Searching journal content for articles similar to Spealman et al. 28 (2): 214.

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  1. Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
    • Ya-Ru Li and
    • Ming-Jung Liu
    Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
    ...alternative TISs are shared across species and also support the findings of previous studies that uORFs are conserved across plants species and are predicted to be initiated from both AUG and non-AUG codons (Hayden and Jorgensen 2007; Jorgensen and Dorantes-Acosta 2012; Takahashi et al. 2012; Vaughn et al...
  2. Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
    • Ting-Ying Wu,
    • Ya-Ru Li,
    • Kai-Jyun Chang,
    • Jhen-Cheng Fang,
    • Daisuke Urano,
    • and Ming-Jung Liu
    Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
    ...of relying on sequence conservation and 3-nt periodicity in revealing protein-coding regions for ORF annotation. Thus, complementary to comparative-genomic approaches and the CHX-based ribosome profiling analyses that have successfully characterized some alternative AUG and nonAUG TIS-initiated ORFs...
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  3. Research: Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
    • Peggy Janich,
    • Alaaddin Bulak Arpat,
    • Violeta Castelo-Szekely,
    • Maykel Lopes,
    • and David Gatfield
    Genome Res. December 2015 25: 1848-1859; Published in Advance October 20, 2015, doi:10.1101/gr.195404.115
    ...-seq reads fell into annotated 5′ UTRs (Fig. 1C), albeit with pronounced transcript-specific variability (Supplemental Fig. S3A), suggestive of abundant uORF usage in the liver. uORFs are short and often poorly conserved (Churbanov et al. 2005) and frequently initiate at near-cognate (non-AUG) start codons...
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  4. Research: Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
    • Can Cenik,
    • Elif Sarinay Cenik,
    • Gun W. Byeon,
    • Fabian Grubert,
    • Sophie I. Candille,
    • Damek Spacek,
    • Bilal Alsallakh,
    • Hagen Tilgner,
    • Carlos L. Araya,
    • Hua Tang,
    • Emiliano Ricci,
    • and Michael P. Snyder
    Genome Res. November 2015 25: 1610-1621; Published in Advance August 21, 2015, doi:10.1101/gr.193342.115
    ...to uORFs affected ribosome occupancy of the main coding region using a linear regression framework. The absolute value of the effect size from the regression was plotted against the P-value of association. For 17 uORF changes shown with red circles, the association was solely with ribosome occupancy...
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  5. Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
    • Marie A. Brunet,
    • Sébastien A. Levesque,
    • Darel J. Hunting,
    • Alan A. Cohen,
    • and Xavier Roucou
    Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
    .... 2016; Pueyo et al. 2016a; Delcourt et al. 2017; Hsu and Benfey 2017; Willems et al. 2017). Three detection methods—ribosome profiling, proteogenomics, and conservation signatures—have been used to identify likely translated and functional alternative ORFs, as further discussed later in this review...
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  6. Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
    • Zhaolian Lu and
    • Zhenguo Lin
    Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
    ...function pathways, such as ribosome and RNA transport (median 5′-UTR lengths ranging from 37–63 bp) (Supplemental Fig. S2C). These results support the hypothesis that 5′-UTR length, which is primarily determined by the location of TSSs, relates to gene functions and their expression profiles (Lin and Li...
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