Searching journal content for articles similar to Ferbeyre et al. 10 (7): 1011.

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  1. Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
    • Uditi Bhatt,
    • Anne Cucchiarini,
    • Yu Luo,
    • Cameron W. Evans,
    • Jean-Louis Mergny,
    • K. Swaminathan Iyer,
    • and Nicole M. Smith
    Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
    ...that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA...
  2. Research: Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
    • Joanna Delimata-Raczek,
    • Natalia Koralewska,
    • Bart Krist,
    • Magdalena Rakoczy,
    • Marek Figlerowicz,
    • and Ireneusz Stolarek
    Genome Res. April 3, 2026 ; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
    ...in contractile cells. Conversely, mRNAs of RBPs like DCN and ANXA1 were enriched in the noncontractile population (Fig. 8B). Finally, to mechanistically link these RBPs to the observed isoform switches, we performed computational motif enrichment analysis within the sequences flanking the D4 to D30 alternative...
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  3. 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...
  4. Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
    • Ishwarya Venkata Narayanan,
    • Karan Bedi,
    • Brian Magnuson,
    • Ariel McShane,
    • Mario Ashaka,
    • Michelle Paulsen,
    • Thomas E Wilson,
    • and Mats Ljungman
    Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
    ...of approximately 50 million read pairs per 609 sample. Raw reads were trimmed using BBDuk (BBTools, v38.46) (Bushnell 2014) to 610 remove adapter sequences and then pre-aligned to the ribosomal RNA (rRNA) 611 repeating unit (GenBank U13369.1), the mitochondrial (chrM), EBV 612 (from the hg38 analysis set...
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  5. 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
    ...splicing (AS) and alternative cleavage and polyadenylation (APA) in humans. Yet, these studies are generally performed with mature mRNA, so they report on the outcome rather than the processes of RNA maturation and thus may overlook how variants directly modulate pre-mRNA processing. The order in which...
  6. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...for its proven efficacy in extracting local sequence motifs and hierarchical patterns from sequence data, which are hypothesized to be relevant features for modeling local RNA sequence conversion dynamics. The output of the CNN layers is flattened and passed to a fully connected dense layer, which...
  7. Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    • Haiyue Liu and
    • Lea H. Gregersen
    Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
    .... Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase...
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  8. Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
    • Kathleen Zeglinski,
    • Christian Montellese,
    • Matthew E. Ritchie,
    • Monther Alhamdoosh,
    • Cédric Vonarburg,
    • Rory Bowden,
    • Monika Jordi,
    • Quentin Gouil,
    • Florian Aeschimann,
    • and Arthur Hsu
    Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
    ...(NCBI GenBank [https://www.ncbi.nlm.nih.gov/genbank/] accession number GGU78775) and from the description of the cloning strategy used by Urbinati et al. (2009) in reverse orientation. A second vector “WAS LV2” contains two A-to-T point mutations in “AG” splice acceptor motifs in the insulator...
  9. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...motif sequences (green, WT; red, Mettl3 knockout). (C) Schematic overview of the strategy used for allelic long-read assignment for ASM analysis. Total RNA from hybrid mESC (C57BL/6J × CAST/EiJ) underwent DRS. To avoid reference bias, we used an N-masked transcriptome for alignment. Reads were...
  10. Research: A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...5290002, Israel; 3Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel A-to-I RNA editing, catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome...
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