Searching journal content for articles similar to Marquez et al. 22 (6): 1184.

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  1. 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
    ...to other plants, is needed.In the transcriptomic landscape, alternative splicing (AS) is regarded as an important mechanism for increasing the coding capacity of s (James et al. 2012; Rühl et al. 2012). Its identification and characterization in plants are widely considered a milestone to understanding...
  2. Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
    • Xingmin Han,
    • Chenghui Xu,
    • Yiyi Ren,
    • Meiling Guo,
    • Jiayue Yan,
    • Xuan Wang,
    • Chao Liu,
    • Qin Gu,
    • Xing-Xing Shen,
    • Zhonghua Ma,
    • and Yun Chen
    Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
    ...; Krogan et al. 2023). Its biological roles exhibit considerable species-specific divergence. Mammals employ at least eight enzymes to catalyze H3K36 methylation, coordinating diverse processes like alternative splicing and DNA repair, with aberrant patterns linked to human diseases (Lucio-Eterovic et al...
  3. Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
    • Yamile Marquez,
    • Markus Höpfler,
    • Zahra Ayatollahi,
    • Andrea Barta,
    • and Maria Kalyna
    Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
    ..., Austria Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also...
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  4. Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
    • Ya-Ru Li and
    • Ming-Jung Liu
    Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
    ...; Gao et al. 2015). Studies in mammalian cells have revealed the widespread presence of alternative TISs (i.e., a TIS different from the annotated AUG site) on transcripts, which tend to be located at AUG or near-cognate codons (i.e., codons one base different from AUG) (Ingolia et al. 2011; Fritsch et...
  5. Resource: A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing
    • Bo Wang,
    • Michael Regulski,
    • Elizabeth Tseng,
    • Andrew Olson,
    • Sara Goodwin,
    • W. Richard McCombie,
    • and Doreen Ware
    Genome Res. June 2018 28: 921-932; Published in Advance April 30, 2018, doi:10.1101/gr.227462.117
    ..., Schilkey F, BenHur A, Reddy AS. 2016. A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun 7: 11706. Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E. 2015. Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA 21: 1521...
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  6. Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
    • Alla Mikheenko,
    • Andrey D. Prjibelski,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
    ..., poly(A)-site, or splice site. Intron-chain disagreement typically arises from alignment errors of microexons and complicated splice sites. Our single-molecule technology comparison reveals that inconsistencies are often caused by sequencing error–induced inaccurate ONT alignments, especially...
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  7. Research: Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
    • Guojie Zhang,
    • Guangwu Guo,
    • Xueda Hu,
    • Yong Zhang,
    • Qiye Li,
    • Ruiqiang Li,
    • Ruhong Zhuang,
    • Zhike Lu,
    • Zengquan He,
    • Xiaodong Fang,
    • Li Chen,
    • Wei Tian,
    • Yong Tao,
    • Karsten Kristiansen,
    • Xiuqing Zhang,
    • Songgang Li,
    • Huanming Yang,
    • Jian Wang,
    • and Jun Wang
    Genome Res. May 2010 20: 646-654; Published in Advance March 19, 2010, doi:10.1101/gr.100677.109
    ...at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis -splicing occurred in ∼33% of all rice genes. This is far more than previously reported. In addition, we...
  8. Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
    • Manuel Tardaguila,
    • Lorena de la Fuente,
    • Cristina Marti,
    • Cécile Pereira,
    • Francisco Jose Pardo-Palacios,
    • Hector del Risco,
    • Marc Ferrell,
    • Maravillas Mellado,
    • Marissa Macchietto,
    • Kenneth Verheggen,
    • Mariola Edelmann,
    • Iakes Ezkurdia,
    • Jesus Vazquez,
    • Michael Tress,
    • Ali Mortazavi,
    • Lennart Martens,
    • Susana Rodriguez-Navarro,
    • Victoria Moreno-Manzano,
    • and Ana Conesa
    Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
    ...-evaluated and curated full-length transcriptomes.Alternative splicing (AS) and alternative polyadenylation (APA) are among the most fascinating and challenging aspects of eukaryotic transcriptomes. AS and APA are considered to be the major mechanisms of generating transcriptome complexity and thus the expansion...
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  9. Research: Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents
    • Anja Paschold,
    • Yi Jia,
    • Caroline Marcon,
    • Steve Lund,
    • Nick B. Larson,
    • Cheng-Ting Yeh,
    • Stephan Ossowski,
    • Christa Lanz,
    • Dan Nettleton,
    • Patrick S. Schnable,
    • and Frank Hochholdinger
    Genome Res. December 2012 22: 2445-2454; Published in Advance October 19, 2012, doi:10.1101/gr.138461.112
    ...Complementation contributes to transcriptome complexity in maize ( Zea mays L.) hybrids relative to their inbred parents Anja Paschold 1 , 6 , Yi Jia 2 , 3 , 6 , 7 , Caroline Marcon 1 , Steve Lund 4 , Nick B. Larson 4 , Cheng...
  10. PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
    • W. Brad Barbazuk,
    • Yan Fu,
    • and Karen M. McGinnis
    Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
    ...is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a global analysis of AS in many plant species. Results of genome analysis have revealed differences between animals and plants in the frequency of alternative splicing. The proportion of plant...
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