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Showing 1–26 of 26 results
Advanced filters: Author: Nicholas T Ingolia Clear advanced filters

  • Following the termination of translation at stop codons, the eukaryotic 60S subunit of the ribosome is removed by the ATPase ABCE1. Here using 40S ribosome footprinting the authors provide a direct demonstration that the yeast orthologs of eIF2D, MCT-1, and DENR recycle the 40S subunits.

    • David J. Young
    • Sezen Meydan
    • Nicholas R. Guydosh
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-16

  • Calcium signals are typically traced through electrophysical, optical and genetic methods. Here the authors report the development of Cal-ID, a calcium-dependent protein proximity labeling tool that can be used to record elevated calcium levels in cells.

    • J. Wren Kim
    • Adeline J. H. Yong
    • Nicholas T. Ingolia
    Research
    Nature Chemical Biology
    Volume: 20, P: 894-905

  • A comprehensive redevelopment of the ribosome profiling workflow involves improved nuclease treatment and sequencing library preparation, enabling richer and more accurate translatome profiling with lower input and fewer technical hurdles.

    • Lucas Ferguson
    • Heather E. Upton
    • Nicholas T. Ingolia
    Research
    Nature Methods
    Volume: 20, P: 1704-1715

  • A systematic survey of the budding yeast proteome identifies hundreds of post-transcriptional regulators. Regulatory activity is enriched in RNA-binding proteins but lies outside the RNA-binding domains, often within intrinsically disordered regions.

    • Kendra Reynaud
    • Anna M. McGeachy
    • Nicholas T. Ingolia
    ResearchOpen Access
    Nature Structural & Molecular Biology
    Volume: 30, P: 740-752

  • Macrolide antibiotics inhibit bacterial translation in a context-specific manner, arresting ribosomes at defined sites within mRNAs and selectively inhibiting synthesis of only a subset of cellular proteins. Here the authors provide a structural basis for the context-specific activity of macrolides on the eukaryotic ribosome.

    • Maxim S. Svetlov
    • Timm O. Koller
    • Alexander S. Mankin
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-14

  • Ribosome profiling is a recently developed technique that uses deep sequencing to study translationin vivo. This approach has provided new insights into the identities and amounts of proteins produced by cells, as well as into the mechanism of protein synthesis itself.

    • Nicholas T. Ingolia
    Reviews
    Nature Reviews Genetics
    Volume: 15, P: 205-213

  • Snakes are notoriously apt at generating 'thermal images' of predators or prey. The underlying physiology has been unclear, although in snakes such as pythons, vipers and boas, infrared signals are initially received by the pit organ. Here it is shown that pit-bearing snakes rely on heat detection by the ion channel TRPA1. This extends the sensory repertoire of the TRPA1 family of proteins, which detect chemical irritants in mammals and thermal variations in insects.

    • Elena O. Gracheva
    • Nicholas T. Ingolia
    • David Julius
    Research
    Nature
    Volume: 464, P: 1006-1011

  • A method, termed hiCLIP, has been developed to determine the RNA duplexes bound by RNA-binding proteins, revealing an unforeseen prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions; the results also show that RNA structure is able to regulate gene expression.

    • Yoichiro Sugimoto
    • Alessandra Vigilante
    • Jernej Ule
    Research
    Nature
    Volume: 519, P: 491-494

  • On-array synthesis of over 20,000 shRNAs at a coverage of ∼30 shRNAs per gene, followed by cloning into lentiviral shRNA libraries and deconvolution of the complex libraries by deep sequencing, ensures high confidence in the observed knockdown phenotypes with low false-negative rates and few off-target hits.

    • Michael C Bassik
    • Robert Jan Lebbink
    • Michael T McManus
    Research
    Nature Methods
    Volume: 6, P: 443-445

  • Borrowing ideas that were originally developed to study electronic circuits, two reports decipher how yeast reacts to changes in its environment by analysing the organism's responses to oscillating input signals.

    • Nicholas T. Ingolia
    • Jonathan S. Weissman
    News & Views
    Nature
    Volume: 454, P: 1061-1062

  • AUF1 is an RNA-binding protein believed to function mostly by regulating the decay of its target transcripts. Here, Yoon et al.systematically identify the targets of AUF1 and provide insights into how AUF1 functions to regulate various cellular processes by enhancing the decay, stability or translation of specific RNAs.

    • Je-Hyun Yoon
    • Supriyo De
    • Myriam Gorospe
    Research
    Nature Communications
    Volume: 5, P: 1-15

  • Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1.

    • Yoshitaka Matsuo
    • Ken Ikeuchi
    • Toshifumi Inada
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-14

  • MicroRNAs are known to affect the levels of both messenger RNA (mRNA) and protein. But as protein production is dependent on the presence of mRNA, it was not clear what the relative contributions of microRNA-mediated mRNA cleavage and translational repression were. These authors have parsed out the two mechanisms, and unexpectedly find that microRNAs function primarily by affecting mRNA levels rather than their translation. This suggests a reassessment of many previous conclusions is necessary.

    • Huili Guo
    • Nicholas T. Ingolia
    • David P. Bartel
    Research
    Nature
    Volume: 466, P: 835-840

  • Detection of weak electrical signals by skates relies on functional coupling of specific calcium and potassium channels, which mediates oscillations in electrosensory cell membrane voltage.

    • Nicholas W. Bellono
    • Duncan B. Leitch
    • David Julius
    Research
    Nature
    Volume: 543, P: 391-396

  • This study shows that a vertebrate-specific ubiquitin ligase modulates neural crest specification in Xenopus development and human embryonic stem-cell differentiation; a proteomics approach reveals that the CUL3KBTBD8 ligase modulates translation by targeting the modulators of ribosomes production NOLC1 and its paralogue TCOF1, which is mutated in a neural-crest-associated syndrome.

    • Achim Werner
    • Shintaro Iwasaki
    • Michael Rape
    Research
    Nature
    Volume: 525, P: 523-527