Papers - Sasaki, Takashi

MEPD: a resource for medaka gene expression patterns

Henrich, T., Ramialison, M., Wittbrodt, B., Assouline, B., Bourrat, F., Berger, A., Himmelbauer, H., Sasaki, T., Shimizu, N., Westerfield, M., Kondoh, H. and Wittbrodt, J.

Bioinformatics 21 ( 14 ) 3195 - 7 2005.07

ISSN  1367-4803

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The Medaka Expression Pattern Database (MEPD) is a database for gene expression patterns determined by in situ hybridization in the small freshwater fish medaka (Oryzias latipes). Data have been collected from various research groups and MEPD is developing into a central expression pattern depository within the medaka community. Gene expression patterns are described by images and terms of a detailed medaka anatomy ontology of over 4000 terms, which we have developed for this purpose and submitted to Open Biological Ontologies. Sequences have been annotated via BLAST match results and using Gene Ontology terms. These new features will facilitate data analyses using bioinformatics approaches and allow cross-species comparisons of gene expression patterns. Presently, MEPD has 19,757 entries, for 1024 of them the expression pattern has been determined.

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Genomic sequences encoding two types of medaka hemopexin-like protein Wap65, and their gene expression profiles in embryos

Nakaniwa, M., Hirayama, M., Shimizu, A., Sasaki, T., Asakawa, S., Shimizu, N. and Watabe, S.

J Exp Biol 208 ( Pt 10 ) 1915 - 25 2005.05

ISSN  0022-0949

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Medaka genomic BAC clones, which contained two types of medaka hemopexin-like protein gene (Wap65), mWap65-1 and mWap65-2, were screened and their genomic sequences were determined by the shotgun strategy. The exon-intron organizations were highly conserved between both mWap65s and human hemopexin genes. The 5'-flanking regions of mWap65-1 and mWap65-2 contained various putative transcription factor binding sites including elements for developmental regulation. The expression patterns of mWap65s during embryonic development were examined by quantitative real-time PCR, demonstrating that both mWap65 transcripts were observed in early embryonic stages, but their expression patterns were different. Interestingly, in situ hybridization revealed that mWap65-2 transcripts were restricted to liver, whereas mWap65-1 transcripts were detected along the edge of pectoral fin buds and the median fin fold of tail buds in embryos at stage 32. Furthermore, we generated transgenic medaka expressing GFP driven by mWap65-1 and mWap65-2 promoters and observed GFP expression patterns during ontogeny. Although localizations of GFP varied among individuals, embryos uniformly expressed GFP 1 day after injection of mWap65-1-hrGFP and mWap65-2-hrGFP constructs, suggesting that mWap65-1 and mWap65-2 promoters were activated in very early stages. The differences between mWap65-1 and mWap65-2 in their expression profiles indicate their distinct roles during ontogeny.

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Finishing the Euchromatic Sequence of the Human Genome

International Human Genome Sequencing Consortium

Nature 431 ( 7011 ) 931-945 2004.10

Research paper (scientific journal), Joint Work, Accepted

Identification and Characterization of a Novel Gene Family YPEL in a Wide Spectrum of Eukaryotic Species

Hosono, K., Sasaki, T., Minoshima, S. and Shimizu, N.

Gene 340 ( 1 ) 31-43 2004.10

Research paper (scientific journal), Joint Work, Accepted

The Minimal Eukaryotic Ribosomal DNA Units in the Primitive Red Alga Cyanidioschyzon merolae

Maruyama, S., Misumi, O., Ishii, Y., Asakawa, S., Shimizu, A., Sasaki, T., Matuszaki, M., Shin-i, T., Nozaki, H., Kohara, Y., Shimizu, N. and Kuroiwa, T.

DNA Research 11 ( 2 ) 83-91 2004.05

Research paper (scientific journal), Joint Work, Accepted

The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae

Maruyama, S., Misumi, O., Ishii, Y., Asakawa, S., Shimizu, A., Sasaki, T., Matsuzaki, M., Shin-i, T., Nozaki, H., Kohara, Y., Shimizu, N. and Kuroiwa, T.

DNA Res 11 ( 2 ) 83 - 91 2004.04

ISSN  1340-2838

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Cyanidioschyzon merolae is a small unicellular red alga that is considered to belong to one of the most deeply branched taxa in the plant kingdom. Its genome size is estimated to be 16.5 Mbp, one of the smallest among free-living eukaryotes. In the nucleus containing this small genome, one nucleolus is clearly observed, but the molecular basis for the intranuclear structure including ribosomal DNA organization is still unclear. We constructed a bacterial artificial chromosome library for C. merolae 10D composed of two subsets with different insert size distributions. The two subsets have average insert sizes of 97 and 48 kb, representing 10.0- and 6.9-fold genome-equivalent coverage of the haploid genome, respectively. For application to whole-genome shotgun sequencing, the termini of each clone were sequenced as sequence-tagged connectors and mapped on the contigs assigned to chromosomes. Screening for rRNA genes by conventional colony hybridization with high-density filter blots and subsequent sequencing revealed that the C. merolae genome contained the smallest number of ribosomal DNA units among all the eukaryotes examined to date. They consist of only 3 single units of rRNA genes distributed on separate chromosomal loci, representing an implication for concerted evolution. Based on these results, the origin and evolution of the nucleolus are discussed.

Comparative genomics of the keratin-associated protein (KAP) gene clusters in human, chimpanzee, and baboon

Shibuya, K., Kudoh, J., Obayashi, I., Shimizu, A., Sasaki, T., Minoshima, S. and Shimizu, N.

Mamm Genome 15 ( 3 ) 179 - 92 2004.03

ISSN  0938-8990

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We have previously identified a cluster of 16 genes that encode hair-specific proteins, called keratin-associated proteins (KAPs), located on human Chromosome (Chr) 21q22.3. Here, we have identified similar KAP gene clusters in two primates, chimpanzee and baboon. DNA sequence comparison revealed the common cluster structure consisting of 16 KAP genes for these three primates, but a significant difference was found in the baboon. Baboon possesses a new KAP gene not found in human and chimpanzee, whereas one KAP gene ( KRTAP18.12) that exists in human and chimpanzee was lost in baboon, making no change in the total number of KAP genes. Interestingly, the sequence for coding regions are highly variable among species owing to insertions and deletions, resulting in variation of gene size. On the contrary, the sequences for the 5' upstream region are highly conserved among species. These findings suggest that the ancestral KAP gene cluster was composed of 17 genes before the divergence of Old World monkeys (baboon) to the anthropoid (human and chimpanzee).

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'Comparative Genomics of the Keratin-associated Protein (KAP) Gene Clusters in Human, Chimpanzee and Baboon'

'Shibuya Kazunori, Kudoh Jun, Obayashi Izumi, Shimizu Atsushi, Sasaki Takashi, Minoshima Shinsei, Shimizu Nobuyoshi'

Mammalian genome 15 ( 3 ) 179-192 2004.03

Research paper (scientific journal), Joint Work, Accepted

Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI)

Schartl, M., Nanda, I., Kondo, M., Schmid, M., Asakawa, S., Sasaki, T., Shimizu, N., Henrich, T., Wittbrodt, J., Furutani-Seiki, M., Kondoh, H., Himmelbauer, H., Hong, Y., Koga, A., Nonaka, M., Mitani, H. and Shima, A.

Methods Cell Biol 77   173 - 99 2004

ISSN  0091-679X

Role of TBX1 in Human Del22q11.2 Syndrome

'Yagi Hisato, Furutani Yoshiyuki, Hamada Hiromichi, Sasaki Takashi, Asakawa Shuichi, Minoshima Shinsei, Ichida Fukiko, Kunitaka, Kimura Misa, Imamura Shinichiro, Kamatani Naoyuki, Momma Kazuo, Takao Atsuyoshi, Nakazawa Makoto, Shimizu Nobuyoshi, Matsuoka Rumiko'

Lancet 362   1366-1373 2003.10

Research paper (scientific journal), Joint Work, Accepted

A Novel Giant Gene CSMD3 Encoding a Protein with CUB and Sushi Multiple Domains: A Candidate Gene for Benign Adult Familial Myoclonic Epilepsy on Human Chromosome 8q23.3-q24.1

'Shimizu Atsushi, Asakawa Shuichi, Sasaki Takashi, Yamazaki Satoru, Yamagata, H., Kudoh Jun, Minoshima Shinsei, Kondo Ikuko, Shimizu Nobuyoshi'

Biochemical and biophysical research communications 309 ( 1 ) 143-154 2003.09

Research paper (scientific journal), Joint Work, Accepted

Identification of Eight Members of the Argonaute Family in the Human Genome

'Sasaki Takashi, Shiohama Aiko, Minoshima Shinsei, Shimizu Nobuyoshi'

Genomics 82 ( 3 ) 323-330 2003.08

Research paper (scientific journal), Joint Work, Accepted

Frequent Translocations Occur between Low Copy Repeats on Chromosome 22q11.2 (LCR22s) and Telomeric Bands of Partner Chromosomes

'Spiteri, E., Babcock, M., Kashork, C.D., Wakui, K., Gogineni, S., Lewis, D. A., Williams, K.M., Minoshima Shinsei, Sasaki Takashi, Shimizu Nobuyoshi, Potocki, L., Pulijaal, V., Shanske, A., Shaffer, L.G., Morrow, B.E.'

Human molecular genetics 12 ( 15 ) 1823-1837 2003.08

Research paper (scientific journal), Joint Work, Accepted

Molecular Cloning and Expression Analysis of a Novel Gene DGCR8 Located in the DiGeorge Syndrome Chromosomal Region (DGCR)

'Shiohama Aiko, Sasaki Takashi, Noda Setsuko, Minoshima Shinsei, Shimizu Nobuyoshi'

Biochemical and biophysical research communications 304 ( 1 ) 184-190 2003.04

Research paper (scientific journal), Joint Work, Accepted

ヒト22番および21番染色体のゲノム解析と疾患関連遺伝子の単離

Kudou Jun，Shibuya Kazunori，Sasaki Takashi，Minoshima Shinsei，Shimizu Nobuyoshi

蛋白質核酸酵素 12月増刊；ゲノムサイエンスの新たなる挑戦 46 ( 16 ) 2262-2270 2001.12

Research paper (scientific journal), Joint Work

Molecular cloning of a member of the facilitative glucose transporter gene family GLUT11 (SLC2A11) and identification of transcription variants

Sasaki Takashi, Minoshima Shinsei, Shiohama Aiko, Shintani Ai, Shimizu Atsushi, Asakawa Shuichi, Kawasaki Kazuhiko, Shimizu Nobuyoshi

Biochemical and Biophysical Research Communications 289 ( 5 ) 1218-1224 2001.12

Research paper (scientific journal), Joint Work

The genomic structure and promoter region of the human Parkin gene

Asakawa Shuichi, Tsunematsu Kennichiro, Takayanagi Atsushi, Sasaki Takashi, Shimizu Atsushi, Shintani Ai, Kawasaki Kazuhiko, Mungall AJ, Beck S, Minoshima Shinsei, Shimizu Nobuyoshi

Biochemical and Biophysical Research Communications 286 ( 5 ) 863-868 2001.09

Research paper (scientific journal), Joint Work

Evolutionary dynamics of the human immunoglobulinκlocus and the germline repertoire of the Vκgenes

Kawasaki Kazuhiko, Minoshima Shinsei, Nakato Eriko, Shibuya Kazunori, Shintani Ai, Asakawa Shuichi, Sasaki Takashi, Klobeck H-G, Combriato G, Zachau HG, Shimizu Nobuyoshi

European Journal of Immunology 31 ( 4 ) 1017-1028 2001.04

Research paper (scientific journal), Joint Work

22番染色体に含まれる高頻度反復配列の分布とその意義（特集　ヒトゲノムプロジェクトの最前線─ヒト22番染色体から学んだこと）

Shimizu Nobuyoshi，Yoshizaki Yuuko，Minoshima Shinsei, Kawasaki Kazuhiko, Sasaki Takashi, Asakawa Sfuuichi, Kudou Jun, Shintani Ai, Shibuya Kazunori, Aoki Norie, Mitsuyama Susumu

最新医学 55 ( 6 ) 1139-1144 2000.06

Research paper (scientific journal), Joint Work

序論：ヒトゲノムプロジェクトの最前線　(特集　ヒトゲノムプロジェクトの最前線─ヒト22番染色体から学んだこと)

Shimizu Nobuyoshi, Minojima Shinsei, Kawasaki Kazuhiko, Sasaki Takashi,asakawa Sfuuichi, kudou Jun, Shintani Ai, Shibuya Kzunori, Yoshizaki Yuuko, Aoki Norie, Mitsuyama Susumu

最新医学 55 ( 6 ) 1097-1098 2000.06

Research paper (scientific journal), Joint Work