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CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

Shintaro Katayama, Mutsumi Kanamori-Katayama, Kazumi Yamaguchi, Piero Carninci, Yoshihide Hayashizaki
2007 Genome Biology  
Promoter-based expression profiling A novel approach that combines CAGE expression analysis with oligonucleotide array technology allows for the accurate and sensitive detection of promoter-based transcriptional activity. Abstract Cap analysis gene expression (CAGE) technology has revealed numerous transcription start sites (TSSs) in mammals and has suggested complex promoter-based patterns of regulation. We developed the CAGE-TSSchip to detect promoter-based transcriptional activity. The
more » ... SSchip is a customized oligonucleotide array that targets known TSSs identified by CAGE. A new labeling method, labeling capped transcripts from the 5'-end, had to be developed. The CAGE-TSSchip is accurate and sensitive, and represents the activity of each TSS.
doi:10.1186/gb-2007-8-3-r42 fatcat:l46dtvevpve7bfadikremfq6qi

Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Kengo Usui, Shintaro Katayama, Mutsumi Kanamori-Katayama, Chihiro Ogawa, Chikatoshi Kai, Makiko Okada, Jun Kawai, Takahiro Arakawa, Piero Carninci, Masayoshi Itoh, Koji Takio, Masashi Miyano (+4 others)
2005 Genome Biology  
Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in Pyrococcus using the mammalian two-hybrid system to determine the function
more » ... f the hypothetical proteins. We examined 960 soluble proteins from Pyrococcus and selected 107 interactions based on luciferase reporter activity, which was then evaluated using a computational approach to assess the reliability of the interactions. We also analyzed the expression of the assay samples by western blot, and a few interactions by in vitro pull-down assays. We identified 11 hetero-interactions that we considered to be located at the same operon, as observed in Helicobacter pylori. We annotated and classified proteins in the selected interactions according to their orthologous proteins. Many enzyme proteins showed self-interactions, similar to those seen in other organisms. We found 13 unannotated proteins that interacted with annotated proteins; this information is useful for predicting the functions of the hypothetical Pyrococcus proteins from the annotations of their interacting partners. Among the heterogeneous interactions, proteins were more likely to interact with proteins within the same ortholog class than with proteins of different classes. The analysis described here can provide global insights into the biological features of the protein-protein interactions in P. horikoshii.
doi:10.1186/gb-2005-6-12-r98 pmid:16356270 pmcid:PMC1414084 fatcat:a6kmsckp3feazonvtr6zyyzwru

Gemin2 Plays an Important Role in Stabilizing the Survival of Motor Neuron Complex

Chihiro Ogawa, Kengo Usui, Makoto Aoki, Fuyu Ito, Masayoshi Itoh, Chikatoshi Kai, Mutsumi Kanamori-Katayama, Yoshihide Hayashizaki, Harukazu Suzuki
2007 Journal of Biological Chemistry  
The survival of motor neuron (SMN) protein, responsible for the neurodegenerative disease spinal muscular atrophy (SMA), oligomerizes and forms a stable complex with seven other major components, the Gemin proteins. Besides the SMN protein, Gemin2 is a core protein that is essential for the formation of the SMN complex, although the mechanism by which it drives formation is unclear. We have found a novel interaction, a Gemin2 self-association, using the mammalian two-hybrid system and the in
more » ... ro pull-down assays. Using in vitro dissociation assays, we also found that the self-interaction of the amino-terminal SMN protein, which was confirmed in this study, became stable in the presence of Gemin2. In addition, Gemin2 knockdown using small interference RNA treatment revealed a drastic decrease in SMN oligomer formation and in the assembly activity of spliceosomal small nuclear ribonucleoprotein (snRNP). Taken together, these results indicate that Gemin2 plays an important role in snRNP assembly through the stabilization of the SMN oligomer/complex via novel self-interaction. Applying the results/techniques to amino-terminal SMN missense mutants that were recently identified from SMA patients, we successfully showed that amino-terminal self-association, Gemin2 binding, the stabilization effect of Gemin2, and snRNP assembly activity were all lowered in the mutant SMN(D44V), suggesting that instability of the amino-terminal SMN self-association may cause SMA in patients carrying this allele.
doi:10.1074/jbc.m609297200 pmid:17308308 fatcat:pjhtfz5ybrhtzjxb7h3rpqzoyi

LRRN4 and UPK3B Are Markers of Primary Mesothelial Cells

Mutsumi Kanamori-Katayama, Ai Kaiho, Yuri Ishizu, Yuko Okamura-Oho, Okio Hino, Masaaki Abe, Takumi Kishimoto, Hisahiko Sekihara, Yukio Nakamura, Harukazu Suzuki, Alistair R. R. Forrest, Yoshihide Hayashizaki (+1 others)
2011 PLoS ONE  
Mesothelioma is a highly malignant tumor that is primarily caused by occupational or environmental exposure to asbestos fibers. Despite worldwide restrictions on asbestos usage, further cases are expected as diagnosis is typically 20-40 years after exposure. Once diagnosed there is a very poor prognosis with a median survival rate of 9 months. Considering this the development of early pre clinical diagnostic markers may help improve clinical outcomes. Methodology: Microarray expression arrays
more » ... mesothelium and other tissues dissected from mice were used to identify candidate mesothelial lineage markers. Candidates were further tested by qRTPCR and in-situ hybridization across a mouse tissue panel. Two candidate biomarkers with the potential for secretion, uroplakin 3B (UPK3B), and leucine rich repeat neuronal 4 (LRRN4) and one commercialized mesothelioma marker, mesothelin (MSLN) were then chosen for validation across a panel of normal human primary cells, 16 established mesothelioma cell lines, 10 lung cancer lines, and a further set of 8 unrelated cancer cell lines. Conclusions: Within the primary cell panel, LRRN4 was only detected in primary mesothelial cells, but MSLN and UPK3B were also detected in other cell types. MSLN was detected in bronchial epithelial cells and alveolar epithelial cells and UPK3B was detected in retinal pigment epithelial cells and urothelial cells. Testing the cell line panel, MSLN was detected in 15 of the 16 mesothelioma cells lines, whereas LRRN4 was only detected in 8 and UPK3B in 6. Interestingly MSLN levels appear to be upregulated in the mesothelioma lines compared to the primary mesothelial cells, while LRRN4 and UPK3B, are either lost or down-regulated. Despite the higher fraction of mesothelioma lines positive for MSLN, it was also detected at high levels in 2 lung cancer lines and 3 other unrelated cancer lines derived from papillotubular adenocarcinoma, signet ring carcinoma and transitional cell carcinoma.
doi:10.1371/journal.pone.0025391 pmid:21984916 pmcid:PMC3184985 fatcat:nzewrxfwqvh2fogsqqckpk6yfe

Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR

Harukazu Suzuki, Rie Okunishi, Wataru Hashizume, Shintaro Katayama, Noriko Ninomiya, Naoki Osato, Kenjiro Sato, Mari Nakamura, Juri Iida, Mutsumi Kanamori, Yoshihide Hayashizaki
2004 FEBS Letters  
We established a medium-scale real-time RT-PCR system focusing on transcription factors and applied it to their expression profiles in the adult mouse 11 brain regions (http:// Almost 90% of the examined genes showed significant expression in at least one region. We successfully extracted 179 region-specific genes by clustering analysis. Interestingly, the transcription factors involved in the development of the pituitary were still expressed in the adult
more » ... , suggesting that they also play important roles in maintenance of the pituitary. These results provide unique molecular markers that may account for the molecular basis of the unique functions of specific brain regions.
doi:10.1016/j.febslet.2004.07.068 pmid:15328000 fatcat:qsyphefv25dtvfoih2foynkvsa

Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer

Masayoshi Itoh, Miki Kojima, Sayaka Nagao-Sato, Eri Saijo, Timo Lassmann, Mutsumi Kanamori-Katayama, Ai Kaiho, Marina Lizio, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki (+1 others)
2012 PLoS ONE  
Acknowledgments We specially thank Shintaro Katayama for the development of manual protocol and data analysis. We thank RIKEN Genome Network Analysis Service for data production, J.  ... 
doi:10.1371/journal.pone.0030809 pmid:22303458 pmcid:PMC3268765 fatcat:a2hevyytynck5py2ij25jfblqm

Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs

Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G. Engström, Boris Lenhard, Rajith N. Aturaliya, Serge Batalov, Kirk W. Beisel, Carol J. Bult, Colin F. Fletcher (+22 others)
2006 PLoS Genetics  
T he international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified.
more » ... pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.
doi:10.1371/journal.pgen.0020062 pmid:16683036 pmcid:PMC1449903 fatcat:seovzd67xffxzlr3xuu7dalyna

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A M Semple, Martin S Taylor, Pär G Engström G, Martin C Frith, Alistair R R Forrest, Wynand B Alkema (+29 others)
2007 Nature Genetics  
doi:10.1038/ng0907-1174b fatcat:w4fkhztmirdcxnwni5mgu37xki

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Harukazu Suzuki, Alistair R R Forrest, Erik van Nimwegen, Carsten O Daub, Piotr J Balwierz, Katharine M Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel J L de Hoon, Shintaro Katayama, Kate Schroder (+148 others)
2009 Nature Genetics  
Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in
more » ... regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.
doi:10.1038/ng.375 pmid:19377474 pmcid:PMC6711855 fatcat:d5jwq2rbt5bfllsd4ej5tprnue

FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima (+166 others)
2017 Scientific Data  
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis
more » ... pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
doi:10.1038/sdata.2017.112 pmid:28850106 pmcid:PMC5574368 fatcat:cel5hhhtardinak67mbl2okvhe

Role of Survival Motor Neuron Complex Components in Small Nuclear Ribonucleoprotein Assembly

Chihiro Ogawa, Kengo Usui, Fuyu Ito, Masayoshi Itoh, Yoshihide Hayashizaki, Harukazu Suzuki
2009 Journal of Biological Chemistry  
Mutsumi Kanamori-Katayama, Chikatoshi Kai, Makoto Aoki, and other members of the Omics Science Center.  ... 
doi:10.1074/jbc.m809031200 pmid:19321448 pmcid:PMC2682908 fatcat:ctc3d5nbfrdzfccdzxupqj75aq

Contents list

2018 Soft Matter  
Univ. 1 Shintaro Katayama 1 , Mutsumi Kanamori-Katayama 1 , Yuki Tsujimura 1 , Noriko Ninomiya 1 , Kazumi Yamaguchi 1,2 , Piero Carninci 1,3 , Yoshihide Hayashizaki 1,3 Genome exploration research  ...  Kanamori-Katayama 1 , Yoshihide Hayashizaki 1,2 and Harukazu Suzuki 1 1 Genome Expl.  ... 
doi:10.1039/c8sm90107d fatcat:tko5byj5izccvgfzmdsssx4mgm


Journal of the Japanese Society of Pediatric Surgeons  
2A-P22-1 続発性偽性低アルドステロン症(Ⅰ型)を呈した左異所性尿管瘤,左重複尿管,左多嚢胞性異型性腎 の 1 例 北九州市立医療センター 小児外科 中村 睦 Pseudohypoaldosteronism type1 in an infant with complex urinary tract's anomalies Kitakyushu Municipal Medical Center Mutsumi  ...  University Shiori Tsuruhisa 1B-P15-4 当科における先天性心疾患を有する小児胆石症患者の治療方針 倉敷中央病院外科,小児外科 片山 修一 Treatment in the pediatric patients with cholelithiasis at a single institution Department of pediatric surgery Shuichi Katayama  ... 
doi:10.11164/jjsps.54.3_423 fatcat:shficcwm7jcvljaosr7fu732iy

General sessions (1A-01 - 3E-13)

2005 Genes & Genetic Systems  
We will discuss evolutionary implications of our observation. 3A -08 FUJIMITSU, Kazuyuki 1 , KATAYAMA, Tsutomu 1 ( 1 Dept. Molec. Biol., Grad. Sch. Pharmaceutical Science, Univ.  ...  Judged from Ka/Ks values, genes expressed in generative organs revealed accelerated evolution during differentiation course between wheat and rice. 1B -09 SANO, Yukie 1,4 , KANAMORI, Hiroyuki 2 , NAMIKI  ... 
doi:10.1266/ggs.80.444 fatcat:yec7vkgtjrbmllw2jgztcp5u2i

Free Communications (Poster Sessions)

2015 Journal of Pharmacological Sciences  
P2-41 Molecular properties of TMEM240, a causative protein of spinocerebellar ataxia type 21 Takahiro Seki 1 , Masahiro Sato 1 , Manami Kawahara 1 , Mutsumi Oshima 1 , Reiho Tsutsumi 1 , Yuki Kurauchi  ...  P2-51 Effects of drugs on cardiac function in a dog model of drug-induced cardiac hypofunction Kazuaki Sasaki, Yasuo Nakamura, Tsuyoshi Higuchi, Masakazu Imaizumi, Seiichi Katayama, Katsuhide Nishi  ...  glycation end product-cholesterol-aggregated proteins increased expression of pro-infl ammatory cytokine mRNA by intracellular acidifi cation in mesangial cells Kenta Sago 1 , Tomohiro Mizuno 1 , Azusa Kanamori  ... 
doi:10.1016/j.jphs.2015.07.029 fatcat:2edp75o6vjefjo2skw7mg4wypa