Searching journal content for articles similar to Scott et al. 14 (10a): 1957.

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  1. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...motif and coding sequences. METTL2A knockdown alters expression of S100A4 mRNA isoforms, which contains METTL2A-mediated m3C sites. Notably, many transcripts with METTL2A-mediated m3C sites are upregulated upon METTL2A knockdown. We reveal the transcriptome-wide presence of m3C sites in poly(A) RNA...
  2. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...sequence is functional, the reporter gene is expressed/induced and the cellular concentration of the gene product is measured (Smale 2010).TF binding predictionTFs bind DNA in a sequence-specific manner based on motifs, with each binding site having a consensus sequence that indicates prerequisites...
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  3. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ...6A sites that are not characterized. (E) Bar plot indicating the total count of m6A sites identified in DRACH and non-DRACH motifs of mRNAs. (F) Venn diagram showing the overlap between high-confident m6A sites identified in this study (CHEUI probability > 0.9999) and sites deposited in RMBase v3...
  4. Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    • Karine Choquet,
    • Louis-Philippe Chaumont,
    • Simon Bache,
    • Autum R. Baxter-Koenigs,
    • and L. Stirling Churchman
    Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
    ...of the last three introns and 3′-end APA in HLA-A, suggesting that the order or timing in which terminal introns are removed relative to their neighbors may be important for 3′-end choice (Kaida 2016). Further experiments are required to establish whether the co-occurrence of splicing order changes and APA...
  5. LETTER: Predicting Protein Cellular Localization Using a Domain Projection Method
    • Richard Mott,
    • Jörg Schultz,
    • Peer Bork,
    • and Chris P. Ponting
    Genome Res. August 1, 2002 12: 1168-1174; doi:10.1101/gr.96802
    ...Kingdom Abstract We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a “small-world network”, linked by no more than seven degrees of separation. Projection of the domains onto two...
  6. Method: Cross-species analysis of enhancer logic using deep learning
    • Liesbeth Minnoye,
    • Ibrahim Ihsan Taskiran,
    • David Mauduit,
    • Maurizio Fazio,
    • Linde Van Aerschot,
    • Gert Hulselmans,
    • Valerie Christiaens,
    • Samira Makhzami,
    • Monika Seltenhammer,
    • Panagiotis Karras,
    • Aline Primot,
    • Edouard Cadieu,
    • Ellen van Rooijen,
    • Jean-Christophe Marine,
    • Giorgia Egidy,
    • Ghanem-Elias Ghanem,
    • Leonard Zon,
    • Jasper Wouters,
    • and Stein Aerts
    Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
    ...Although motif enrichment can predict candidate regulators, we sought to build a more comprehensive model of the MEL enhancers, which would allow cross-species predictions and in-depth analysis of enhancer architecture. To this end, we trained a deep learning (DL) model on the human ATAC-seq data. First...
    OPEN ACCESS ARTICLE
  7. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...neighborhood; red, gene fusions; dark blue, gene co-occurrence; black, coexpression; and purple, protein homology. Proteins belonging to the glycolysis and TCA cycle network are marked in red; proteins of the ribosome biogenesis cluster are colored in blue. (F) KEGG, Gene Ontology, and STRINGdb cluster terms...
  8. Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
    • Sanjana Pillay,
    • Hazuki Takahashi,
    • Piero Carninci,
    • and Aditi Kanhere
    Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
    ...and in predicting their function in regulating sense-strand gene expression.ResultsComparison of NATs with long intergenic RNAs during early developmentFirst, we sought to understand if NATs have features that are distinct from other long ncRNAs. We compared them to the other major category of lncRNAs, long...
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  9. Resource: Identification of protein features encoded by alternative exons using Exon Ontology
    • Léon-Charles Tranchevent,
    • Fabien Aubé,
    • Louis Dulaurier,
    • Clara Benoit-Pilven,
    • Amandine Rey,
    • Arnaud Poret,
    • Emilie Chautard,
    • Hussein Mortada,
    • François-Olivier Desmet,
    • Fatima Zahra Chakrama,
    • Maira Alejandra Moreno-Garcia,
    • Evelyne Goillot,
    • Stéphane Janczarski,
    • Franck Mortreux,
    • Cyril F. Bourgeois,
    • and Didier Auboeuf
    Genome Res. June 2017 27: 1087-1097; Published in Advance April 18, 2017, doi:10.1101/gr.212696.116
    ...). The co-occurrence of phospho-residues, IUPRs, and/or protein bindingmotifs in the protein segments coded by the 81 Mes-Epi exons suggested that alternative splicing of these exons may affect protein–protein interaction networks. We therefore looked within the IntAct database (http://www. ebi...
    OPEN ACCESS ARTICLE
  10. Method: Proteome-wide discovery of mislocated proteins in cancer
    • KiYoung Lee,
    • Kyunghee Byun,
    • Wonpyo Hong,
    • Han-Yu Chuang,
    • Chan-Gi Pack,
    • Enkhjargal Bayarsaikhan,
    • Sun Ha Paek,
    • Hyosil Kim,
    • Hye Young Shin,
    • Trey Ideker,
    • and Bonghee Lee
    Genome Res. August 2013 23: 1283-1294; Published in Advance May 14, 2013, doi:10.1101/gr.155499.113
    ...). Figure 1. Proteome-wide prediction of protein mislocation. (A) A protein is described by its sequence, chemical properties, motifs, and functions (single protein features) together with a description of its network neighborhood (capturing the features of its neighbors and their subcellular locations...
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