Searching journal content for articles similar to Li and Liu 30 (10): 1418.

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  1. 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
    ...on alternative AUG and nonAUG TIS recognition, the observations also found in a model species, Arabidopsis (Figs. 1⇑⇑–4). We identified CU-rich elements in plant mRNAs that promote translation initiation (Fig. 5) and were evolutionarily conversed for accurate TIS prediction within and across plant species...
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  2. Research: Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
    • Pieter Spealman,
    • Armaghan W. Naik,
    • Gemma E. May,
    • Scott Kuersten,
    • Lindsay Freeberg,
    • Robert F. Murphy,
    • and Joel McManus
    Genome Res. February 2018 28: 214-222; Published in Advance December 18, 2017, doi:10.1101/gr.221507.117
    ...with UUG are particularly common and are shared between species at rates similar to that of AUG uORFs. However, non-AUG uORFs are translated less efficiently than AUG-uORFs and are less subject to removal via alternative transcription initiation under normal growth conditions. These results suggest...
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  3. Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
    • Jack A.S. Tierney,
    • Michał Świrski,
    • Håkon Tjeldnes,
    • Jonathan M. Mudge,
    • Joanna Kufel,
    • Nicola Whiffin,
    • Eivind Valen,
    • and Pavel V. Baranov
    Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
    ...to proteoforms with alternative N termini (PANTs) (Fig. 1B). A potentially large number of start codons may be used to initiate translation within the same stop-stop ORF, as is the case with the well-explored human PTEN gene, in which functionally distinct extended proteoforms are produced from multiple non-AUG...
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  4. Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
    • Hsin-Yen Larry Wu,
    • Isaiah D. Kaufman,
    • and Polly Yingshan Hsu
    Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
    ...as the main ORF and extends from 5′ or 3′. The fExtend and tExtend parameters allow extending the main ORF frames into the 5′ UTR and 3′ UTR, respectively. This enables investigating translation from alternative AUG or non-AUG start codons in the 5′ UTR or stop-codon readthrough events in the 3′ UTR...
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  5. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...), the fragmented RNA products may be translated into a toxic truncated protein (Sznajder et al. 2018). GOF due to repeat-associated non-ATG/AUG-mediated translation (RAN-translation): in SCA31, FXTAS, C9orf72-associated ALS/FTD, and SCA8, expanded RNA aberrantly recruits translation machinery and produces toxic...
  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
    ...al. 2011; The ENCODE Project Consortium 2012; Lu and Lin 2019). Transcription can be initiated from multiple TSSs in most genes, and alternative usage of TSSs in different cell types or growth conditions is prevalent in mammals, the fruit fly, and yeast (Davuluri et al. 2008; Batut et al. 2013; Lu...
  7. Research: Evidence of abundant stop codon readthrough in Drosophila and other metazoa
    • Irwin Jungreis,
    • Michael F. Lin,
    • Rebecca Spokony,
    • Clara S. Chan,
    • Nicolas Negre,
    • Alec Victorsen,
    • Kevin P. White,
    • and Manolis Kellis
    Genome Res. December 2011 21: 2096-2113; Published in Advance October 12, 2011, doi:10.1101/gr.119974.110
    ...-frame ATGs (as second cistrons would follow lowerscoring untranslated regions). While we cannot rule out the possibility that some of the remaining candidates are translated through a non-AUG IRES (Sugiharas et al. 1990; DeSimone andWhite 1993; Takahashia et al. 2005), we have used a similar analysis to show...
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