Searching journal content for articles similar to Ritter et al. 34 (11): 2000.

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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. 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
    ...from the 3′-end of the transcript and proceeds toward the 5′-end. Some of the mRNAs are sequenced to completion (full-length reads), whereas others are truncated at their 5′-end. We estimated the number of full-length reads by mapping the reads to the gene annotations and then comparing the length...
  3. 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...
  4. Research: Systematic identification and characterization of exon–intron circRNAs
    • Yinchun Zhong,
    • Yan Yang,
    • Xiaolin Wang,
    • Bingbing Ren,
    • Xueren Wang,
    • Ge Shan,
    • and Liang Chen
    Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
    ...with the functional role of LIRs in regulating mRNA translation and decay (Braunschweig et al. 2014; Mauger et al. 2016; Schmitz et al. 2017; Wong and Schmitz 2022).A -wide CRISPR-Cas9 screen for genes regulating CIRs identifies SRSF1The introns retained in CIR were unique, and we subsequently sought to identify...
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  5. Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
    • Christopher J. Playfoot,
    • Julien Duc,
    • Shaoline Sheppard,
    • Sagane Dind,
    • Alexandre Coudray,
    • Evarist Planet,
    • and Didier Trono
    Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
    ...regulated TE-derived promoter (Supplemental Fig. S7B,C). It was also detected in the PacBio data, represented by four long-read mRNA molecules (Fig. 5A) with the same splicing profile (Supplemental Fig. S7D). Only 14% of TcGTs from Figure 3A represented in Supplemental Figure S7A had a median of one spliced...
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  6. Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
    • Joana Carlevaro-Fita,
    • Taisia Polidori,
    • Monalisa Das,
    • Carmen Navarro,
    • Tatjana I. Zoller,
    • and Rory Johnson
    Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
    ...in Uchl1os increases translational rate of its sense mRNA (Carrieri et al. 2012). In parallel, transcriptome-wide maps of lncRNA-linked TEs have shown how TEs have contributed extensively to lncRNA gene evolution (Kelley and Rinn 2012; Kapusta et al. 2013; Hezroni et al. 2015; Schmitt et al. 2016...
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  7. Editorial: Revolutionizing genomics and medicine—one long molecule at a time
    • Ana Conesa,
    • Alexander Hoischen,
    • and Fritz J. Sedlazeck
    Genome Res. November 2024 34: ix-xi; doi:10.1101/gr.280179.124
    ...fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation. Genome Res (this issue) 34: 2000–2011. doi:10.1101/gr.279170.124 ↵Slizovskiy IB, Bonin N, Bravo JE, Ferm PM, Singer J, Boucher C, Noyes NR. 2024. Factors impacting target-enriched long-read...
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