Searching journal content for articles similar to Rappsilber et al. 12 (8): 1231.

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  1. Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
    • Heidi Dvinge,
    • Jamie Guenthoer,
    • Peggy L. Porter,
    • and Robert K. Bradley
    Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
    ...enable these RNAs to regulate alternative splicing. However, it is unknown whether such variation occurs in healthy cells. Only 100–200 nt in length, snRNAs are not detected by most large-scale assays routinely used in functional genomics (e.g., microarrays and most RNA-seq protocols), unless those...
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  2. LETTER: Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    • Schraga Schwartz,
    • João Silva,
    • David Burstein,
    • Tal Pupko,
    • Eduardo Eyras,
    • and Gil Ast
    Genome Res. January 2008 18: 88-103; Published in Advance November 21, 2007, doi:10.1101/gr.6818908
    ...Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes Schraga Schwartz 1 , João Silva 2 , David Burstein 3 , Tal Pupko 3 , Eduardo Eyras 2 , 4 , and Gil Ast 1 , 5...
  3. Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
    • Mayank Murali,
    • Jamie Saquing,
    • Senbao Lu,
    • Ziyang Gao,
    • Emily F. Watts,
    • Ben Jordan,
    • Zachary Peters Wakefield,
    • Ana Fiszbein,
    • David R. Cooper,
    • Peter J. Castaldi,
    • Dmitry Korkin,
    • and Gloria M. Sheynkman
    Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
    ...sets. As long-read RNA-seq approaches are increasingly adopted in large-scale studies of hundreds of samples (Glinos et al. 2022; Reese et al. 2023) and are maturing into stable tools being adopted by the community (Pardo-Palacios et al. 2021), extracting all sources of biological molecular diversity...
  4. Method: Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae
    • Daniel M. Klass,
    • Marion Scheibe,
    • Falk Butter,
    • Gregory J. Hogan,
    • Matthias Mann,
    • and Patrick O. Brown
    Genome Res. June 2013 23: 1028-1038; Published in Advance May 1, 2013, doi:10.1101/gr.153031.112
    ...). We also examined a published data set of ‘‘high-confidence’’ protein–protein interactions based on large-scale affinity mass spectrometry studies (Gavin et al. 2006; Krogan et al. 2006; Collins et al. 2007), and we discovered that themajority of the previously published physically interacting...
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  5. 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
    ...identified in large scale (Veiga et al. 2022), but most of the studies have been focused on the p95HER2 and delta16 HER2 (Δ16HER2) isoforms (Scaltriti et al. 2007; Turpin et al. 2016). p95HER2 (also known as CTF611 or HER2-CTF; here and after, P95) is an incomplete isoform of the HER2 protein (molecular...
  6. 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
    ...proteomic diversity for the fine tuning of stress responses in plants, but the exact mechanism through which AS functions in plant stress responses is not thoroughly understood. Here, we investigated how AS functions in poplar (Populus trichocarpa), a popular plant for bioremediation, in response to lead...
  7. Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
    • Aliza B. Rubenstein,
    • Gregory R. Smith,
    • Zidong Zhang,
    • Xi Chen,
    • Toby L. Chambers,
    • Frederique Ruf-Zamojski,
    • Natalia Mendelev,
    • Wan Sze Cheng,
    • Michel Zamojski,
    • Mary Anne S. Amper,
    • Venugopalan D. Nair,
    • Andrew R. Marderstein,
    • Stephen B. Montgomery,
    • Olga G. Troyanskaya,
    • Elena Zaslavsky,
    • Todd Trappe,
    • Scott Trappe,
    • and Stuart C. Sealfon
    Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
    ...). In contrast, an LV associated with mTOR, spliceosome, and circadian expression pathways showed significant decreases with exercise in gene expression and chromatin accessibility in all three fiber types (Fig. 3C,D; Supplemental Fig. S5B).View larger version: In this window In a new window Figure 3. PLIER...
  8. Research: DDX54 regulates transcriptome dynamics during DNA damage response
    • Miha Milek,
    • Koshi Imami,
    • Neelanjan Mukherjee,
    • Francesca De Bortoli,
    • Ulrike Zinnall,
    • Orsalia Hazapis,
    • Christian Trahan,
    • Marlene Oeffinger,
    • Florian Heyd,
    • Uwe Ohler,
    • Matthias Selbach,
    • and Markus Landthaler
    Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
    ...2016). Several recent large-scale proteomic studies have reported that RNA processing and translation factors are post-translationally modified by DDR signaling (Matsuoka et al. 2007; Bennetzen et al. 2010; Bensimon et al. 2010; Beli et al. 2012; Jungmichel et al. 2013), and many RBPs are essential...
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  9. Research: Systematic identification and characterization of exon–intron circRNAs
    • Yinchun Zhong,
    • Yan Yang,
    • Xiaolin Wang,
    • Bingbing Ren,
    • Xueren Wang,
    • Ge Shan,
    • and Liang Chen
    Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
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  10. Method: Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing
    • Laura M. Agosto,
    • Matthew R. Gazzara,
    • Caleb M. Radens,
    • Simone Sidoli,
    • Josue Baeza,
    • Benjamin A. Garcia,
    • and Kristen W. Lynch
    Genome Res. December 2019 29: 2046-2055; Published in Advance November 14, 2019, doi:10.1101/gr.248435.119
    ...that improves isoform detection in large-scale proteomic experiments.Eukaryotic proteome diversity arises via multiple mechanisms, including alternative premessenger RNA (pre-mRNA) splicing. Alternative splicing (AS) is a highly regulated process by which a single gene may code for multiple proteins through...
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