Searching journal content for articles similar to Litterman et al. 29 (6): 896.

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  1. Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
    • Alexander J. Ritter,
    • Jolene M. Draper,
    • Christopher Vollmers,
    • and Jeremy R. Sanford
    Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
    ...al. 2019). The other 70% of lowly ribosome-associated isoforms showed the opposite characteristic regarding 3′ UTR GC-content, which is concordant with reports that suggest an inverse relationship between 3′ UTR GC-content and mRNA stability (Litterman et al. 2019). Overall, broad measurements like...
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  2. Research: An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease
    • Farhoud Faraji,
    • Ying Hu,
    • Gang Wu,
    • Natalie E. Goldberger,
    • Renard C. Walker,
    • Jinghui Zhang,
    • and Kent W. Hunter
    Genome Res. February 2014 24: 227-240; Published in Advance December 9, 2013, doi:10.1101/gr.166223.113
    ...2000; Ezzeddine et al. 2007) and Rngtt is anmRNA 59-guanyltransferase capping enzyme (Pillutla et al. 1998). To our knowledge, this is the first report implicating modulation of mRNA processing and stability in metastasis. Analysis of expression data reveals modulation of network expression...
  3. Research: DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast
    • Joel H. Graber,
    • Fathima I. Nazeer,
    • Pei-chun Yeh,
    • Jason N. Kuehner,
    • Sneha Borikar,
    • Derick Hoskinson,
    • and Claire L. Moore
    Genome Res. October 2013 23: 1690-1703; Published in Advance June 20, 2013, doi:10.1101/gr.144964.112
    ...observe after 4NQO treatment, especially if these RNAs are inherently unstable. Two types of yeast mRNAs fall in this category. First, transcripts with very long 39 UTRs are subject to destabilization through nonsense-mediated decay (NMD) (Nicholson et al. 2010; Parker 2012). In our data set, eight...
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  4. Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
    • Isabel X. Wang,
    • Christopher Grunseich,
    • Youree G. Chung,
    • Hojoong Kwak,
    • Girish Ramrattan,
    • Zhengwei Zhu,
    • and Vivian G. Cheung
    Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
    ...–DNA sequence differences (RDDs) in the mRNA. We showed these sequence differences are propagated to proteins, as we identified peptides encoded by the RNA sequences in addition to those by the DNA sequences at RDD sites. RDDs are significantly enriched at regions with R-loops. A screen of yeast mutants showed...
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  5. Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
    • Stanislav Volik,
    • Benjamin J. Raphael,
    • Guiqing Huang,
    • Michael R. Stratton,
    • Graham Bignel,
    • John Murnane,
    • John H. Brebner,
    • Krystyna Bajsarowicz,
    • Pamela L. Paris,
    • Quanzhou Tao,
    • David Kowbel,
    • Anna Lapuk,
    • Dmitri A. Shagin,
    • Irina A. Shagina,
    • Joe W. Gray,
    • Jan-Fang Cheng,
    • Pieter J. de Jong,
    • Pavel Pevzner,
    • and Colin Collins
    Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
    ...-normalized first-strand cDNA independently synthesized from the same preparation of mRNA. In order to increase specificity and sensitivity of the assay, we utilized nested primer strategy. Only clones positive in both assays were considered validated. PCR primers were successfully designed for 21 of the 24...
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