Publications by authors named "Yuko Nobe"

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Dual synthesis pathways of scaRNA28 via intronic processing of transformation/transcription domain-associated protein transcripts and a novel independent transcription unit.
Keiichi Izumikawa, Tatsuya Shida, Hideaki Ishikawa, Sotaro Miyao, Takayuki Ohga, Yuko Nobe

RNA Biol· December 2025

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Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome.
Miguel A Garcia-Campos, Joe Georgeson, Ronit Nir, Robert Reichelt, Kristin A Fluke, Yuko Nobe

Cell· November 2025

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Involvement of Escherichia coli unconventional G protein, YchF, in cell growth at the stationary phase.
Yuto Kotaka, Takahiro Nagai, Kento Tominaga, Tatsuaki Kurata, Wataru Iwasaki, Yuko Nobe

Genes Genet Syst· June 2025

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The ionic liquid-assisted sample preparation method pTRUST allows sensitive proteome characterization of a variety of bacterial endospores to aid in the search for protein biomarkers.
Masato Taoka, Ritsuko Kuwana, Yoshinari Murakami, Akiko Kashima, Yuko Nobe

PLoS One· May 2025

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Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Disha-Gajanan Hiregange, Sarit Samiya, Danuta Mizgalska, Efrat Ben-Zeev, Miriam Waghalter, Yuko Nobe

Nucleic Acids Res· May 2025

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Pre-ribosomal WDR74 module coordinates the early and late pre-rRNA processing stages for the NVL2-mediated regulation of 60S ribosome biogenesis.
Yuya Hirooka, Keiichi Izumikawa, Sotaro Miyao, Takayuki Ohga, Yuko Nobe

Biochem Biophys Res Commun· January 2025

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Ionic liquid-assisted sample preparation mediates sensitive proteomic analysis of Bacillus subtilis spores.
Masato Taoka, Ritsuko Kuwana, Tatsumi Fukube, Akiko Kashima, Yuko Nobe

Sci Rep· July 2024

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Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.
K Shanmugha Rajan, Saurav Aryal, Disha-Gajanan Hiregange, Anat Bashan, Hava Madmoni, Yuko Nobe

Cell Rep· May 2024

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Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Vivek Singh, Yuzuru Itoh, Samuel Del'Olio, Asem Hassan, Andreas Naschberger, Yuko Nobe

Nat Commun· May 2024

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An ionic liquid-assisted sample preparation method for sensitive integral-membrane proteome analysis.
Masato Taoka, Kota Kamei, Akiko Kashima, Yuko Nobe, Takahiro Takekiyo

Anal Biochem· December 2023

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A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei.
K Shanmugha Rajan, Hava Madmoni, Anat Bashan, Masato Taoka, Saurav Aryal, Yuko Nobe

Nat Commun· November 2023

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The Feeder Effects of Cultured Rice Cells on the Early Development of Rice Zygotes.
Yoriko Watanabe, Yuko Nobe, Masato Taoka, Takashi Okamoto

Int J Mol Sci· November 2023

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Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications.
Vivek Singh, Yuzuru Itoh, Samuel Del'Olio, Asem Hassan, Andreas Naschberger, Yuko Nobe

bioRxiv· July 2023

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Liquid Chromatography-Mass Spectrometry-Based Qualitative Profiling of mRNA Therapeutic Reagents Using Stable Isotope-Labeled Standards Followed by the Automatic Quantitation Software Ariadne.
Hiroshi Nakayama, Yuko Nobe, Masami Koike, Masato Taoka

Anal Chem· January 2023

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Cryo-EM structure and rRNA modification sites of a plant ribosome.
Patrick Cottilli, Yuzuru Itoh, Yuko Nobe, Anton S Petrov, Purificación Lisón

Plant Commun· September 2022

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Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis.
Donna Matzov, Masato Taoka, Yuko Nobe, Yoshio Yamauchi, Yehuda Halfon

Nucleic Acids Res· November 2020

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DKC1 Overexpression Induces a More Aggressive Cellular Behavior and Increases Intrinsic Ribosomal Activity in Immortalized Mammary Gland Cells.
Ania Naila Guerrieri, Federico Zacchini, Carmine Onofrillo, Sara Di Viggiano, Marianna Penzo, Yuko Nobe

Cancers (Basel)· November 2020

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Direct Determination of Pseudouridine in RNA by Mass Spectrometry Coupled with Stable Isotope Labeling.
Yuka Yamaki, Yuko Nobe, Masami Koike, Yoshio Yamauchi, Kouji Hirota

Anal Chem· August 2020

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Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
Aldema Sas-Chen, Justin M Thomas, Donna Matzov, Masato Taoka, Kellie D Nance, Yuko Nobe

Nature· July 2020

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Method for Direct Mass-Spectrometry-Based Identification of Monomethylated RNA Nucleoside Positional Isomers and Its Application to the Analysis of rRNA.
Hiroshi Nakayama, Yoshio Yamauchi, Yuko Nobe, Ko Sato, Nobuhiro Takahashi

Anal Chem· December 2019

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TDP-43 regulates site-specific 2'-O-methylation of U1 and U2 snRNAs via controlling the Cajal body localization of a subset of C/D scaRNAs.
Keiichi Izumikawa, Yuko Nobe, Hideaki Ishikawa, Yoshio Yamauchi, Masato Taoka

Nucleic Acids Res· March 2019

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Landscape of the complete RNA chemical modifications in the human 80S ribosome.
Masato Taoka, Yuko Nobe, Yuka Yamaki, Ko Sato, Hideaki Ishikawa

Nucleic Acids Res· October 2018

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Truncated forms of U2 snRNA (U2-tfs) are shunted toward a novel uridylylation pathway that differs from the degradation pathway for U1-tfs.
Hideaki Ishikawa, Yuko Nobe, Keiichi Izumikawa, Masato Taoka, Yoshio Yamauchi

RNA Biol· February 2018

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Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Moran Shalev-Benami, Yan Zhang, Haim Rozenberg, Yuko Nobe, Masato Taoka

Nat Commun· November 2017

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TDP-43 stabilises the processing intermediates of mitochondrial transcripts.
Keiichi Izumikawa, Yuko Nobe, Harunori Yoshikawa, Hideaki Ishikawa, Yutaka Miura

Sci Rep· August 2017

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