Searching journal content for articles similar to Zacchi et al. 13 (5): 980.

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  1. Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
    • Matthew D.C. Neville,
    • Robin Kohze,
    • Chaitanya Erady,
    • Narendra Meena,
    • Matthew Hayden,
    • David N. Cooper,
    • Matthew Mort,
    • and Sudhakaran Prabakaran
    Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
    ...: sp339@cam.ac.ukAbstractRecent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic s contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans...
  2. Method: k-mer manifold approximation and projection for visualizing DNA sequences
    • Chengbo Fu,
    • Einari A. Niskanen,
    • Gong-Hong Wei,
    • Zhirong Yang,
    • Marta Sanvicente-García,
    • Marc Güell,
    • and Lu Cheng
    Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
    ...resolution allow a higher rate of success to achieve certain outcomes, like efficient knockouts with out-of-frame deletions. From the gene editing results (FASTQ files) of the aforementioned experiment, we first removed DNA reads that were identical to the reference sequence, which represented unedited DNA...
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  3. Research: Distinct types of short open reading frames are translated in plant cells
    • Igor Fesenko,
    • Ilya Kirov,
    • Andrey Kniazev,
    • Regina Khazigaleeva,
    • Vassili Lazarev,
    • Daria Kharlampieva,
    • Ekaterina Grafskaia,
    • Viktor Zgoda,
    • Ivan Butenko,
    • Georgy Arapidi,
    • Anna Mamaeva,
    • Vadim Ivanov,
    • and Vadim Govorun
    Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
    ...author: fesigor@gmail.comAbstractGenomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been...
  4. Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
    • Yu-Chi Chen,
    • David L.J. Vendrami,
    • Maximilian L. Huber,
    • Luisa E.Y. Handel,
    • Christopher R. Cooney,
    • Joseph I. Hoffman,
    • and Toni I. Gossmann
    Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
    ....gossmann@tu-dortmund.deAbstractSporadically, genetic material that originates from an organelle integrates into the nuclear . However, it is unclear what processes maintain such integrations over evolutionary time. Recently, it was shown that nuclear DNA of mitochondrial origin (NUMT) may harbor genes with intact mitochondrial reading frames despite...
  5. Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
    • Jonathan Cahn,
    • James P.B. Lloyd,
    • Ino D. Karemaker,
    • Pascal W.T.C. Jansen,
    • Jahnvi Pflueger,
    • Owen Duncan,
    • Jakob Petereit,
    • Ozren Bogdanovic,
    • A. Harvey Millar,
    • Michiel Vermeulen,
    • and Ryan Lister
    Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
    ...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...
  6. Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
    • Chenbo Gong,
    • Yicheng Huang,
    • Mengmeng Liu,
    • Yong Zhou,
    • Yinwei Xu,
    • Nahed Mohammed,
    • Xintong Qiao,
    • Andrea Zuccolo,
    • Weibo Xie,
    • Rod A. Wing,
    • Jianwei Zhang,
    • Fei Zhou,
    • and Yongjun Lin
    Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
    ...into the regulation regions, such as promoters, untranslated regions, and introns, or land in the nuclear with intact reading frames or protein domains, which help contribute the raw genetic material needed for gene expression regulation and de novo gene birth.Our data demonstrated that inter- and intra...
  7. Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
    • Anna Grandchamp,
    • Lucas Kühl,
    • Marie Lebherz,
    • Kathrin Brüggemann,
    • John Parsch,
    • and Erich Bornberg-Bauer
    Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
    ...sister s. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating s. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors...
  8. Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
    ...substantially from the reference , a DNA-based alignment process sometimes produces transcripts with invalid open reading frames (ORFs) or with erroneous splice sites. DNA-based mapping becomes even more challenging when the new is less closely related to the available reference.By comparison with DNA, protein...
  9. Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
    • Veronica Astro,
    • Kelly Yojanna Cardona-Londoño,
    • Lorena Viridiana Cortés-Medina,
    • Rawan Alghamdi,
    • Gustavo Ramírez-Calderón,
    • Fotios Kefalas,
    • Jair Dilmé-Capó,
    • Santiago Radío,
    • and Antonio Adamo
    Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
    ...,XYY iPSC clones generated in this study. (B) Representative DNA-FISH images of X Chromosome (green) and Y Chromosome (red) in JS iPSCs. DNA was stained with DAPI (blue). Scale bar, 5 µm. (C) KaryoStat+ whole- view. The whole- view displays all somatic and sex chromosomes in one frame with a high...
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  10. Research: Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
    • Peggy Janich,
    • Alaaddin Bulak Arpat,
    • Violeta Castelo-Szekely,
    • Maykel Lopes,
    • and David Gatfield
    Genome Res. December 2015 25: 1848-1859; Published in Advance October 20, 2015, doi:10.1101/gr.195404.115
    ...Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames Peggy Janich 1 , 3 , Alaaddin Bulak Arpat 1 , 2 , 3 , Violeta Castelo-Szekely 1 , Maykel Lopes 1 and David Gatfield 1...
    OPEN ACCESS ARTICLE
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