Searching journal content for articles similar to Yang et al. 13 (8): 1863.

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  1. Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
    • Marcus J. Viscardi,
    • Enisha Sehgal,
    • and Joshua A. Arribere
    Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
    ...truncated and dominantly acting proteins that harm cells. Eukaryotic cells protect themselves by degrading such mRNAs via the nonsense-mediated mRNA decay (NMD) pathway. The precise reactions by which cells attack NMD-target mRNAs remain obscure, precluding a biochemical understanding of NMD and hampering...
  2. Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
    • Felicia Peng,
    • C. Erik Nordgren,
    • and John Isaac Murray
    Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
    ...and developmental stages, and identify differentially regulated mRNA decay throughout embryonic development. We identify transcript features that are correlated with mRNA stability and find that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that...
  3. Research: Plasma cell-free RNA characteristics in COVID-19 patients
    • Yanqun Wang,
    • Jie Li,
    • Lu Zhang,
    • Hai-Xi Sun,
    • Zhaoyong Zhang,
    • Jinjin Xu,
    • Yonghao Xu,
    • Yu Lin,
    • Airu Zhu,
    • Yuxue Luo,
    • Haibo Zhou,
    • Yan Wu,
    • Shanwen Lin,
    • Yuzhe Sun,
    • Fei Xiao,
    • Ruiying Chen,
    • Liyan Wen,
    • Wei Chen,
    • Fang Li,
    • Rijing Ou,
    • Yanjun Zhang,
    • Tingyou Kuo,
    • Yuming Li,
    • Lingguo Li,
    • Jing Sun,
    • Kun Sun,
    • Zhen Zhuang,
    • Haorong Lu,
    • Zhao Chen,
    • Guoqiang Mai,
    • Jianfen Zhuo,
    • Puyi Qian,
    • Jiayu Chen,
    • Huanming Yang,
    • Jian Wang,
    • Xun Xu,
    • Nanshan Zhong,
    • Jingxian Zhao,
    • Junhua Li,
    • Jincun Zhao,
    • and Xin Jin
    Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
    ...in COVID-19 patients (Yang et al. 2021).Cell-free circulating RNAs (cfRNAs) consist of a variety of RNA molecules, such as messenger RNAs (mRNAs) (Ng et al. 2002), microRNAs (miRNAs) (Pritchard et al. 2012) and long noncoding RNAs (lncRNAs) (Kumarswamy et al. 2014). cfRNAs present in various body fluids...
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  4. Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
    • Marta Melé,
    • Kaia Mattioli,
    • William Mallard,
    • David M. Shechner,
    • Chiara Gerhardinger,
    • and John L. Rinn
    Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
    .... LincRNAs are less efficiently spliced, which cannot be explained by differences in U1 binding or the density of exonic splicing enhancers but may be partially attributed to lower U2AF65 binding and weaker splicing-related motifs. Conversely, the stability of lincRNAs and mRNAs is similar, differing...
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  5. Research: Heritable variation of mRNA decay rates in yeast
    • Jennifer M. Andrie,
    • Jon Wakefield,
    • and Joshua M. Akey
    Genome Res. December 2014 24: 2000-2010; Published in Advance September 25, 2014, doi:10.1101/gr.175802.114
    .... Figure 2. Characteristics of genes that exhibit allele-specific mRNA decay. (A) Posterior probability that a gene exhibits allele-specific mRNA decay rates, as calculated from our Bayesian hierarchical Markov chainMonte Carlomodel. The dashed line at posterior probability = 0.67 corresponds...
  6. Research: Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline
    • Toshiaki Watanabe,
    • Ee-chun Cheng,
    • Mei Zhong,
    • and Haifan Lin
    Genome Res. March 2015 25: 368-380; Published in Advance December 5, 2014, doi:10.1101/gr.180802.114
    ...KOandMov10l1CKOmice, respectively (Fig. 2B). When comparing RNA levels between Piwil1 andMov10l1mutant mice, a lower correlation of fold-change in lncRNA levels (R = 0.57) was observed as compared with mRNA levels (R = 0.74). This is at least partly due to the relatively lower expression level of lnc...
  7. Research: Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing
    • Joshua A. Arribere and
    • Wendy V. Gilbert
    Genome Res. June 2013 23: 977-987; Published in Advance April 11, 2013, doi:10.1101/gr.150342.112
    ...their function in translation. Using TATL-seq to address relationships between TL features and translation of the downstream ORF, we observed that upstream AUGs (uAUGs), and no other upstream codons, were associated with poor translation and nonsense-mediated mRNA decay (NMD). We also identified hundreds...
  8. Research: 3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts
    • Noah Spies,
    • Christopher B. Burge,
    • and David P. Bartel
    Genome Res. December 2013 23: 2078-2090; Published in Advance September 26, 2013, doi:10.1101/gr.156919.113
    ..., respectively. Nonetheless, both the decay and translation rates were highly correlated for proximal and distal 3′ UTR isoforms from the same genes, implying that in 3T3 cells, alternative 3′ UTR sequences play a surprisingly small regulatory role compared to other mRNA regions. Footnotes ↵ 5...
  9. Methods: Most mammalian mRNAs are conserved targets of microRNAs
    • Robin C. Friedman,
    • Kyle Kai-How Farh,
    • Christopher B. Burge,
    • and David P. Bartel
    Genome Res. January 2009 19: 92-105; Published in Advance October 27, 2008, doi:10.1101/gr.082701.108
    ...Most mammalian mRNAs are conserved targets of microRNAs Robin C. Friedman 1 , 2 , 3 , Kyle Kai-How Farh 1 , 2 , 4 , Christopher B. Burge 1 , 5 and David P. Bartel 1 , 2 , 5 1 Department of Biology, Massachusetts Institute...
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  10. Method: Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
    • Lukas Windhager,
    • Thomas Bonfert,
    • Kaspar Burger,
    • Zsolt Ruzsics,
    • Stefan Krebs,
    • Stefanie Kaufmann,
    • Georg Malterer,
    • Anne L'Hernault,
    • Markus Schilhabel,
    • Stefan Schreiber,
    • Philip Rosenstiel,
    • Ralf Zimmer,
    • Dirk Eick,
    • Caroline C. Friedel,
    • and Lars Dölken
    Genome Res. October 2012 22: 2031-2042; Published in Advance April 26, 2012, doi:10.1101/gr.131847.111
    ...with reduced duration of 4sU-tagging from 18.9% in untagged RNA to 75.9% in 5-min 4sU-RNA (Fig. 1B). As excised introns are generally believed to be rapidly degraded (Lamond et al. 1988; Nam et al. 1997; Clement et al. 1999) this indicates the presence of large amounts of unspliced pre-mRNAs in the newly...
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