Affiliation: National Institute for Basic Biology
- Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiaeKoji Kasahara
Division of Molecular and Cellular Biology, Science of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, Japan
Mol Cell Biol 27:6686-705. 2007..Reporter gene assays indicate that these functional properties are determined by the promoter sequence...
- Phylogenetic footprinting to find functional DNA elementsAusten R D Ganley
Division of Cytogenetics, National Institutes of Genetics
Methods Mol Biol 395:367-80. 2007..Our methods are broadly applicable and should appeal to molecular biologists with little experience in bioinformatics...
- A new role of the rDNA and nucleolus in the nucleus--rDNA instability maintains genome integrityTakehiko Kobayashi
National Institute of Genetics and The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima 411 8540 Japan
Bioessays 30:267-72. 2008..Here I would like to propose a new model regarding the roles of the rDNA and nucleolus. The key point of this model is that they act to preserve genome stability and trigger aging...
- Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiaeT Kobayashi
National Institute for Basic Biology, Okazaki 444 8585, Japan
Mol Cell Biol 21:136-47. 2001..This approximately 400-bp DNA element is not required for the RFB activity or the HOT1 activity and therefore defines a function unique to rDNA repeat expansion (and presumably contraction) separate from HOT1 and RFB activities...
- Strategies to maintain the stability of the ribosomal RNA gene repeats--collaboration of recombination, cohesion, and condensationTakehiko Kobayashi
National Institute for Basic Biology and The Graduate University for Advanced Studies SOKENDAI, School of Life Science, Okazaki, Japan
Genes Genet Syst 81:155-61. 2006....
- Recombination regulation by transcription-induced cohesin dissociation in rDNA repeatsTakehiko Kobayashi
National Institute for Basic Biology, SOKENDAI, School of Life Science, 38 Nishigonaka, Myodaijicho, Okazaki, 444 8585 Japan
Science 309:1581-4. 2005..This transcription is regulated by the silencing gene, SIR2, and by copy number. Transcription-induced cohesin dissociation may be a general mechanism of recombination regulation...
- [Recombination regulation by noncoding transcription in yeast rDNA repeats]Takehiko Kobayashi
Tanpakushitsu Kakusan Koso 51:2141-3. 2006
- SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeastTakehiko Kobayashi
National Institute for Basic Biology, Okazaki, Japan
Cell 117:441-53. 2004..From these and other experiments, we conclude that SIR2 prevents unequal sister-chromatid recombination, probably by forming special cohesin structures, without significant effects on recombinational events within individual rRNA genes...
- The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication forkTakehiko Kobayashi
National Institute for Basic Biology, 38 Nishigonaka, Myodaijicho, Okazaki 444 8585, Japan
Mol Cell Biol 23:9178-88. 2003..The RFB seems to wrap around Fob1p, and this wrapping structure may be important for function in the rDNA repeats...
- Transcription-mediated hyper-recombination in HOT1Naomi Serizawa
National Institute for Basic Biology, School of Life Science, 38 Nishigonaka, Myodaijicho, Okazaki, 444-8585, Japan
Genes Cells 9:305-15. 2004..This suggests that Fob1p is functioning as a PolI transcriptional activator in the wild-type strain...
- Transcription-dependent recombination and the role of fork collision in yeast rDNAYasushi Takeuchi
National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan
Genes Dev 17:1497-506. 2003..These results suggest that such a transcription-dependent fork collision induces recombination, and may function as a general recombination trigger for multiplication of highly transcribed single-copy genes...
- Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence dataAusten R D Ganley
National Institute for Basic Biology, Okazaki, 444 8585, Japan
Genome Res 17:184-91. 2007..These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays...
- Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprintingAusten R D Ganley
National Institute for Basic Biology, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaijicho, Okazaki 444-8585, Japan
Proc Natl Acad Sci U S A 102:11787-92. 2005....
- Amplification of Hot DNA segments in Escherichia coliKen-Ichi Kodama
National Institute for Basic Biology, Myodaiji, Okazaki, Aichi, Japan
Mol Microbiol 45:1575-88. 2002....
- Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeastTakehiko Kobayashi
Division of Cytogenetics, National Institute of Genetics The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, Japan
Cell Mol Life Sci 68:1395-403. 2011..In this review, I would like to introduce a new aspect of the rRNA gene repeat (called rDNA) as a center of maintenance of genome integrity and discuss its contribution to evolution...
- How does genome instability affect lifespan?: roles of rDNA and telomeresTakehiko Kobayashi
Division of Cytogenetics, National Institute of Genetics The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411 8540, Japan
Genes Cells 16:617-24. 2011..However, rDNA may also act as a NOC with respect to cellular senescence by limiting the number of times a cell can divide. Here, I discuss how rDNA might function as a NOC to influence life span in a manner analogous to telomeres...
- Abnormality in initiation program of DNA replication is monitored by the highly repetitive rRNA gene array on chromosome XII in budding yeastSatoru Ide
Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama cho 8916 5, Ikoma, Nara 630 0192, Japan
Mol Cell Biol 27:568-78. 2007..These results suggest that the rDNA locus primarily signals abnormalities in the initiation program to the DNA damage checkpoint and that the rDNA copy number modulates the sensitivity of this monitoring function...
- Oxaliplatin in treatment of the cisplatin-resistant MKN45 cell line of gastric cancerKatsuyuki Tozawa
Division of Lower Gastroenterology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
Anticancer Res 28:2087-92. 2008..Here, we studied oxaliplatin in vitro to reveal the mechanism of acquiring drug resistance and whether a cisplatin-resistant gastric cancer cell line has susceptibility to oxaliplatin...