Searching journal content for articles similar to Bénitière et al. 35 (3): 446.

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  1. 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
    ...modulate ribosome occupancy—many of these differences lie close to start codons and upstreamORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. [Supplemental material...
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  2. Research: nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
    • Valentina Gandin,
    • Laia Masvidal,
    • Laura Hulea,
    • Simon-Pierre Gravel,
    • Marie Cargnello,
    • Shannon McLaughlan,
    • Yutian Cai,
    • Preetika Balanathan,
    • Masahiro Morita,
    • Arjuna Rajakumar,
    • Luc Furic,
    • Michael Pollak,
    • John A. Porco, Jr.,
    • Julie St-Pierre,
    • Jerry Pelletier,
    • Ola Larsson,
    • and Ivan Topisirovic
    Genome Res. May 2016 26: 636-648; Published in Advance March 16, 2016, doi:10.1101/gr.197566.115
    ...RNAs lack the 5′ TOP motif but that 5′ UTR features distinguish two functionally and translationally distinct subsets of MTOR-sensitive mRNAs: (1) mRNAs with short 5′ UTRs enriched for mitochondrial functions, which require EIF4E but are less EIF4A1-sensitive; and (2) long 5′ UTR mRNAs encoding...
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  3. Research: Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
    • Alaaddin Bulak Arpat,
    • Angélica Liechti,
    • Mara De Matos,
    • René Dreos,
    • Peggy Janich,
    • and David Gatfield
    Genome Res. July 2020 30: 985-999; Published in Advance July 23, 2020, doi:10.1101/gr.257741.119
    .... We did not notice any selectivity in the region occupied by the upstream ribosome or at the boundary between the ribosomes. These findings fit the model that the leading ribosome defined the pause site (with preference for specific codons) and an upstream ribosome colliding sequence independently...
  4. Research: Saturation mutagenesis reveals manifold determinants of exon definition
    • Shengdong Ke,
    • Vincent Anquetil,
    • Jorge Rojas Zamalloa,
    • Alisha Maity,
    • Anthony Yang,
    • Mauricio A. Arias,
    • Sergey Kalachikov,
    • James J. Russo,
    • Jingyue Ju,
    • and Lawrence A. Chasin
    Genome Res. January 2018 28: 11-24; Published in Advance December 14, 2017, doi:10.1101/gr.219683.116
    ...at each exonic position in the 10 HMs are compared in Figure 2F. The region from position 2 to ∼15 shows great variation among HMs as expected since this stretch overlaps the distinctive six-base substitutions they contain. That is, if two mutations are within about 6 nt, they may be creating an entirely...
  5. Research: Transcriptional consequences of genomic structural aberrations in breast cancer
    • Koichiro Inaki,
    • Axel M. Hillmer,
    • Leena Ukil,
    • Fei Yao,
    • Xing Yi Woo,
    • Leah A. Vardy,
    • Kelson Folkvard Braaten Zawack,
    • Charlie Wah Heng Lee,
    • Pramila Nuwantha Ariyaratne,
    • Yang Sun Chan,
    • Kartiki Vasant Desai,
    • Jonas Bergh,
    • Per Hall,
    • Thomas Choudary Putti,
    • Wai Loon Ong,
    • Atif Shahab,
    • Valere Cacheux-Rataboul,
    • Radha Krishna Murthy Karuturi,
    • Wing-Kin Sung,
    • Xiaoan Ruan,
    • Guillaume Bourque,
    • Yijun Ruan,
    • and Edison T. Liu
    Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
    ...points and the assessment of the directionality to the gene components allowed us to categorize the impact of genomic rearrangements to gene structures into four categories (Supplemental Glossary; Supplemental Fig. 2A): fusion genes (FG), in which two distinct RefSeq genes are fused together in the same...
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