Research Topics
| Yasushi YukawaSummaryAffiliation: Nagoya City University Country: Japan Publications
| Collaborators
|
Detail Information
Publications
The context of transcription start site regions is crucial for transcription of a plant tRNA(Lys)(UUU) gene group both in vitro and in vivoYasushi 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...
[Plant in vitro transcription systems]Yasushi Yukawa
Tanpakushitsu Kakusan Koso 47:583-9. 2002- A common sequence motif involved in selection of transcription start sites of Arabidopsis and budding yeast tRNA genesYasushi 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... - A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcriptsTadamasa 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... 
Translation of partially overlapping psbD-psbC mRNAs in chloroplasts: the role of 5'-processing and translational couplingYuka 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...- The downstream atpE cistron is efficiently translated via its own cis-element in partially overlapping atpB-atpE dicistronic mRNAs in chloroplastsHaruka 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... - A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in ArabidopsisJuan 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... - A survey of expressed tRNA genes in the chromosome I of Arabidopsis using an RNA polymerase III-dependent in vitro transcription systemYasushi 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... - Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplastsHiroshi 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... - Plant 7SL RNA genes belong to type 4 of RNA polymerase III- dependent genes that are composed of mixed promotersYasushi Yukawa
Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
Plant J 43:97-106. 2005.... - 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 editingTadamasa 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... - Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plantsGiorgio 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... - In vitro analysis of the sequences required for transcription of the Arabidopsis thaliana 5S rRNA genesCatherine Cloix
U. M. R. 6547 BIOMOVE, , 24 avenue des Landais, , 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... - Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thalianaOlivier 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... - 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 systemKeiko 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... - Plant 7SL RNA and tRNA(Tyr) genes with inserted antisense sequences are efficiently expressed in an in vitro transcription system from Nicotiana tabacum cellsYasushi Yukawa
, , Biozentrum, Germany
Plant Mol Biol 50:713-23. 2002.... - Organization and transcription of the gene family encoding chlorophyll a/b-binding proteins in Nicotiana sylvestrisKeiko 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... - 5S rRNA genes expression is not inhibited by DNA methylation in ArabidopsisOlivier Mathieu
U.M.R. 6547 BIOMOVE, , 24 avenue des Landais, , 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... - Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNACatherine Cloix
U.M.R. 6547 BIOMOVE, , 24 avenue des Landais, , 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...