Searching journal content for articles similar to Mata and Bähler 13 (12): 2686.

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  1. Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
    • Thomas D. Lewin,
    • Isabel Jiah-Yih Liao,
    • Mu-En Chen,
    • John D.D. Bishop,
    • Peter W.H. Holland,
    • and Yi-Jyun Luo
    Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
    ...are highly conserved, although the chromosome containing ALG a underwent a fission event to form Chr 10 and Chr 12 in C. pallasiana. These ALGs are not conserved in the phylactolaemate species C. mucedo. Links between chromosomes sharing five or fewer genes between chromosomes are removed for clarity but can...
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  2. 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
    ...(fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here...
  3. Method: Delineating yeast cleavage and polyadenylation signals using deep learning
    • Emily Kunce Stroup and
    • Zhe Ji
    Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
    ...are highly degenerate and variable across genes.Previous experimental and computational characterization of yeast poly(A) sites identified cis-elements promoting site formation: the UA-rich elements located 40 nt upstream (designated as the efficiency element) bound by the cleavage and polyadenylation factor...
  4. Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
    • Yang Li and
    • Jianzhi Zhang
    Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
    ...function, we compare the transcriptomic and proteomic effects of systematic gene deletions in budding yeast (Saccharomyces cerevisiae) with those effects in fission yeast (Schizosaccharomyces pombe). Despite evidence for functional conservation of orthologous genes, their deletions result in no more...
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  5. 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
    ...into newly born genes seems likely. Together, the results of this study highlight the diversity and dynamics at the isoform level in the sexual development of fission yeast. [Supplemental material is available for this article.] Splicing is a fundamental process which removes intragenic noncoding regions...
  6. Research: Transposable element insertions in fission yeast drive adaptation to environmental stress
    • Caroline Esnault,
    • Michael Lee,
    • Chloe Ham,
    • and Henry L. Levin
    Genome Res. January 2019 29: 85-95; Published in Advance December 12, 2018, doi:10.1101/gr.239699.118
    ...://go.princeton.edu/cgi-bin/GOTermFinder), Fission Yeast Phenotype Ontology annotation (Harris et al. 2013), the set of genes up-regulated in tor2 mutants (Matsuo et al. 2007), the set of genes up-regulated and down-regulated in tor1Δ strain (Schonbrun et al. 2009), and the set of genes induced by environmental stresses (Chen et al. 2003...
  7. Method: System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA–protein complexes
    • Cornelia Kilchert,
    • Tea Kecman,
    • Emily Priest,
    • Svenja Hester,
    • Ebru Aydin,
    • Krzysztof Kus,
    • Oliver Rossbach,
    • Alfredo Castello,
    • Shabaz Mohammed,
    • and Lidia Vasiljeva
    Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
    ...in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA...
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  8. Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
    • Gregory T. Booth,
    • Isabel X. Wang,
    • Vivian G. Cheung,
    • and John T. Lis
    Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
    ...@cornell.edu AbstractComplex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run...
  9. Research: Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
    • Danny A. Bitton,
    • Sophie R. Atkinson,
    • Charalampos Rallis,
    • Graeme C. Smith,
    • David A. Ellis,
    • Yuan Y.C. Chen,
    • Michal Malecki,
    • Sandra Codlin,
    • Jean-François Lemay,
    • Cristina Cotobal,
    • François Bachand,
    • Samuel Marguerat,
    • Juan Mata,
    • and Jürg Bähler
    Genome Res. June 2015 25: 884-896; Published in Advance April 16, 2015, doi:10.1101/gr.185371.114
    ..., physiological, and genetic perturbations in the fission yeast Schizosaccharomyces pombe. Approximately 47% of the S. pombe genes contain annotated introns, and the splicing machinery is conserved (Käufer and Potashkin 2000). Limited evidence suggests alternative splicing via intron retention (Moldón et al. 2008...
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  10. Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
    • Danny Zeevi,
    • Shai Lubliner,
    • Maya Lotan-Pompan,
    • Eran Hodis,
    • Rita Vesterman,
    • Adina Weinberger,
    • and Eran Segal
    Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
    ...by expressing in S. cerevisiae 668 ribosomal protein (RP) gene promoters taken from nine yeast species and by further examining several pairs of orthologous promoters through a library of 91 chimeric promoters. Our results shed new light on how yeast promoters can evolve in sequencewhile preserving...
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