Yasushi Yukawa

Summary

Affiliation: Nagoya City University
Country: Japan

Publications

  1. doi request reprint The context of transcription start site regions is crucial for transcription of a plant tRNA(Lys)(UUU) gene group both in vitro and in vivo
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, Nagoya 467 8501, Japan
    Gene 512:286-93. 2013
  2. ncbi request reprint [Plant in vitro transcription systems]
    Yasushi Yukawa
    Tanpakushitsu Kakusan Koso 47:583-9. 2002
  3. doi request reprint A common sequence motif involved in selection of transcription start sites of Arabidopsis and budding yeast tRNA genes
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, 467 8501 Nagoya, Japan
    Genomics 97:166-72. 2011
  4. ncbi request reprint A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts
    Tadamasa Sasaki
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Plant J 47:802-10. 2006
  5. pmc Translation of partially overlapping psbD-psbC mRNAs in chloroplasts: the role of 5'-processing and translational coupling
    Yuka Adachi
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Nucleic Acids Res 40:3152-8. 2012
  6. pmc The downstream atpE cistron is efficiently translated via its own cis-element in partially overlapping atpB-atpE dicistronic mRNAs in chloroplasts
    Haruka Suzuki
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Nucleic Acids Res 39:9405-12. 2011
  7. doi request reprint A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis
    Juan Wu
    Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
    RNA Biol 9:302-13. 2012
  8. ncbi request reprint A survey of expressed tRNA genes in the chromosome I of Arabidopsis using an RNA polymerase III-dependent in vitro transcription system
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, Nagoya 467 8501, Japan
    Gene 392:7-13. 2007
  9. ncbi request reprint Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplasts
    Hiroshi Kuroda
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya, Japan
    Plant Cell Physiol 48:1374-8. 2007
  10. ncbi request reprint Plant 7SL RNA genes belong to type 4 of RNA polymerase III- dependent genes that are composed of mixed promoters
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, Nagoya 467 8501, Japan
    Plant J 43:97-106. 2005

Collaborators

Detail Information

Publications19

  1. doi request reprint The context of transcription start site regions is crucial for transcription of a plant tRNA(Lys)(UUU) gene group both in vitro and in vivo
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, Nagoya 467 8501, Japan
    Gene 512:286-93. 2013
    ..The above transcription regulation by context around TSS differed between tRNA genes and other Pol III-dependent genes...
  2. ncbi request reprint [Plant in vitro transcription systems]
    Yasushi Yukawa
    Tanpakushitsu Kakusan Koso 47:583-9. 2002
  3. doi request reprint A common sequence motif involved in selection of transcription start sites of Arabidopsis and budding yeast tRNA genes
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, 467 8501 Nagoya, Japan
    Genomics 97:166-72. 2011
    ..In plant, this motif caused multiple TSSs to converge at one site and enhanced transcription. The TATA-like sequence upstream of Arabidopsis tRNA genes also contributed to TSS selection...
  4. ncbi request reprint A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts
    Tadamasa Sasaki
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Plant J 47:802-10. 2006
    ..These results suggest that distinct editing mechanisms are present in chloroplasts...
  5. pmc Translation of partially overlapping psbD-psbC mRNAs in chloroplasts: the role of 5'-processing and translational coupling
    Yuka Adachi
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Nucleic Acids Res 40:3152-8. 2012
    ..These observations, together with the presence of monocistronic psbC mRNAs, suggest that the psbD and psbC cistrons are translated via multiple processes to produce necessary amounts of D2 and CP43 proteins...
  6. pmc The downstream atpE cistron is efficiently translated via its own cis-element in partially overlapping atpB-atpE dicistronic mRNAs in chloroplasts
    Haruka Suzuki
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Nucleic Acids Res 39:9405-12. 2011
    ..These results indicate that atpE translation is independent of atpB translation. Mutation analysis showed that the atpE cistron possesses its own cis-element(s) for translation, located ~25 nt upstream from the start codon...
  7. doi request reprint A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis
    Juan Wu
    Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
    RNA Biol 9:302-13. 2012
    ..The RNA was not processed into a smaller fragment and no short open reading frame was included. Remarkably, expression of the AtR8 RNA responded negatively to hypoxic stress, and this regulation evidently differed from that of U6 snRNA...
  8. ncbi request reprint A survey of expressed tRNA genes in the chromosome I of Arabidopsis using an RNA polymerase III-dependent in vitro transcription system
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, Nagoya 467 8501, Japan
    Gene 392:7-13. 2007
    ..Based on previous reports on pseudo-tRNA genes (e.g., Beier and Beier, Mol. Gen. Genet. 1992; 233: 201-208) and the present results, we estimated that 16% or more of the annotated tRNA genes in the chromosome I are not functional...
  9. ncbi request reprint Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplasts
    Hiroshi Kuroda
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya, Japan
    Plant Cell Physiol 48:1374-8. 2007
    ..Point mutations in this sequence abolished translation, suggesting that a strong interaction between this extended SD-like sequence and the 3' end of 16S rRNA facilitates translation initiation from the GUG...
  10. ncbi request reprint Plant 7SL RNA genes belong to type 4 of RNA polymerase III- dependent genes that are composed of mixed promoters
    Yasushi Yukawa
    Graduate School of Natural Sciences, Nagoya City University, Nagoya 467 8501, Japan
    Plant J 43:97-106. 2005
    ....
  11. ncbi request reprint Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing
    Tadamasa Sasaki
    Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya, Japan
    Mol Biol Evol 20:1028-35. 2003
    ..tomentosiformis ndhD mRNAs. Four to six sites are edited partially in green leaves. Some of these sites may represent evolutionary intermediates in the process of losing editing events...
  12. ncbi request reprint Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plants
    Giorgio Dieci
    Department of Biochemistry and Molecular Biology, University of Parma, Parco Area delle Scienze 23A, 43100 Parma, Italy
    Gene 379:12-25. 2006
    ..Interactions involving components other than TBP are thus responsible for the strong TATA box requirement of plant tDNA transcription...
  13. ncbi request reprint In vitro analysis of the sequences required for transcription of the Arabidopsis thaliana 5S rRNA genes
    Catherine Cloix
    U M R 6547 BIOMOVE, Universite Blaise Pascal, 24 avenue des Landais, 63177 Aubiere Cedex, France
    Plant J 35:251-61. 2003
    ..A stretch of four T is sufficient for transcription termination. Transcription of Arabidopsis 5S rDNA requires 30 bp of 5'-flanking region, a promoter internal to the transcribed region, and a stretch of T for transcription termination...
  14. pmc Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thaliana
    Olivier Mathieu
    UMR CNRS 6547 BIOMOVE, Universite Blaise Pascal, 24 avenue des Landais, 63177 Aubiere Cedex, France
    Nucleic Acids Res 31:2424-33. 2003
    ..AtL5 protein accumulates in the nucleus, especially in the nucleolus, and is also present in the cytoplasm...
  15. ncbi request reprint A tRNA(Leu)-like sequence located immediately upstream of an Arabidopsis clock-regulated gene is transcriptionally active: efficient transcription by an RNA polymerase III-dependent in vitro transcription system
    Keiko Hasegawa
    Center for Gene Research, Nagoya University, Nagoya 464 8602, Japan
    Gene 307:133-9. 2003
    ..Mutation of a basic promoter element of the tRNA gene exerted no influence on the transcription of the downstream protein-coding gene, suggesting that no apparent interference occurs between the two adjacent genes...
  16. ncbi request reprint Plant 7SL RNA and tRNA(Tyr) genes with inserted antisense sequences are efficiently expressed in an in vitro transcription system from Nicotiana tabacum cells
    Yasushi Yukawa
    Institut fur Biochemie, Universitat Wurzburg, Biozentrum, Germany
    Plant Mol Biol 50:713-23. 2002
    ....
  17. ncbi request reprint Organization and transcription of the gene family encoding chlorophyll a/b-binding proteins in Nicotiana sylvestris
    Keiko Hasegawa
    Center for Gene Research, Nagoya University, Nagoya 464 8602, Japan
    Gene 289:161-8. 2002
    ..The genes with single initiation sites belong to the first group. A consensus motif for the initiation region is CTC*A (C* for initiation site), which differs from those of other plant genes or mammalian genes...
  18. ncbi request reprint 5S rRNA genes expression is not inhibited by DNA methylation in Arabidopsis
    Olivier Mathieu
    U M R 6547 BIOMOVE, Universite Blaise Pascal, 24 avenue des Landais, 63177 Aubiere Cedex, France
    Plant J 29:313-23. 2002
    ..As there were no detectable differences in methylation, this implies more efficient repair and/or selection pressure in transcribed 5S-blocks...
  19. pmc Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA
    Catherine Cloix
    U M R 6547 BIOMOVE, Universite Blaise Pascal, 24 avenue des Landais, 63177 Aubiere Cedex, France
    Genome Res 12:132-44. 2002
    ..Other 5S loci are either not transcribed or produce rapidly degraded 5S transcripts. Analysis of the 5'- and 3'-DNA flanking sequence has permitted the definition of specific signatures for each 5S rDNA array...