Searching journal content for articles similar to Zhang et al. 13 (12): 2637.

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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
    ...alternative transcripts (>50% proportion). Comparison of SeqSplice findings for 28 variants with published data shows the value and limitations of using construct-based results for variant classification. Overall, our findings inform use of construct-derived data for clinical variant classification. We show...
  2. Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
    • Kyu-Hyeon Yeom,
    • Zhicheng Pan,
    • Chia-Ho Lin,
    • Han Young Lim,
    • Wen Xiao,
    • Yi Xing,
    • and Douglas L. Black
    Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
    ..., the maturation of pre-messenger RNA (pre-mRNA) requires splicing, polyadenylation, and release of the RNA from the chromatin template before export to the cytoplasm for translation. For many genes, the bulk of expressed RNA exists in the cytoplasm as mature mRNA, whereas nascent, intron-containing transcripts...
  3. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
  4. Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
    • Konstantin Licht,
    • Utkarsh Kapoor,
    • Fabian Amman,
    • Ernesto Picardi,
    • David Martin,
    • Prajakta Bajad,
    • and Michael F. Jantsch
    Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
    .... In contrast to other editing sites, editing of the Gria2 Q/R site is close to 100% and required to support mammalian life (Higuchi et al. 2000). Seemingly, only edited Gria2 pre-mRNA can be spliced efficiently to release the mature transcript (Higuchi et al. 2000; Schoft et al. 2007; Penn et al. 2013...
    OPEN ACCESS ARTICLE
  5. 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
    ...to abrogate the use of splice site 2 (SSU < 0.01) while activating the usage of splice site 1 (SSU = 0.97) (Fig. 3, bottom panel). These results support the notion that this single-nucleotide change likely played a critical role in the lineage-specific splicing and the introduction of the seven...
    OPEN ACCESS ARTICLE
  6. Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
    • Minjie Zhang,
    • Irena T. Hwang,
    • Kongpan Li,
    • Jianhui Bai,
    • Jian-Fu Chen,
    • Tsachy Weissman,
    • James Y. Zou,
    • and Zhipeng Lu
    Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
    ..., and homodimers. The rearrangements also enable the visualization and of complex alignments in browsers and facilitate intuitive understanding of their corresponding structures.Third, densely packed noncontinuous alignments are difficult to deconvolve into distinct groups that support individual RNA duplexes...
  7. Research: In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
    • F.X. Reymond Sutandy,
    • Stefanie Ebersberger,
    • Lu Huang,
    • Anke Busch,
    • Maximilian Bach,
    • Hyun-Seo Kang,
    • Jörg Fallmann,
    • Daniel Maticzka,
    • Rolf Backofen,
    • Peter F. Stadler,
    • Kathi Zarnack,
    • Michael Sattler,
    • Stefan Legewie,
    • and Julian König
    Genome Res. May 2018 28: 699-713; Published in Advance April 11, 2018, doi:10.1101/gr.229757.117
    ...are either not regulated or cleared in vivo (Fig. 3C; Supplemental Fig. S3A). The widespread clearance supports the existence of proofreading mechanisms that suppress the recognition of cryptic sites to ensure accurate splicing. In addition, we observe a substantial number of stabilized U2AF2 binding sites...
  8. Resource: Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
    • Angela N. Brooks,
    • Michael O. Duff,
    • Gemma May,
    • Li Yang,
    • Mohan Bolisetty,
    • Jane Landolin,
    • Ken Wan,
    • Jeremy Sandler,
    • Benjamin W. Booth,
    • Susan E. Celniker,
    • Brenton R. Graveley,
    • and Steven E. Brenner
    Genome Res. November 2015 25: 1771-1780; Published in Advance August 20, 2015, doi:10.1101/gr.192518.115
    ...components of the spliceosome and components of the EJC, further supporting their function in alternative pre-mRNA processing. We would not expect the target genes of the D. melanogaster splicing regulators to be broadly conserved in distant eukaryotes; however, there is evidence that regulatory specificity...
    OPEN ACCESS ARTICLE
  9. Resource: Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
    • Yamile Marquez,
    • John W.S. Brown,
    • Craig Simpson,
    • Andrea Barta,
    • and Maria Kalyna
    Genome Res. June 2012 22: 1184-1195; Published in Advance March 5, 2012, doi:10.1101/gr.134106.111
    ...from the alignment with two mismatches (see Methods) were removed if the splice junction in question was within 10 nt of another splice junction with better support and if it was not supported by the alignment of perfectly aligned reads (alignment with no mismatches) (Supplemental Fig. S1; see Methods...
    OPEN ACCESS ARTICLE
  10. Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
    • Sahar Gelfman,
    • David Burstein,
    • Osnat Penn,
    • Anna Savchenko,
    • Maayan Amit,
    • Schraga Schwartz,
    • Tal Pupko,
    • and Gil Ast
    Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
    ...of how the mode of splicing is determined. Toward this aim, we used three different classification algorithms: Naı¨ve Bayes (Morrison 1990; Langley et al. 1992), Bayesian networks (Heckerman et al. 1995), and Support Vector Machine (SVM) (Burges 1998; Vapnik 2000). For each classification algorithm...
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