Searching journal content for articles similar to Schmitt et al. 24 (11): 1797.

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  1. Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
    • William Gao,
    • Carlos J. Gallardo-Dodd,
    • and Claudia Kutter
    Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
    ...be biased because of experimental challenges (Wong et al. 2012). The development of bulk high-throughput sequencing (Stark et al. 2019) in the past two decades has allowed for examination of these mRNA and tRNA pools across a few mammalian tissues, revealing some tissue-specific differences but an overall...
  2. Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
    • Xiaoli Ma,
    • Tom Denyer,
    • Marie Javelle,
    • Antje Feller,
    • and Marja C.P. Timmermans
    Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
    ...the contribution of miRNA-directed RNA cleavage to developmental patterning, the ratio of PARE signatures over target mRNA levels in the miRNA precursor domain was calculated (Methods). Based on the principles that 3′ cleavage products are stable and not selectively degraded, the relative number of PARE signatures...
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  3. Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
    • Keyi Geng,
    • Lara G. Merino,
    • Linda Wedemann,
    • Aniek Martens,
    • Małgorzata Sobota,
    • Yerma P. Sanchez,
    • Jonas Nørskov Søndergaard,
    • Robert J. White,
    • and Claudia Kutter
    Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
    ...-bound tRNA genes reside in euchromatic genomic regions, which are marked by active histone modifications, such as histone H3 lysine 4 trimethylation (H3K4me3) (White 2011; Schmitt et al. 2014; Ottenburghs et al. 2021). tRNAs represent one of the most abundant RNA types, well known for decoding mRNA...
  4. Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
    • Mattia Furlan,
    • Eugenia Galeota,
    • Nunzio Del Gaudio,
    • Erik Dassi,
    • Michele Caselle,
    • Stefano de Pretis,
    • and Mattia Pelizzola
    Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
    ..., both the new level of transcript abundance and the speed of the transition (responsiveness) depend on RNA kinetic rates. In the most straightforward case, differential expression—the regulation of the cellular abundance of premature (P) and mature (M) RNA species—derives from changes in the rate of RNA...
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  5. Research: Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest
    • Andrea Orioli,
    • Viviane Praz,
    • Philippe Lhôte,
    • and Nouria Hernandez
    Genome Res. May 2016 26: 624-635; Published in Advance March 3, 2016, doi:10.1101/gr.201400.115
    ...by global tRNA levels but also by the balance between the supply of different tRNA isoacceptors and the decoding requirements of the mRNAs expressed in a certain tissue or developmental state (Gingold et al. 2014; Schmitt et al. 2014). These studies point to a more subtle regulation of Pol III transcription...
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  6. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...represent candidate active enhancers and 206 promoters that are primed for activation but may require additional regulatory inputs for 207 transcriptional induction (Figure 3C), (3) genes where mRNA expression is increased but 208 lacking changes in chromatin accessibility (1,008 genes; set 3) (Figure 3D...
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  7. Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
    • Amy R. Vandiver,
    • Allen Herbst,
    • Paul Stothard,
    • and Jonathan Wanagat
    Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
    ...processing, or impair mt-mRNA degradation/turnover pathways. Effects of chimeric mtRNAs on protein translation could include the sequestration of ribosomes and tRNAs on these aberrant transcripts. Chimeric mtRNAs could also bind other mtRNA transcripts or even leak into the cytoplasm (Kim et al. 2017...
  8. Method: Predicting transfer RNA gene activity from sequence and genome context
    • Bryan P. Thornlow,
    • Joel Armstrong,
    • Andrew D. Holmes,
    • Jonathan M. Howard,
    • Russell B. Corbett-Detig,
    • and Todd M. Lowe
    Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
    ...for several reasons (Hanada et al. 2013; Schaffer et al. 2014; Yoo et al. 2016). Measuring expression of unique mRNA transcripts has become relatively straightforward. However, tRNA sequencing by the methods originally developed for unmodified small RNAs (e.g., microRNAs) is frequently impeded by numerous RNA...
  9. Resource: The developmental proteome of Drosophila melanogaster
    • Nuria Casas-Vila,
    • Alina Bluhm,
    • Sergi Sayols,
    • Nadja Dinges,
    • Mario Dejung,
    • Tina Altenhein,
    • Dennis Kappei,
    • Benjamin Altenhein,
    • Jean-Yves Roignant,
    • and Falk Butter
    Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
    ...(Yamanaka et al. 2013). Previousmicroarray studies focused on 20E-induced gene regulation of mRNA transcripts between the L3 larval stage and 12 h after puparium formation (Beckstead et al. 2005; Gonsalves et al. 2011). However, for the ecdysone-induced gene family 71E (Eig71E), we find intriguing...
  10. Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
    • Seung Cho Lee,
    • Evan Ernst,
    • Benjamin Berube,
    • Filipe Borges,
    • Jean-Sebastien Parent,
    • Paul Ledon,
    • Andrea Schorn,
    • and Robert A. Martienssen
    Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
    ...in the small interfering RNA pathway, and their mutation results in increased somatic retrotransposition (Xie et al. 2013). In mammalian embryos, 3′ tRNA fragments (3′-tRF) control transposition of LTR retrotransposons both after transcription and by direct inhibition of reverse transcription (Schorn et al...
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