Professional Education

  • Doctor of Philosophy, Kyoto University (2011)
  • Bachelor of Science, Tohoku University (2005)

Stanford Advisors


All Publications

  • Pervasive translational regulation of the cell signalling circuitry underlies mammalian development NATURE COMMUNICATIONS Fujii, K., Shi, Z., Zhulyn, O., Denans, N., Barna, M. 2017; 8


    The degree and dynamics of translational control during mammalian development remain poorly understood. Here we monitored translation of the mammalian genome as cells become specified and organize into tissues in vivo. This identified unexpected and pervasive translational regulation of most of the core signalling circuitry including Shh, Wnt, Hippo, PI3K and MAPK pathways. We further identify and functionally characterize a complex landscape of upstream open reading frames (uORFs) across 5'-untranslated regions (UTRs) of key signalling components. Focusing on the Shh pathway, we demonstrate the importance of uORFs within the major SHH receptor, Ptch1, in control of cell signalling and neuronal differentiation. Finally, we show that the expression of hundreds of mRNAs underlying critical tissue-specific developmental processes is largely regulated at the translation but not transcript levels. Altogether, this work reveals a new layer of translational control to major signalling components and gene regulatory networks that diversifies gene expression spatially across developing tissues.

    View details for DOI 10.1038/ncomms14443

    View details for Web of Science ID 000393859100001

    View details for PubMedID 28195124

  • Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Molecular cell Shi, Z., Fujii, K., Kovary, K. M., Genuth, N. R., Röst, H. L., Teruel, M. N., Barna, M. 2017


    Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) exists and enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. We find that heterogeneity in RP composition endows ribosomes with differential selectivity for translating subpools of transcripts, including those controlling metabolism, cell cycle, and development. As an example, mRNAs enriched in binding to RPL10A/uL1-containing ribosomes are shown to require RPL10A/uL1 for their efficient translation. Within several of these transcripts, this level of regulation is mediated, at least in part, by internal ribosome entry sites. Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression.

    View details for DOI 10.1016/j.molcel.2017.05.021

    View details for PubMedID 28625553

  • Crt10 directs the cullin-E3 ligase Rtt101 to nonfunctional 25S rRNA decay BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS Sakata, T., Fujii, K., Ohno, M., Kitabatake, M. 2015; 457 (1): 90-94


    Nonfunctional mutant ribosomal RNAs in 40S or 60S subunits are selectively degraded in eukaryotic cells (nonfunctional rRNA decay, NRD). We previously reported that NRD of 25S rRNA required cullin-E3 ligase Rtt101 and its associating factor Mms1, both of which are involved in DNA repair. Although Mms22, an accessory component of the E3 complex, was suggested to direct the E3 complex to DNA repair, the factor that directs the complex to 25S NRD currently remains unknown. We herein demonstrated that another accessory component, Crt10 was required for 25S NRD, but not for DNA repair, suggesting that this accessory component specifies the function of the E3 complex differently. We also identified two distinct Crt10-containing E3 complexes, one of which contained the Paf1 complex, a Pol-II binding complex that modulates the transcription of stress-related genes. Our results showed the convergence of multiple pathways for stresses that harm nucleic acids and provided a molecular framework for the substrate diversity of the E3 complex.

    View details for DOI 10.1016/j.bbrc.2014.12.072

    View details for Web of Science ID 000350187000015

    View details for PubMedID 25534857

  • RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Nature Xue, S., Tian, S., Fujii, K., Kladwang, W., Das, R., Barna, M. 2015; 517 (7532): 33-38


    Emerging evidence suggests that the ribosome has a regulatory function in directing how the genome is translated in time and space. However, how this regulation is encoded in the messenger RNA sequence remains largely unknown. Here we uncover unique RNA regulons embedded in homeobox (Hox) 5' untranslated regions (UTRs) that confer ribosome-mediated control of gene expression. These structured RNA elements, resembling viral internal ribosome entry sites (IRESs), are found in subsets of Hox mRNAs. They facilitate ribosome recruitment and require the ribosomal protein RPL38 for their activity. Despite numerous layers of Hox gene regulation, these IRES elements are essential for converting Hox transcripts into proteins to pattern the mammalian body plan. This specialized mode of IRES-dependent translation is enabled by an additional regulatory element that we term the translation inhibitory element (TIE), which blocks cap-dependent translation of transcripts. Together, these data uncover a new paradigm for ribosome-mediated control of gene expression and organismal development.

    View details for DOI 10.1038/nature14010

    View details for PubMedID 25409156

  • 40S subunit dissociation and proteasome-dependent RNA degradation in nonfunctional 25S rRNA decay EMBO JOURNAL Fujii, K., Kitabatake, M., Sakata, T., Ohno, M. 2012; 31 (11): 2579-2589


    Eukaryotic cells have quality control systems that eliminate nonfunctional rRNAs with deleterious mutations (nonfunctional rRNA decay, NRD). We have previously reported that 25S NRD requires an E3 ubiquitin ligase complex, which is involved in ribosomal ubiquitination. However, the degradation process of nonfunctional ribosomes has remained unknown. Here, using genetic screening, we identified two ubiquitin-binding complexes, the Cdc48-Npl4-Ufd1 complex (Cdc48 complex) and the proteasome, as the factors involved in 25S NRD. We show that the nonfunctional 60S subunit is dissociated from the 40S subunit in a Cdc48 complex-dependent manner, before it is attacked by the proteasome. When we examined the nonfunctional 60S subunits that accumulated under proteasome-depleted conditions, the majority of mutant 25S rRNAs retained their full length at a single-nucleotide resolution. This indicates that the proteasome is an essential factor triggering rRNA degradation. We further showed that ribosomal ubiquitination can be stimulated solely by the suppression of the proteasome, suggesting that ubiquitin-proteasome-dependent RNA degradation occurs in broader situations, including in general rRNA turnover.

    View details for DOI 10.1038/emboj.2012.85

    View details for Web of Science ID 000304600300015

    View details for PubMedID 22505030

    View details for PubMedCentralID PMC3365426

  • A role for ubiquitin in the clearance of nonfunctional rRNAs GENES & DEVELOPMENT Fujii, K., Kitabatake, M., Sakata, T., Miyata, A., Ohno, M. 2009; 23 (8): 963-974


    Quality control mechanisms operate in various steps of ribosomal biogenesis to ensure the production of functional ribosome particles. It was reported previously that mature ribosome particles containing nonfunctional mutant rRNAs are also recognized and selectively removed by a cellular quality control system (nonfunctional rRNA decay [NRD]). Here, we show that the NRD of 25S rRNA requires a ubiquitin E3 ligase component Rtt101p and its associated protein Mms1p, identified previously as factors involved in DNA repair. We revealed that a group of proteins associated with nonfunctional ribosome particles are ubiquitinated in a Rtt101-Mms1-dependent manner. 25S NRD was disrupted when ubiquitination was inhibited by the overexpression of modified ubiquitin molecules, demonstrating a direct role for ubiquitin in this pathway. These results uncovered an unexpected connection between DNA repair and the quality control of rRNAs. Our findings support a model in which responses to DNA and rRNA damages are triggered by a common ubiquitin ligase complex during genotoxic stress harmful to both molecules.

    View details for DOI 10.1101/gad.1775609

    View details for Web of Science ID 000265449900009

    View details for PubMedID 19390089

    View details for PubMedCentralID PMC2675866

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