Searching journal content for articles similar to Garg and Green 17 (7): 1015.

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  1. 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
    ...from a known BRCA1 exon 5 variant (c.188T>C) that produces a naturally occurring alternative isoform containing a 22 bp deletion (Δ5q22), in addition to the full-length (FL) transcript. As part of this experiment, we also assessed construction of SeqSplice libraries at different input concentrations...
  2. 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
    ...comprehensively characterize the HER2 alternative splicing isoforms, assess their expression in primary BC patients and cell lines, and explore their role in resistance to anti-HER2 therapies. We expand the catalog of known HER2 protein-coding isoforms from 13 to 90, revealing distinct patterns of protein domains...
  3. 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 alternative splicing patterns and histone post-translational modifications (hPTMs) across mouse brain development finds that enrichment of chromatin modifications correlates with, and predicts, alternative exon inclusion (Hu et al. 2017, 2020; Xu et al. 2017, 2018). Alternative splicing of neurexin I (Nrxn1...
  4. 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
    ...from replicate samples were pooled for the calculation. SSU is independent of constitutive or alternative splicing patterns. Unlike the standard percentage spliced in (PSI), which measures the relative usage of a splice site among two or more compared isoforms, SSU provides a measure of each splice...
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  5. Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
    • Irmgard U. Haussmann,
    • Thomas C. Dix,
    • David W.J. McQuarrie,
    • Veronica Dezi,
    • Abdullah I. Hans,
    • Roland Arnold,
    • and Matthias Soller
    Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
    ...to study Dscam alternative splicing from introducing mutations by gap repair recombineering (Fig. 1A,B; Supplemental Fig. S1A; Supplemental Table S1A; Hemani and Soller 2012; Haussmann et al. 2019). Similarly, the first sgRNAs flanking the Drosophila Ythdf gene, a reader for m6A mRNA methylation did...
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  6. Research: Exonic splice regulation imposes strong selection at synonymous sites
    • Rosina Savisaar and
    • Laurence D. Hurst
    Genome Res. October 2018 28: 1442-1454; Published in Advance August 24, 2018, doi:10.1101/gr.233999.117
    ...elements is a major contributor to this strong selection in human. In Drosophila, Machado et al. (2017) found that alternatively spliced genes contributed more to the signal of strong selection at synonymous sites than did constitutively spliced genes. However, this effect was dwarfed by a much greater...
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  7. Method: The dynamic landscape of fission yeast meiosis alternative-splice isoforms
    • Zheng Kuang,
    • Jef D. Boeke,
    • and Stefan Canzar
    Genome Res. January 2017 27: 145-156; Published in Advance November 17, 2016, doi:10.1101/gr.208041.116
    ...splicing duringmeiosis. (A) Trends of different types of alternative splicing duringmeiosis. Red lines represent numbers of isoforms and blue lines represent numbers of FL CCS reads. (B) Heat map showing the temporal pattern of novel isoforms. (C ) Histogram showing the correlation between annotated...
  8. 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
    ...that negatively constitute self-regulatory circuits in plants under cold stress. Moreover, a number of SFs involved in RNA binding, splice site selection, and spliceosome assembly are also affected by temperature fluctuations (Seo et al. 2013). These findings support a close association between TFs and SFs...
  9. 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
    ...transcripts by choosing different initiation/termination sites or by selecting different exons (Graveley 2001). Alternative splicing, as well as alternative promoter usage or alternative polyadenylation (hereafter referred to as AS), concerns almost all multiexon genes in vertebrates (Wang et al. 2008...
  10. Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
    • José Carlos Montañés,
    • Marta Huertas,
    • Simone G. Moro,
    • William R. Blevins,
    • Mercè Carmona,
    • José Ayté,
    • Elena Hidalgo,
    • and M. Mar Albà
    Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
    ...).View larger version: In this window In a new window Figure 2. Identification of alternative isoforms using dRNA-seq. (A) Alternative splicing (AS) isoform classes. We built a transcriptome using the dRNA reads with StringTie2. We identified 332 alternative isoforms in 263 different genes. The plot shows one...
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