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Your search keyword '"Hamaguchi, Makoto"' showing total 11 results
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11 results on '"Hamaguchi, Makoto"'

1. Exploratory analysis on crosstalk between intra-tumor immunity and FGF/FGFR pathway in clear cell renal cell carcinoma.

Author

Narisawa, Takafumi, primary, Naito, Sei, additional, Mitsuda, Yoshihide, additional, Oe, Rintaro, additional, Sato, Hidenori, additional, Kobayashi, Chizuru, additional, Fukuda, Mizuki, additional, Kitaoka, Takumi, additional, Miyano, Yuki, additional, Ito, Hiromi, additional, Kimura, Mizuki, additional, Hamaguchi, Makoto, additional, Aoshima, Ken, additional, Futakuchi, Mitsuru, additional, and Tsuchiya, Norihiko, additional

Published
2022
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2. Genome-wide network of regulatory genes for construction of a chordate embryo

Author

Shoguchi, Eiichi, Hamaguchi, Makoto, and Satoh, Nori

Subjects
Genetic research, Gene expression, DNA binding proteins, Genomes, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2008.01.009 Byline: Eiichi Shoguchi, Makoto Hamaguchi, Nori Satoh Keywords: Chordate early embryos; Cell fate determination; Networks of regulatory genes; Chromosomal positioning; Genome-wide control Abstract: Animal development is controlled by gene regulation networks that are composed of sequence-specific transcription factors (TF) and cell signaling molecules (ST). Although housekeeping genes have been reported to show clustering in the animal genomes, whether the genes comprising a given regulatory network are physically clustered on a chromosome is uncertain. We examined this question in the present study. Ascidians are the closest living relatives of vertebrates, and their tadpole-type larva represents the basic body plan of chordates. The Ciona intestinalis genome contains 390 core TF genes and 119 major ST genes. Previous gene disruption assays led to the formulation of a basic chordate embryonic blueprint, based on over 3000 genetic interactions among 79 zygotic regulatory genes. Here, we mapped the regulatory genes, including all 79 regulatory genes, on the 14 pairs of Ciona chromosomes by fluorescent in situ hybridization (FISH). Chromosomal localization of upstream and downstream regulatory genes demonstrates that the components of coherent developmental gene networks are evenly distributed over the 14 chromosomes. Thus, this study provides the first comprehensive evidence that the physical clustering of regulatory genes, or their target genes, is not relevant for the genome-wide control of gene expression during development. Author Affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Article History: Received 7 November 2007; Revised 29 December 2007; Accepted 9 January 2008 Article Note: (footnote) [star] Genome-wide gene regulatory network is superimposed onto chromosomal map. The viewpoint provides the first comprehensive evidence that the physical clustering of regulatory genes is not relevant for the genome-wide control of gene expression during development.

Published
2008

7. Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis

Author

Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Tadasu Sin-I, Kohara, Yuji, Putnam, Nik, Rokhsar, Daniel S., and Satoh, Nori

Subjects
Cytogenetics -- Research, Nucleotide sequence -- Research, Health
Abstract

The molecular cytogenic characterization of all 14 pairs Ciona intestinalis chromosomes, as well as initial large-scale mapping of genomic sequences onto chromosomes by fluorescent in situ hybridization (FISH) is reported. This map lays the foundation for future studies of the protochordate Ciona intestinalis genome at the chromosomal level.

Published
2006

9. A cDNA resource from the basal chordate Ciona intestinalis

Author

Satou, Yutaka, primary, Yamada, Lixy, additional, Mochizuki, Yasuaki, additional, Takatori, Naohito, additional, Kawashima, Takeshi, additional, Sasaki, Akane, additional, Hamaguchi, Makoto, additional, Awazu, Satoko, additional, Yagi, Kasumi, additional, Sasakura, Yasunori, additional, Nakayama, Akie, additional, Ishikawa, Hisayoshi, additional, Inaba, Kazuo, additional, and Satoh, Nori, additional

Published
2002
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10. Gene expression profiles inCiona intestinalistailbud embryos

Author

Satou, Yutaka, primary, Takatori, Naohito, additional, Yamada, Lixy, additional, Mochizuki, Yasuaki, additional, Hamaguchi, Makoto, additional, Ishikawa, Hisayoshi, additional, Chiba, Shota, additional, Imai, Kaoru, additional, Kano, Shungo, additional, Murakami, Seiko D., additional, Nakayama, Akie, additional, Nishino, Atsuo, additional, Sasakura, Yasunori, additional, Satoh, Gohki, additional, Shimotori, Taishin, additional, Shin-i, Tadasu, additional, Shoguchi, Eiichi, additional, Suzuki, Miho M., additional, Takada, Norio, additional, Utsumi, Nanami, additional, Yoshida, Natsue, additional, Saiga, Hidetoshi, additional, Kohara, Yuji, additional, and Satoh, Nori, additional

Published
2001
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11. Gene expression profiles in Ciona intestinalis tailbud embryos

Author

Satou, Yutaka, Takatori, Naohito, Yamada, Lixy, Mochizuki, Yasuaki, Hamaguchi, Makoto, Ishikawa, Hisayoshi, Chiba, Shota, Imai, Kaoru, Kano, Shungo, Murakami, Seiko D., Nakayama, Akie, Nishino, Atsuo, Sasakura, Yasunori, Satoh, Gohki, Shimotori, Taishin, Shin-i, Tadasu, Shoguchi, Eiichi, Suzuki, Miho M., Takada, Norio, Utsumi, Nanami, Yoshida, Natsue, Saiga, Hidetoshi, Kohara, Yuji, and Satoh, Nori

Abstract

A set of 3423 expressed sequence tags derived from the Ciona intestinalis tailbud embryos was categorized into 1213 independent clusters. When compared with DNA Data Bank of Japan database, 502 clusters of them showed significant matches to reported proteins with distinct function, whereas 184 lacked sufficient information to be categorized (including reported proteins with undefined function) and 527 had no significant similarities to known proteins. Sequence similarity analyses of the 502 clusters in relation to the biosynthetic function, as well as the structure of the message population at this stage, demonstrated that 390 of them were associated with functions that many kinds of cells use, 85 with cell-cell communication and 27 with transcription factors and other gene regulatory proteins. All of the 1213 clusters were subjected to whole-mount in situ hybridization to analyze the gene expression profiles at this stage. A total of 387 clusters showed expression specific to a certain tissue or organ; 149 showed epidermis-specific expression; 34 were specific to the nervous system; 29 to endoderm; 112 to mesenchyme; 32 to notochord; and 31 to muscle. Many genes were also specifically expressed in multiple tissues. The study also highlighted characteristic gene expression profiles dependent on the tissues. In addition, several genes showed intriguing expression patterns that have not been reported previously; for example, four genes were expressed specifically in the nerve cord cells and one gene was expressed only in the posterior part of muscle cells. This study provides molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. The sequence information will also be used for further genome scientific approach to explore molecular mechanisms involved in the formation of one of the most primitive chordate body plans.

Published
2001
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