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2. A single-cell atlas of transcribed cis-regulatory elements in the human genome

Author

Moody, Jonathan, primary, Kouno, Tsukasa, additional, Kojima, Miki, additional, Koya, Ikuko, additional, Leon, Julio, additional, Suzuki, Akari, additional, Hasegawa, Akira, additional, Akiyama, Taishin, additional, Akiyama, Nobuko, additional, Amagai, Masayuki, additional, Chang, Jen-Chien, additional, Fukushima-Nomura, Ayano, additional, Handa, Mika, additional, Hino, Kazunori, additional, Hino, Mizuki, additional, Hirata, Tomoko, additional, Imai, Yuuki, additional, Inoue, Kazunori, additional, Kawasaki, Hiroshi, additional, Kimura, Toshihiro, additional, Kinoshita, Tomofumi, additional, Kubo, Ken-ichiro, additional, Kunii, Yasuto, additional, Lopez-Redondo, Fernando, additional, Manabe, Ri-ichiroh, additional, Miyai, Tomohiro, additional, Morimoto, Satoru, additional, Nagaoka, Atsuko, additional, Nakajima, Jun, additional, Noma, Shohei, additional, Okazaki, Yasushi, additional, Ozaki, Kokoro, additional, Saeki, Noritaka, additional, Sakai, Hiroshi, additional, Seyama, Kuniaki, additional, Shibayama, Youtaro, additional, Sujino, Tomohisa, additional, Tagami, Michihira, additional, Takahashi, Hayato, additional, Takao, Masaki, additional, Takeshita, Masaru, additional, Takiuchi, Tsuyoshi, additional, Terao, Chikashi, additional, Yip, Chi Wai, additional, Yoshinaga, Satoshi, additional, Okano, Hideyuki, additional, Yamamoto, Kazuhiko, additional, Kasukawa, Takeya, additional, Ando, Yoshinari, additional, Carninci, Piero, additional, Shin, Jay W., additional, and Hon, Chung-Chau, additional

Published
2023
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3. Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets

Author

Ohta, Atsushi, primary, Tanada, Mikimasa, additional, Shinohara, Shojiro, additional, Morita, Yuya, additional, Nakano, Kazuhiko, additional, Yamagishi, Yusuke, additional, Takano, Ryusuke, additional, Kariyuki, Shiori, additional, Iida, Takeo, additional, Matsuo, Atsushi, additional, Ozeki, Kazuhisa, additional, Emura, Takashi, additional, Sakurai, Yuuji, additional, Takano, Koji, additional, Higashida, Atsuko, additional, Kojima, Miki, additional, Muraoka, Terushige, additional, Takeyama, Ryuuichi, additional, Kato, Tatsuya, additional, Kimura, Kaori, additional, Ogawa, Kotaro, additional, Ohara, Kazuhiro, additional, Tanaka, Shota, additional, Kikuchi, Yasufumi, additional, Hisada, Nozomi, additional, Hayashi, Ryuji, additional, Nishimura, Yoshikazu, additional, Nomura, Kenichi, additional, Tachibana, Tatsuhiko, additional, Irie, Machiko, additional, Kawada, Hatsuo, additional, Torizawa, Takuya, additional, Murao, Naoaki, additional, Kotake, Tomoya, additional, Tanaka, Masahiko, additional, Ishikawa, Shiho, additional, Miyake, Taiji, additional, Tamiya, Minoru, additional, Arai, Masako, additional, Chiyoda, Aya, additional, Akai, Sho, additional, Sase, Hitoshi, additional, Kuramoto, Shino, additional, Ito, Toshiya, additional, Shiraishi, Takuya, additional, Kojima, Tetsuo, additional, and Iikura, Hitoshi, additional

Published
2023
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4. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Author

FANTOM Consortium, Arner, Erik, Daub, Carsten O., Vitting-Seerup, Kristoffer, Andersson, Robin, Lilje, Berit, Drabløs, Finn, Lennartsson, Andreas, Rönnerblad, Michelle, Hrydziuszko, Olga, Vitezic, Morana, Freeman, Tom C., Alhendi, Ahmad M. N., Arner, Peter, Axton, Richard, Baillie, J. Kenneth, Beckhouse, Anthony, Bodega, Beatrice, Briggs, James, Brombacher, Frank, Davis, Margaret, Detmar, Michael, Ehrlund, Anna, Endoh, Mitsuhiro, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley, Goldowitz, Daniel, Guler, Reto, Ha, Thomas, Hara, Mitsuko, Herlyn, Meenhard, Ikawa, Tomokatsu, Kai, Chieko, Kawamoto, Hiroshi, Khachigian, Levon M., Klinken, S. Peter, Kojima, Soichi, Koseki, Haruhiko, Klein, Sarah, Mejhert, Niklas, Miyaguchi, Ken, Mizuno, Yosuke, Morimoto, Mitsuru, Morris, Kelly J., Mummery, Christine, Nakachi, Yutaka, Ogishima, Soichi, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry, Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Qin, Xian-Yang, Roy, Sugata, Sato, Hiroki, Savvi, Suzana, Saxena, Alka, Schwegmann, Anita, Sugiyama, Daisuke, Swoboda, Rolf, Tanaka, Hiroshi, Tomoiu, Andru, Winteringham, Louise N., Wolvetang, Ernst, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Zabierowski, Susan, Zhang, Peter, Abugessaisa, Imad, Bertin, Nicolas, Diehl, Alexander D., Fukuda, Shiro, Furuno, Masaaki, Harshbarger, Jayson, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Ishizu, Yuri, Itoh, Masayoshi, Kawashima, Tsugumi, Kojima, Miki, Kondo, Naoto, Lizio, Marina, Meehan, Terrence F., Mungall, Christopher J., Murata, Mitsuyoshi, Nishiyori-Sueki, Hiromi, Sahin, Serkan, Nagao-Sato, Sayaka, Severin, Jessica, de Hoon, Michiel J. L., Kawai, Jun, Kasukawa, Takeya, Lassmann, Timo, Suzuki, Harukazu, Kawaji, Hideya, Summers, Kim M., Wells, Christine, Hume, David A., Forrest, Alistair R. R., Sandelin, Albin, Carninci, Piero, and Hayashizaki, Yoshihide

Published
2015

5. GENE REGULATION: Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Author

Arner, Erik, Daub, Carsten O., Vitting-Seerup, Kristoffer, Andersson, Robin, Lilje, Berit, Drabløs, Finn, Lennartsson, Andreas, Rönnerblad, Michelle, Hrydziuszko, Olga, Vitezic, Morana, Freeman, Tom C., Alhendi, Ahmad M. N., Arner, Peter, Axton, Richard, Baillie, Kenneth J., Beckhouse, Anthony, Bodega, Beatrice, Briggs, James, Brombacher, Frank, Davis, Margaret, Detmar, Michael, Ehrlund, Anna, Endoh, Mitsuhiro, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley, Goldowitz, Daniel, Guler, Reto, Ha, Thomas, Hara, Mitsuko, Herlyn, Meenhard, Ikawa, Tomokatsu, Kai, Chieko, Kawamoto, Hiroshi, Khachigian, Levon M., Klinken, Peter S., Kojima, Soichi, Koseki, Haruhiko, Klein, Sarah, Mejhert, Niklas, Miyaguchi, Ken, Mizuno, Yosuke, Morimoto, Mitsuru, Morris, Kelly J., Mummery, Christine, Nakachi, Yutaka, Ogishima, Soichi, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry, Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Qin, Xian-Yang, Roy, Sugata, Sato, Hiroki, Savvi, Suzana, Saxena, Alka, Schwegmann, Anita, Sugiyama, Daisuke, Swoboda, Rolf, Tanaka, Hiroshi, Tomoiu, Andru, Winteringham, Louise N., Wolvetang, Ernst, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Zabierowski, Susan, Zhang, Peter, Abugessaisa, Imad, Bertin, Nicolas, Diehl, Alexander D., Fukuda, Shiro, Furuno, Masaaki, Harshbarger, Jayson, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Ishizu, Yuri, Itoh, Masayoshi, Kawashima, Tsugumi, Kojima, Miki, Kondo, Naoto, Lizio, Marina, Meehan, Terrence F., Mungall, Christopher J., Murata, Mitsuyoshi, Nishiyori-Sueki, Hiromi, Sahin, Serkan, Nagao-Sato, Sayaka, Severin, Jessica, de Hoon, Michiel J. L., Kawai, Jun, Kasukawa, Takeya, Lassmann, Timo, Suzuki, Harukazu, Kawaji, Hideya, Summers, Kim M., Wells, Christine, Hume, David A., Forrest, Alistair R. R., Sandelin, Albin, Carninci, Piero, and Hayashizaki, Yoshihide

Published
2015
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8. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
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9. Functional annotation of human long noncoding RNAs via molecular phenotyping

Author

Ramilowski, Jordan A., Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V., Mendez, Mickaël, Ooi, Jasmine Li Ching, Ouyang, John F., Parkinson, Nicholas J., Petri, Andreas, Roos, Leonie, Severin, Jessica, Yasuzawa, Kayoko, Abugessaisa, Imad, Akalin, Altuna, Antonov, Ivan V., Arner, Erik, Bonetti, Alessandro, Bono, Hidemasa, Borsari, Beatrice, Brombacher, Frank, Cameron, Christopher J.F., Cannistraci, Carlo V., Cardenas, Ryan, Cardon, Melissa, Chang, Howard, Dostie, Josée, Ducoli, Luca, Favorov, Alexander V., Fort, Alexandre, Garrido, Diego, Gil, Noa, Gimenez, Juliette, Guler, Reto, Handoko, Lusy, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Kosuke, Hayatsu, Norihito, Heutink, Peter, Hirose, Tetsuro, Imada, Eddie L., Itoh, Masayoshi, Kaczkowski, Bogumil, Kanhere, Aditi S., Kawabata, Emily, Kawaji, Hideya, Kawashima, Tsugumi, Kelly, S. Thomas, Kojima, Miki, Kondo, Naoto, Koseki, Haruhiko, Kouno, Tsukasa, Kratz, Anton, Kurowska-Stolarska, Mariola S., Kwon, Andrew Tae Jun, Leek, Jeffrey T., Lennartsson, Andreas, Lizio, Marina, López-Redondo, Fernando, Luginbühl, Joachim, Maeda, Shiori, Makeev, Vsevolod, Marchionni, Luigi, Medvedeva, Yulia A., Minoda, Aki, Müller, Ferenc, Muñoz-Aguirre, Manuel, Murata, Mitsuyoshi, Nishiyori, Hiromi, Nitta, Kazuhiro R., Noguchi, Shuhei, Noro, Yukihiko, Nurtdinov, Ramil N., Okazaki, Yasushi, Orlando, Valerio, Paquette, Denis, Parr, Callum J.C., Rackham, Owen J.L., Rizzu, Patrizia, Sánchez Martinez, Diego Fernando, Sandelin, Albin, Sanjana, Pillay, Semple, Colin A.M., Shibayama, Youtaro, Sivaraman, Divya M., Szumowski, Suzannah C., Tagami, Michihira, Taylor, Martin S., Terao, Chikashi, Thodberg, Malte, Thongjuea, Supat, Tripathi, Vidisha, Ulitsky, Igor, Verardo, Roberto, Vorontsov, Ilya E., Yamamoto, Chinatsu, Baillie, J. Kenneth, Forrest, Alistair R.R., Guigó, Roderic, Hoffman, Michael, Hon, Chungchau, Kasukawa, Takeya, Kauppinen, Sakari, Kere, Jura, Lenhard, Boris, Schneider, Claudio, Suzuki, Harukazu, Yagi, Ken, de Hoon, Michiel J.L., Shin, Jay W., and Carninci, Piero

Abstract

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2., Genome Research, 30 (7), ISSN:1088-9051, ISSN:1549-5469

Published
2020

13. Ynolate chemistry. reaction of a silylynolate with aziridines leading to gamma-lactams

Author

Iwamoto, Keiji, Kojima, Miki, Chatani, Naoto, and Murai, Shinji

Subjects
Chemistry, Organic -- Research, Antibiotics -- Structure-activity relationships, Ring formation (Chemistry) -- Methods, Biological sciences, Chemistry
Abstract

The five-membered lactams are generated by reacting a silylynolate with N-tosyl aziridines via ring-opening ketenylation of aziridines by silylynolate. The gamma-lactams are derived from alpha-silylated lactam enolates following aldehyde treatment.

Published
2001

14. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Author

Ramilowski, Jordan A., primary, Yip, Chi Wai, additional, Agrawal, Saumya, additional, Chang, Jen-Chien, additional, Ciani, Yari, additional, Kulakovskiy, Ivan V., additional, Mendez, Mickaël, additional, Ooi, Jasmine Li Ching, additional, Ouyang, John F., additional, Parkinson, Nick, additional, Petri, Andreas, additional, Roos, Leonie, additional, Severin, Jessica, additional, Yasuzawa, Kayoko, additional, Abugessaisa, Imad, additional, Akalin, Altuna, additional, Antonov, Ivan V., additional, Arner, Erik, additional, Bonetti, Alessandro, additional, Bono, Hidemasa, additional, Borsari, Beatrice, additional, Brombacher, Frank, additional, Cameron, Christopher J.F., additional, Cannistraci, Carlo Vittorio, additional, Cardenas, Ryan, additional, Cardon, Melissa, additional, Chang, Howard, additional, Dostie, Josée, additional, Ducoli, Luca, additional, Favorov, Alexander, additional, Fort, Alexandre, additional, Garrido, Diego, additional, Gil, Noa, additional, Gimenez, Juliette, additional, Guler, Reto, additional, Handoko, Lusy, additional, Harshbarger, Jayson, additional, Hasegawa, Akira, additional, Hasegawa, Yuki, additional, Hashimoto, Kosuke, additional, Hayatsu, Norihito, additional, Heutink, Peter, additional, Hirose, Tetsuro, additional, Imada, Eddie L., additional, Itoh, Masayoshi, additional, Kaczkowski, Bogumil, additional, Kanhere, Aditi, additional, Kawabata, Emily, additional, Kawaji, Hideya, additional, Kawashima, Tsugumi, additional, Kelly, S. Thomas, additional, Kojima, Miki, additional, Kondo, Naoto, additional, Koseki, Haruhiko, additional, Kouno, Tsukasa, additional, Kratz, Anton, additional, Kurowska-Stolarska, Mariola, additional, Kwon, Andrew Tae Jun, additional, Leek, Jeffrey, additional, Lennartsson, Andreas, additional, Lizio, Marina, additional, López-Redondo, Fernando, additional, Luginbühl, Joachim, additional, Maeda, Shiori, additional, Makeev, Vsevolod J., additional, Marchionni, Luigi, additional, Medvedeva, Yulia A., additional, Minoda, Aki, additional, Müller, Ferenc, additional, Muñoz-Aguirre, Manuel, additional, Murata, Mitsuyoshi, additional, Nishiyori, Hiromi, additional, Nitta, Kazuhiro R., additional, Noguchi, Shuhei, additional, Noro, Yukihiko, additional, Nurtdinov, Ramil, additional, Okazaki, Yasushi, additional, Orlando, Valerio, additional, Paquette, Denis, additional, Parr, Callum J.C., additional, Rackham, Owen J.L., additional, Rizzu, Patrizia, additional, Martinez, Diego Fernando Sánchez, additional, Sandelin, Albin, additional, Sanjana, Pillay, additional, Semple, Colin A.M., additional, Shibayama, Youtaro, additional, Sivaraman, Divya M., additional, Suzuki, Takahiro, additional, Szumowski, Suzannah C., additional, Tagami, Michihira, additional, Taylor, Martin S., additional, Terao, Chikashi, additional, Thodberg, Malte, additional, Thongjuea, Supat, additional, Tripathi, Vidisha, additional, Ulitsky, Igor, additional, Verardo, Roberto, additional, Vorontsov, Ilya E., additional, Yamamoto, Chinatsu, additional, Young, Robert S., additional, Baillie, J. Kenneth, additional, Forrest, Alistair R.R., additional, Guigó, Roderic, additional, Hoffman, Michael M., additional, Hon, Chung Chau, additional, Kasukawa, Takeya, additional, Kauppinen, Sakari, additional, Kere, Juha, additional, Lenhard, Boris, additional, Schneider, Claudio, additional, Suzuki, Harukazu, additional, Yagi, Ken, additional, de Hoon, Michiel J.L., additional, Shin, Jay W., additional, and Carninci, Piero, additional

Published
2020
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24. Data Descriptor : FANTOM5 CAGE profiles of human and mouse samples

Author

Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru, Kaiho, Ai, Kanamori-Katayama, Mutsumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakazato, Kenichi, Ninomiya, Noriko, Nishiyori-Sueki, Hiromi, Noma, Shohei, Saijyo, Eri, Saka, Akiko, Sakai, Mizuho, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Watanabe, Shoko, Yoshida, Shigehiro, Arner, Peter, Axton, Richard A., Babina, Magda, Baillie, J. Kenneth, Barnett, Timothy C., Beckhouse, Anthony G., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Carlisle, Ailsa J., Clevers, Hans C., Davis, Carrie A., Detmar, Michael, Dohi, Taeko, Edge, Albert S. B., Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Farach-Carson, Mary C., Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley M., Fujita, Rie, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gingeras, Thomas, Goldowitz, Daniel, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Hasegawa, Yuki, Herlyn, Meenhard, Heutink, Peter, Hitchens, Kelly J., Hume, David A., Ikawa, Tomokatsu, Ishizu, Yuri, Kai, Chieko, Kawamoto, Hiroshi, Kawamura, Yuki I., Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klein, Sarah, Klinken, S. Peter, Knox, Alan J., Kojima, Soichi, Koseki, Haruhiko, Koyasu, Shigeo, Lee, Weonju, Lennartsson, Andreas, Mackay-sim, Alan, Mejhert, Niklas, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Morris, Kelly J., Motohashi, Hozumi, Mummery, Christine L., Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Pradhan-Bhatt, Swati, Qin, Xian-Yang, Rehli, Michael, Rizzu, Patrizia, Roy, Sugata, Sajantila, Antti, Sakaguchi, Shimon, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schmidl, Christian, Schneider, Claudio, Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sheng, Guojun, Shin, Jay W., Sugiyama, Daisuke, Sugiyama, Takaaki, Summers, Kim M., Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tomoiu, Andru, Toyoda, Hiroo, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Yamaguchi, Yoko, Yamamoto, Masayuki, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Yonekura, Yohei, Zhang, Peter G., Zucchelli, Silvia, Abugessaisa, Imad, Arner, Erik, Harshbarger, Jayson, Kondo, Atsushi, Lassmann, Timo, Lizio, Marina, Sahin, Serkan, Sengstag, Thierry, Severin, Jessica, Shimoji, Hisashi, Suzuki, Masanori, Suzuki, Harukazu, Kawai, Jun, Kondo, Naoto, Itoh, Masayoshi, Daub, Carsten O., Kasukawa, Takeya, Kawaji, Hideya, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Medicum, University of Helsinki, Forensic Medicine, Department of Forensic Medicine, and PaleOmics Laboratory

Subjects
ENHANCERS, MAMMALIAN-CELLS, UCSC GENOME BROWSER, VISUALIZATION, UPDATE, GROWTH, IN-VITRO, TRANSCRIPTION, 3111 Biomedicine, ATLAS, GENE-EXPRESSION
Abstract

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 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.

Published
2017

25. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Author

Hurst, Laurence D., Ghanbarian, Avazeh T., Forrest, Alistair R R, Huminiecki, Lukasz, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J L, Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Baker, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan, Swati Bhatt, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun ichi, Geijtenbeek, Teunis B., Gibson, Andrew, Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori, Mutsumi Katayama, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay, Alan sim, Manabe, Riichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao, Sayaka Sato, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada, Mariko Hatakeyama, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 't Hoen, Peter A C, Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Suzan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, Hayashizaki, Yoshihide, Hubrecht Institute for Developmental Biology and Stem Cell Research, Barton, Nick H, Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Male, Medical and Health Sciences, Essential, Models, Gene expression, Databases, Genetic, Biology (General), Non-U.S. Gov't, X-linked recessive inheritance, X chromosome, Cells, Cultured, Regulation of gene expression, Genetics, Sex Characteristics, Dosage compensation, Tumor, Cultured, Genes, Essential, Genome, Agricultural and Biological Sciences(all), General Neuroscience, Research Support, Non-U.S. Gov't, Biological Sciences, Organ Specificity, Female, General Agricultural and Biological Sciences, Research Article, Human, X Chromosome, Retroelements, QH301-705.5, Neuroscience(all), 1.1 Normal biological development and functioning, Cells, Down-Regulation, Biology, Research Support, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Cell Line, Databases, Genetic, Species Specificity, Underpinning research, Immunology and Microbiology(all), Cell Line, Tumor, Journal Article, Animals, Humans, Comparative Study, Gene, Chromosomes, Human, X, Autosome, General Immunology and Microbiology, Agricultural and Veterinary Sciences, Models, Genetic, Biochemistry, Genetics and Molecular Biology(all), Genome, Human, Mammalian, Human Genome, Chromosomes, Mammalian, Genes, Gene Expression Regulation, Human genome, FANTOM consortium, Developmental Biology
Abstract

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution., Laurence Hurst, Lukasz Huminiecki, and the FANTOM5 consortium propose a new explanation for the peculiar expression properties of genes on the human X chromosome, based on the premise that very high expression levels cannot be achieved on a haploid-expressed chromosome., Author Summary Genes located on the human X chromosome are not a random mix of genes: they tend to be expressed in relatively few tissues or are specific for a particular set of tissues, e.g., brain regions. Prior attempts to explain this skewed gene content have hypothesized that the X chromosome might be peculiar because it has to balance mutations that are advantageous to one sex but deleterious to the other, or because it has to shut down during the process of sperm manufacture in males. Here we suggest and test a third possible explanation: that genes on the X chromosome are limited in their transcription levels and thus tend to be genes that are lowly or specifically expressed. We consider the suggestion that since these genes can only be expressed from one chromosome, as males only have one X, the ability to express a gene at very high rates is limited owing to potential transcriptional traffic jams. As predicted, we find that human X-located genes have maximal expression rates far below that of genes residing on autosomes. When we look at genes that have moved onto or off the X chromosome during recent evolution, we find the maximal expression is higher when not on the X chromosome. We also find that X-located genes that are relatively highly expressed are not able to increase their expression level further. Our model explains both the enrichment for tissue specificity and the paucity of certain tissues with X-located genes. Genes underrepresented on the X are either expressed in many tissues—such genes tend to have high maximal expression—or are from tissues that require a lot of transcription (e.g., fast secreting tissues like the liver). Just as many of the findings cannot be explained by the two earlier models, neither can the traffic jam model explain all the peculiar features of the genes found on the X chromosome. Indeed, we find evidence of a reproduction-related bias in X-located genes, even after allowing for the traffic jam problem.

Published
2015

26. 脳卒中後片麻痺患者に対する，反復性経頭蓋磁気刺激と集中的リハビリテーションの併用療法：歩行機能および下肢運動機能への影響について (原著)

Author

Yoshida, Yutaka, Watanabe, Shigehito, Kakuda, Wataru, Ono, Akiko, Kojima, Miki, Sato, Toshihiro, Ikehara, Eri, Harashima, Hiroaki, and Abo, Masahiro

Subjects
liver failure, hepatitis C cirrhosis, hepatocellular carcinoma, living donor liver transplantation
Abstract

article

Published
2011

27. Activation of Circularly Permutated beta-Lactamase Tethered to Antibody Domains by Specific Small Molecules

Author

Kojima, Miki, Iwai, Hiroto, Dong, Jinhua, Lim, Shean-Lee, Ito, Shigekazu, Okumura, Koichi, Ihara, Masaki, and Ueda, Hiroshi

Subjects
Pharmacology, Expression vector, biology, Chemistry, Effector, Organic Chemistry, Allosteric regulation, Biomedical Engineering, Imidazoles, Pharmaceutical Science, Active site, Bioengineering, Nitro Compounds, Fusion protein, beta-Lactamases, Neonicotinoids, Antigen, Biochemistry, biology.protein, Antibody, Linker, Immunoglobulin Fragments, Biotechnology
Abstract

Regulation of enzyme activity either by its substrates or by effectors is generally known as allostery. However, it has been considered hard to alter its effector specificity, despite its potential utility as a sensitive molecular sensor. To this end, we made fusion proteins consisting of an antibody variable region Fv and a circularly permutated TEM-1 β-lactamase cpBLA. Two expression vectors encoding Fv-cpBLA with different antigen specificities were made, in which cpBLA was inserted into the linker region of the single chain Fv that specifically binds either bone-related disease marker osteocalcin (BGP) C-terminal peptide or neonicotinoid insecticide imidacloprid (ICP). The cpBLA having new termini near the active site was activated upon binding with its cognate antigen, owing to the stabilization of tethered Fv by bound antigen. As a result, both Fv-cpBLA showed specific antigen binding as well as antigen-induced enhancement in catalytic activity. Moreover, E. coli cells expressing Fv-cpBLA for ICP showed ICP concentration dependent growth in the medium containing ampicillin. The system was also applied to select for Fv-cpBLA linker mutants that confer faster growth. This will be the first of an antibody-based small molecule indicator enzyme.

Published
2011

28. FANTOM5 CAGE profiles of human and mouse samples

Author

Noguchi, Shuhei, primary, Arakawa, Takahiro, additional, Fukuda, Shiro, additional, Furuno, Masaaki, additional, Hasegawa, Akira, additional, Hori, Fumi, additional, Ishikawa-Kato, Sachi, additional, Kaida, Kaoru, additional, Kaiho, Ai, additional, Kanamori-Katayama, Mutsumi, additional, Kawashima, Tsugumi, additional, Kojima, Miki, additional, Kubosaki, Atsutaka, additional, Manabe, Ri-ichiroh, additional, Murata, Mitsuyoshi, additional, Nagao-Sato, Sayaka, additional, Nakazato, Kenichi, additional, Ninomiya, Noriko, additional, Nishiyori-Sueki, Hiromi, additional, Noma, Shohei, additional, Saijyo, Eri, additional, Saka, Akiko, additional, Sakai, Mizuho, additional, Simon, Christophe, additional, Suzuki, Naoko, additional, Tagami, Michihira, additional, Watanabe, Shoko, additional, Yoshida, Shigehiro, additional, Arner, Peter, additional, Axton, Richard A., additional, Babina, Magda, additional, Baillie, J. Kenneth, additional, Barnett, Timothy C., additional, Beckhouse, Anthony G., additional, Blumenthal, Antje, additional, Bodega, Beatrice, additional, Bonetti, Alessandro, additional, Briggs, James, additional, Brombacher, Frank, additional, Carlisle, Ailsa J., additional, Clevers, Hans C., additional, Davis, Carrie A., additional, Detmar, Michael, additional, Dohi, Taeko, additional, Edge, Albert S.B., additional, Edinger, Matthias, additional, Ehrlund, Anna, additional, Ekwall, Karl, additional, Endoh, Mitsuhiro, additional, Enomoto, Hideki, additional, Eslami, Afsaneh, additional, Fagiolini, Michela, additional, Fairbairn, Lynsey, additional, Farach-Carson, Mary C., additional, Faulkner, Geoffrey J., additional, Ferrai, Carmelo, additional, Fisher, Malcolm E., additional, Forrester, Lesley M., additional, Fujita, Rie, additional, Furusawa, Jun-ichi, additional, Geijtenbeek, Teunis B., additional, Gingeras, Thomas, additional, Goldowitz, Daniel, additional, Guhl, Sven, additional, Guler, Reto, additional, Gustincich, Stefano, additional, Ha, Thomas J., additional, Hamaguchi, Masahide, additional, Hara, Mitsuko, additional, Hasegawa, Yuki, additional, Herlyn, Meenhard, additional, Heutink, Peter, additional, Hitchens, Kelly J., additional, Hume, David A., additional, Ikawa, Tomokatsu, additional, Ishizu, Yuri, additional, Kai, Chieko, additional, Kawamoto, Hiroshi, additional, Kawamura, Yuki I., additional, Kempfle, Judith S., additional, Kenna, Tony J., additional, Kere, Juha, additional, Khachigian, Levon M., additional, Kitamura, Toshio, additional, Klein, Sarah, additional, Klinken, S. Peter, additional, Knox, Alan J., additional, Kojima, Soichi, additional, Koseki, Haruhiko, additional, Koyasu, Shigeo, additional, Lee, Weonju, additional, Lennartsson, Andreas, additional, Mackay-sim, Alan, additional, Mejhert, Niklas, additional, Mizuno, Yosuke, additional, Morikawa, Hiromasa, additional, Morimoto, Mitsuru, additional, Moro, Kazuyo, additional, Morris, Kelly J., additional, Motohashi, Hozumi, additional, Mummery, Christine L., additional, Nakachi, Yutaka, additional, Nakahara, Fumio, additional, Nakamura, Toshiyuki, additional, Nakamura, Yukio, additional, Nozaki, Tadasuke, additional, Ogishima, Soichi, additional, Ohkura, Naganari, additional, Ohno, Hiroshi, additional, Ohshima, Mitsuhiro, additional, Okada-Hatakeyama, Mariko, additional, Okazaki, Yasushi, additional, Orlando, Valerio, additional, Ovchinnikov, Dmitry A., additional, Passier, Robert, additional, Patrikakis, Margaret, additional, Pombo, Ana, additional, Pradhan-Bhatt, Swati, additional, Qin, Xian-Yang, additional, Rehli, Michael, additional, Rizzu, Patrizia, additional, Roy, Sugata, additional, Sajantila, Antti, additional, Sakaguchi, Shimon, additional, Sato, Hiroki, additional, Satoh, Hironori, additional, Savvi, Suzana, additional, Saxena, Alka, additional, Schmidl, Christian, additional, Schneider, Claudio, additional, Schulze-Tanzil, Gundula G., additional, Schwegmann, Anita, additional, Sheng, Guojun, additional, Shin, Jay W., additional, Sugiyama, Daisuke, additional, Sugiyama, Takaaki, additional, Summers, Kim M., additional, Takahashi, Naoko, additional, Takai, Jun, additional, Tanaka, Hiroshi, additional, Tatsukawa, Hideki, additional, Tomoiu, Andru, additional, Toyoda, Hiroo, additional, van de Wetering, Marc, additional, van den Berg, Linda M., additional, Verardo, Roberto, additional, Vijayan, Dipti, additional, Wells, Christine A., additional, Winteringham, Louise N., additional, Wolvetang, Ernst, additional, Yamaguchi, Yoko, additional, Yamamoto, Masayuki, additional, Yanagi-Mizuochi, Chiyo, additional, Yoneda, Misako, additional, Yonekura, Yohei, additional, Zhang, Peter G., additional, Zucchelli, Silvia, additional, Abugessaisa, Imad, additional, Arner, Erik, additional, Harshbarger, Jayson, additional, Kondo, Atsushi, additional, Lassmann, Timo, additional, Lizio, Marina, additional, Sahin, Serkan, additional, Sengstag, Thierry, additional, Severin, Jessica, additional, Shimoji, Hisashi, additional, Suzuki, Masanori, additional, Suzuki, Harukazu, additional, Kawai, Jun, additional, Kondo, Naoto, additional, Itoh, Masayoshi, additional, Daub, Carsten O., additional, Kasukawa, Takeya, additional, Kawaji, Hideya, additional, Carninci, Piero, additional, Forrest, Alistair R.R., additional, and Hayashizaki, Yoshihide, additional

Published
2017
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29. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

Author

Valen, Eivind, Pascarella, Giovanni, Chalk, Alistair, Maeda, Norihiro, Kojima, Miki, Kawazu, Chika, Murata, Mitsuyoshi, Nishiyori, Hiromi, Lazarevic, Dejan, Motti, Dario, Marstrand, Troels Torben, Tang, Man-Hung Eric, Xiaobei Zhao, Krogh, Anders, Winther, Ole, Arakawa, Takahiro, Kawai, Jun, Wells, Christine, Daub, Carsten, Harbers, Matthias, Hayashizaki, Yoshihide, Gustincich, Stefano, Sandelin, Albin, and Carninci, Piero

Subjects
Messenger RNA -- Analysis, Gene expression -- Analysis, Genetic transcription -- Research, Sea horses -- Analysis, Health
Published
2009

30. Quotient of cerebrospinal fluid/serum immunoglobulin G as a predictive factor for non-responders to intravenous methylprednisolone therapy in patients with relapsing neuromyelitis optica spectrum disorder: Implication for early initiation of plasmapheresi

Author

Oji, Satoru, primary, Tanaka, Satoru, additional, Kojima, Miki, additional, Fukaura, Hikoaki, additional, Mori, Masahiro, additional, Takahashi, Toshiyuki, additional, Fujihara, Kazuo, additional, and Nomura, Kyoichi, additional

Published
2016
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31. Telomerase Reverse Transcriptase Regulates microRNAs

Author

Lassmann, Timo, primary, Maida, Yoshiko, additional, Tomaru, Yasuhiro, additional, Yasukawa, Mami, additional, Ando, Yoshinari, additional, Kojima, Miki, additional, Kasim, Vivi, additional, Simon, Christophe, additional, Daub, Carsten, additional, Carninci, Piero, additional, Hayashizaki, Yoshihide, additional, and Masutomi, Kenkichi, additional

Published
2015
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32. Interdependence in the parent and adolescent child relationship

Author

Kurokawa, Masaru, Hayashi, Haruo, Kojima, Miki, and 国立情報学研究所

Subjects
Fate-control, Behavior-control, parent-child relationship, interdependence, outcome matrix, Reflexive-control
Abstract

On the basis of Thibaut and Kelley's interdependence theory, this study attempted to clarify the structure of parent-child relationship, one of the most vital personal relationships. We created three hypothetical decision-making situations (vignettes) that would occur for the majority of relationships between parents and their adolescent children. Each situation can be conceptually described in terms of 2×2 matrix format, in which both a parent and a child have two behavioral alternatives to choose from. The subjects were first graders at junior- and senior-high school and their parents. Both the parent and the child expressed their own preferences for each of the possible four combinations of the behavioral alternatives as to the three vignettes. Control scores were calculated for reflexive control (RC), fate control (FC), and behavior control (BC). Results indicated that; (1) Interdependence patterns were quite stable across the three situations, suggesting that parent and child are interdependent more at the dispositional than the given matrix level; (2) The parents showed consistent interdependence patterns with almost no RC, but a high degree of BC. High school children, however, indicated much higher degrees of RC and FC compared with Junior High school children. These results suggest that children become more self-interested and try to exert their control as they get older, while the parents will basically be happy as long as it corresponds with what the children want to do.

Published
1992

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

Author

Itoh, Masayoshi, primary, Kojima, Miki, additional, Nagao-Sato, Sayaka, additional, Saijo, Eri, additional, Lassmann, Timo, additional, Kanamori-Katayama, Mutsumi, additional, Kaiho, Ai, additional, Lizio, Marina, additional, Kawaji, Hideya, additional, Carninci, Piero, additional, Forrest, Alistair R. R., additional, and Hayashizaki, Yoshihide, additional

Published
2012
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36. Unamplified cap analysis of gene expression on a single-molecule sequencer

Author

Kanamori-Katayama, Mutsumi, primary, Itoh, Masayoshi, additional, Kawaji, Hideya, additional, Lassmann, Timo, additional, Katayama, Shintaro, additional, Kojima, Miki, additional, Bertin, Nicolas, additional, Kaiho, Ai, additional, Ninomiya, Noriko, additional, Daub, Carsten O., additional, Carninci, Piero, additional, Forrest, Alistair R.R., additional, and Hayashizaki, Yoshihide, additional

Published
2011
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43. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

Author

Valen, Eivind, primary, Pascarella, Giovanni, additional, Chalk, Alistair, additional, Maeda, Norihiro, additional, Kojima, Miki, additional, Kawazu, Chika, additional, Murata, Mitsuyoshi, additional, Nishiyori, Hiromi, additional, Lazarevic, Dejan, additional, Motti, Dario, additional, Marstrand, Troels Torben, additional, Tang, Man-Hung Eric, additional, Zhao, Xiaobei, additional, Krogh, Anders, additional, Winther, Ole, additional, Arakawa, Takahiro, additional, Kawai, Jun, additional, Wells, Christine, additional, Daub, Carsten, additional, Harbers, Matthias, additional, Hayashizaki, Yoshihide, additional, Gustincich, Stefano, additional, Sandelin, Albin, additional, and Carninci, Piero, additional

Published
2008
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47. CAGE: cap analysis of gene expression

Author

Kodzius, Rimantas, primary, Kojima, Miki, additional, Nishiyori, Hiromi, additional, Nakamura, Mari, additional, Fukuda, Shiro, additional, Tagami, Michihira, additional, Sasaki, Daisuke, additional, Imamura, Kengo, additional, Kai, Chikatoshi, additional, Harbers, Matthias, additional, Hayashizaki, Yoshihide, additional, and Carninci, Piero, additional

Published
2006
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50. The role of interface framework residues in determining antibody VH/VL interaction strength and antigen-binding affinity.

Author

Masuda, Kenji, Sakamoto, Kenzo, Kojima, Miki, Aburatani, Takahide, Ueda, Takuya, and Ueda, Hiroshi

Subjects
ANTIGEN-antibody reactions, BACTERIOPHAGES, IMMUNOGLOBULIN G, SURFACE plasmon resonance, IMMUNOGLOBULINS, IMMUNOASSAY, MUTAGENESIS
Abstract

While many antibodies with strong antigen-binding affinity have stable variable regions with a strong antibody heavy chain variable region fragment (VH)/antibody light chain variable region fragment (VL) interaction, the anti-lysozyme IgG HyHEL-10 has a fairly strong affinity, yet a very weak VH/VL interaction strength, in the absence of antigen. To investigate the possible relationship between antigen-binding affinity and VH/VL interaction strength, a novel phage display system that can switch two display modes was employed. We focused on the two framework region 2 regions of the HyHEL-10 VH and VL, facing each other at the domain interface, and a combinatorial library was made in which each framework region 2 residue was mixed with that of D1.3, which has a far stronger VH/VL interaction. The phagemid library, encoding VH gene 7 and VL amber codon gene 9, was used to transform TG-1 ( sup+), and the phages displaying functional variable regions were selected. The selected phages were then used to infect a nonsuppressing strain, and the culture supernatant containing VH-displaying phages and soluble VL fragment was used to evaluate the VH/VL interaction strength. The results clearly showed the existence of a key framework region 2 residue (H39) that strongly affects VH/VL interaction strength, and a marked positive correlation between the antigen-binding affinity and the VH/VL interaction, especially in the presence of a set of particular VL residues. The effect of the H39 mutation on the wild-type variable region was also confirmed by a SPR biosensor as a several-fold increase in antigen-binding affinity owing to an increased association rate, while a slight decrease was observed for the single-chain variable region. [ABSTRACT FROM AUTHOR]

Published
2006
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