ramos,
- Mihai Gagea,
- Guillermo Garcia Manero,
- and George A. Calin
Genome Res. April 2018 28: 432-447; Published in Advance March 22, 2018, doi:10.1101/gr.225128.117
...that human CCAT2 sequence played an important role in the incidence of rs6983267-RE.rs6983267-RE causes significant immune dysregulation in CCAT2-induced myeloid malignanciesTo study the global alterations induced by rs6983267-RE, we performed a -wide expression profiling (Affymetrix microarray) on BM cells...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...cultivated strawberry individuals are analyzed by whole sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 × 10−8–3.0 × 10−6 mutations per site. CG methylation shows a stable reduction (0...
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Research: Alu insertion variants alter gene transcript levels
- Lindsay M. Payer,
- Jared P. Steranka,
- Maria S. Kryatova,
- Giacomo Grillo,
- Mathieu Lupien,
- Pedro P. Rocha,
- and Kathleen H. Burns
Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
...Alu sequences. Recently, we showed that a subset of those mapping to introns can alter mRNA splicing of nearby exons (Payer et al. 2019), and that is likely just one of many functional consequences of polymorphic Alu elements.Retrotransposons have intrinsic sequences that regulate expression...

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