Sakurai, Tetsuya, Plata, Germán, Rodríguez-Zapata, Fausto, Seki, Motoaki, Salcedo, Andrés, Toyoda, Atsushi, ...
Abstract Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial...
Functional annotation of 19,841 Populus nigrafull-length enriched cDNA clones (2007)
Nanjo, Tokihiko, Sakurai, Tetsuya, Totoki, Yasushi, Toyoda, Atsushi, Nishiguchi, Mitsuru, Kado, Tomoyuki, ...
Abstract Background Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been...
Sugaya, Nobuyoshi, Ikeda, Kazuyoshi, Tashiro, Toshiyuki, Takeda, Shizu, Otomo, Jun, Ishida, Yoshiko, ...
Abstract Background Protein-protein interactions (PPIs) are challenging but attractive targets for small chemical drugs. Whole PPIs, called the 'interactome', have been emerged in several organisms,...
Generation of medaka gene knockout models by target-selected mutagenesis (2006)
Taniguchi, Yoshihito, Takeda, Shunichi, Furutani-Seiki, Makoto, Kamei, Yasuhiro, Todo, Takeshi, Sasado, Takao, ...
Abstract We have established a reverse genetics approach for the routine generation of medaka ( Oryzias latipes ) gene knockouts. A cryopreserved library of N -ethyl- N -nitrosourea (ENU) mutagenized...
Genome Informatics 14: 408--409 (2003) Detection of Tissue Specific Genes by Putative (2004)
Katsuhiko Murakami, Toshio Kojima, Yoshiyuki Sakaki
Introduction Gene expression of multi-cellular organisms is regulated by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To find the functional regulatory...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Murakami, Katsuhiko, Kojima, Toshio, Sakaki, Yoshiyuki
Abstract Background Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis -elements on DNA sequences. To identify functional regulatory elements,...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
Abstract Background Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian...
Construction and Analysis of a Human-Chimpanzee Comparative Clone Map (2002)
Fujiyama,Asao, Watanabe,Hidemi, Toyoda,Atsushi, Taylor,Todd D., Itoh,Takehiko, Tsai,Shih-Feng, ...
The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes...
Construction and Analysis of a Human-Chimpanzee Comparative Clone Map (2002)
Fujiyama, Asao, Watanabe, Hidemi, Toyoda, Atsushi, Taylor, Todd D., Itoh, Takehiko, Tsai, Shih-Feng, ...
The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes...
Todd Taylor, Masahira Hattori, Kiyoteru Noguchi, Tomomi Shobu, Kazuo Ishii, Atsushi Toyoda, ...
Introduction Down syndrome (MIM 190685) is the most common genetic form of mental retardation. It is caused by trisomy of all or a portion of chromosome 21. The 2.5-Mb region [3, 4] between DNA...
Todd Taylor, Masahira Hattori, Kiyoteru Noguchi, Tomomi Shobu, Kazuo Ishii, Atsushi Toyoda, ...
Introduction Down syndrome (MIM 190685) is the most common genetic form of mental retardation. It is caused by trisomy of all or a portion of chromosome 21. The 2.5-Mb region [3, 4] between DNA...
古谷, 博和, 堂浦, 克美, 三島, 浩道, 榊, 佳之, 川崎, 晃一, Furuya, Hirokazu, ...
Haplotype analysis has been served for the study of molecular evolution by means of comparing of amino acid, at first and later, DNA sequences. This technique has allowed construction of evolutionary...
Ito, Takashi, Tashiro, Kosuke, Muta, Shigeru, Ozawa, Ritsuko, Chiba, Tomoko, Nishizawa, Mayumi, ...
Protein–protein interactions play pivotal roles in various aspects of the structural and functional organization of the cell, and their complete description is indispensable to thorough...
Hagiwara, Yuriko, Hirai, Momoki, Nishiyama, Kazutoshi, Kanazawa, Ichiro, Ueda, Takayuki, Sakaki, Yoshiyuki, ...
A systematic screen termed the allelic message display (AMD) was developed for the hunting of imprinted genes. In AMD, differential display PCR is adopted to image allelic expression status of...
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, Takashi, Chiba, Tomoko, Ozawa, Ritsuko, Yoshida, Mikio, Hattori, Masahira, Sakaki, Yoshiyuki
Protein–protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional...
Ōmura, Satoshi, Ikeda, Haruo, Ishikawa, Jun, Hanamoto, Akiharu, Takahashi, Chigusa, Shinose, Mayumi, ...
Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is...
Effects of aging on central and peripheral mammalian clocks
Yamazaki, Shin, Straume, Marty, Tei, Hajime, Sakaki, Yoshiyuki, Menaker, Michael, Block, Gene D.
Circadian organization changes with age, but we do not know the extent to which age-related changes are the result of alterations in the central pacemakers, the peripheral oscillators, or the...
Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region
Toyoda, Atsushi, Noguchi, Hideki, Taylor, Todd D., Ito, Takehiko, Pletcher, Mathew T., Sakaki, Yoshiyuki, ...
Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse...
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from...
A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q
Yamada, Yoichi, Watanabe, Hidemi, Miura, Fumihito, Soejima, Hidenobu, Uchiyama, Michiko, Iwasaka, Tsuyoshi, ...
Approximately half of all human genes have CpG islands (CGIs)around their promoter regions. Although CGIs usually escape methylation, those on Chromosome X in females and those in the vicinity of...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
The ATP-dependent DNase activity of Escherichia coli disappeared or was markedly reduced after infection with double-stranded DNA phages, T2, T3, T4, T5, T6, T7, λ, φ80, and P1, but not with the...
Site-specific mutagenesis of the calcium-binding photoprotein aequorin
Tsuji, Frederick I., Inouye, Satoshi, Goto, Toshio, Sakaki, Yoshiyuki
The luminescent protein aequorin from the jellyfish Aequoria victoria emits light by an intramolecular reaction in the presence of a trace amount of Ca2+. In order to understand the mechanism of the...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Sakaki, Yoshiyuki, Karu, Alexander E., Linn, Stuart, Echols, Harrison
Previous experiments have indicated that the gam gene of bacteriophage λ is responsible for an inhibition of the RecBC DNase—an enzyme that is essential for the major host pathway of genetic...
Abe, Kuniya, Noguchi, Hideki, Tagawa, Keiko, Yuzuriha, Misako, Toyoda, Atsushi, Kojima, Toshio, ...
MSM/Ms is an inbred strain derived from the Japanese wild mouse, Mus musculus molossinus. It is believed that subspecies molossinus has contributed substantially to the genome constitution of common...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
Suzuki, Yutaka, Taira, Hirotoshi, Tsunoda, Tatsuhiko, Mizushima-Sugano, Junko, Sese, Jun, Hata, Hiroko, ...
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method...
Constitutive expression of the Period1 gene impairs behavioral and molecular circadian rhythms
Numano, Rika, Yamazaki, Shin, Umeda, Nanae, Samura, Tomonori, Sujino, Mitsugu, Takahashi, Ri-ichi, ...
Three mammalian Period (Per) genes, termed Per1, Per2, and Per3, have been identified as structural homologues of the Drosophila circadian clock gene, period (per). The three Per genes are...
Katsube, Takanori, Sakamoto, Norihiro, Kobayashi, Yasushi, Seki, Ritsuko, Hirano, Masami, Tanishima, Kiyoh, ...
We analyzed the NADH-cytochrome b5 reductase gene of hereditary methemoglobinemia type I and type III, by using PCR-related techniques. The mutation in type I is a guanine-to-adenine substitution in...
Ito, Takashi, Tashiro, Kosuke, Muta, Shigeru, Ozawa, Ritsuko, Chiba, Tomoko, Nishizawa, Mayumi, ...
Protein–protein interactions play pivotal roles in various aspects of the structural and functional organization of the cell, and their complete description is indispensable to thorough...
Hagiwara, Yuriko, Hirai, Momoki, Nishiyama, Kazutoshi, Kanazawa, Ichiro, Ueda, Takayuki, Sakaki, Yoshiyuki, ...
A systematic screen termed the allelic message display (AMD) was developed for the hunting of imprinted genes. In AMD, differential display PCR is adopted to image allelic expression status of...
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, Takashi, Chiba, Tomoko, Ozawa, Ritsuko, Yoshida, Mikio, Hattori, Masahira, Sakaki, Yoshiyuki
Protein–protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional...
Ōmura, Satoshi, Ikeda, Haruo, Ishikawa, Jun, Hanamoto, Akiharu, Takahashi, Chigusa, Shinose, Mayumi, ...
Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is...
Effects of aging on central and peripheral mammalian clocks
Yamazaki, Shin, Straume, Marty, Tei, Hajime, Sakaki, Yoshiyuki, Menaker, Michael, Block, Gene D.
Circadian organization changes with age, but we do not know the extent to which age-related changes are the result of alterations in the central pacemakers, the peripheral oscillators, or the...
Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region
Toyoda, Atsushi, Noguchi, Hideki, Taylor, Todd D., Ito, Takehiko, Pletcher, Mathew T., Sakaki, Yoshiyuki, ...
Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse...
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from...
A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q
Yamada, Yoichi, Watanabe, Hidemi, Miura, Fumihito, Soejima, Hidenobu, Uchiyama, Michiko, Iwasaka, Tsuyoshi, ...
Approximately half of all human genes have CpG islands (CGIs)around their promoter regions. Although CGIs usually escape methylation, those on Chromosome X in females and those in the vicinity of...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
The ATP-dependent DNase activity of Escherichia coli disappeared or was markedly reduced after infection with double-stranded DNA phages, T2, T3, T4, T5, T6, T7, λ, φ80, and P1, but not with the...
Site-specific mutagenesis of the calcium-binding photoprotein aequorin
Tsuji, Frederick I., Inouye, Satoshi, Goto, Toshio, Sakaki, Yoshiyuki
The luminescent protein aequorin from the jellyfish Aequoria victoria emits light by an intramolecular reaction in the presence of a trace amount of Ca2+. In order to understand the mechanism of the...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Sakaki, Yoshiyuki, Karu, Alexander E., Linn, Stuart, Echols, Harrison
Previous experiments have indicated that the gam gene of bacteriophage λ is responsible for an inhibition of the RecBC DNase—an enzyme that is essential for the major host pathway of genetic...
Abe, Kuniya, Noguchi, Hideki, Tagawa, Keiko, Yuzuriha, Misako, Toyoda, Atsushi, Kojima, Toshio, ...
MSM/Ms is an inbred strain derived from the Japanese wild mouse, Mus musculus molossinus. It is believed that subspecies molossinus has contributed substantially to the genome constitution of common...
Yokomine, Takaaki, Shirohzu, Hisao, Purbowasito, Wahyu, Toyoda, Atsushi, Iwama, Hisakazu, Ikeo, Kazuho, ...
Previous studies revealed that Igf2 and Mpr/Igf2r are imprinted in eutherian mammals and marsupials but not in monotremes or birds. Igf2 lies in a large imprinted cluster in eutherians, and its...
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
Suzuki, Yutaka, Taira, Hirotoshi, Tsunoda, Tatsuhiko, Mizushima-Sugano, Junko, Sese, Jun, Hata, Hiroko, ...
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method...
Constitutive expression of the Period1 gene impairs behavioral and molecular circadian rhythms
Numano, Rika, Yamazaki, Shin, Umeda, Nanae, Samura, Tomonori, Sujino, Mitsugu, Takahashi, Ri-ichi, ...
Three mammalian Period (Per) genes, termed Per1, Per2, and Per3, have been identified as structural homologues of the Drosophila circadian clock gene, period (per). The three Per genes are...
Katsube, Takanori, Sakamoto, Norihiro, Kobayashi, Yasushi, Seki, Ritsuko, Hirano, Masami, Tanishima, Kiyoh, ...
We analyzed the NADH-cytochrome b5 reductase gene of hereditary methemoglobinemia type I and type III, by using PCR-related techniques. The mutation in type I is a guanine-to-adenine substitution in...
Generation of medaka gene knockout models by target-selected mutagenesis
Taniguchi, Yoshihito, Takeda, Shunichi, Furutani-Seiki, Makoto, Kamei, Yasuhiro, Todo, Takeshi, Sasado, Takao, ...
A reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts is described and applied to create a cryopreserved resource containing knockouts for most medaka...
Cysteine 10 Is a Key Residue in Amyloidogenesis of Human Transthyretin Val30Met
Takaoka, Yutaka, Ohta, Mika, Miyakawa, Kazuhisa, Nakamura, Osamu, Suzuki, Misao, Takahashi, Kiyoshi, ...
Type I familial amyloidotic polyneuropathy (FAP), a systemic amyloidosis, is characterized by aggregation of variant transthyretin (TTR Val30Met) into stable, insoluble fibrils. This aggregation is...
LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1
Kojima, Shihoko, Matsumoto, Ken, Hirose, Matsumi, Shimada, Miyuki, Nagano, Mamoru, Shigeyoshi, Yasufumi, ...
The mammalian molecular clock is composed of feedback loops to keep circadian 24-h rhythms. Although much focus has been on transcriptional regulation, it is clear that posttranscriptional controls...
Sugaya, Nobuyoshi, Ikeda, Kazuyoshi, Tashiro, Toshiyuki, Takeda, Shizu, Otomo, Jun, Ishida, Yoshiko, ...
Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
Nanjo, Tokihiko, Sakurai, Tetsuya, Totoki, Yasushi, Toyoda, Atsushi, Nishiguchi, Mitsuru, Kado, Tomoyuki, ...
Kurochkin, Igor V, Mizuno, Yumi, Konagaya, Akihiko, Sakaki, Yoshiyuki, Schönbach, Christian, Okazaki, Yasushi
Peroxisomes play an important role in β-oxidation of fatty acids. All peroxisomal matrix proteins are synthesized in the cytosol and post-translationally sorted to the organelle. Two distinct...