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1. DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells

Author

Shinriki, Satoru, Hirayama, Mayumi, Nagamachi, Akiko, Yokoyama, Akihiko, Kawamura, Takeshi, Kanai, Akinori, Kawai, Hidehiko, Iwakiri, Junichi, Liu, Rin, Maeshiro, Manabu, Tungalag, Saruul, Tasaki, Masayoshi, Ueda, Mitsuharu, Tomizawa, Kazuhito, Kataoka, Naoyuki, Ideue, Takashi, Suzuki, Yutaka, Asai, Kiyoshi, Tani, Tokio, Inaba, Toshiya, and Matsui, Hirotaka

Published
2022
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4. Generalized Centroid Estimators in Bioinformatics

Author

Hamada, Michiaki, Kiryu, Hisanori, Iwasaki, Wataru, and Asai, Kiyoshi

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Learning
Abstract

In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which representmany fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics., Comment: 35 pages. This is a corrected version of the published paper: PLoS ONE 6(2):e16450, 2011. The original version is available from http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016450

Published
2013

6. Approximating Incomplete Kernel Matrices by the em Algorithm

Author

Tsuda, Koji, Akaho, Shotaro, and Asai, Kiyoshi

Subjects
Computer Science - Learning, I2.6, I5.2
Abstract

In biological data, it is often the case that observed data are available only for a subset of samples. When a kernel matrix is derived from such data, we have to leave the entries for unavailable samples as missing. In this paper, we make use of a parametric model of kernel matrices, and estimate missing entries by fitting the model to existing entries. The parametric model is created as a set of spectral variants of a complete kernel matrix derived from another information source. For model fitting, we adopt the em algorithm based on the information geometry of positive definite matrices. We will report promising results on bacteria clustering experiments using two marker sequences: 16S and gyrB., Comment: 17 pages, 4 figures

Published
2002

7. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Author

Katayama, Toshiaki, Wilkinson, Mark D, Micklem, Gos, Kawashima, Shuichi, Yamaguchi, Atsuko, Nakao, Mitsuteru, Yamamoto, Yasunori, Okamoto, Shinobu, Oouchida, Kenta, Chun, Hong-Woo, Aerts, Jan, Afzal, Hammad, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Belleau, Francois, Bolleman, Jerven, Bonnal, Raoul JP, Chapman, Brad, Cock, Peter JA, Eriksson, Tore, Gordon, Paul MK, Goto, Naohisa, Hayashi, Kazuhiro, Horn, Heiko, Ishiwata, Ryosuke, Kaminuma, Eli, Kasprzyk, Arek, Kawaji, Hideya, Kido, Nobuhiro, Kim, Young Joo, Kinjo, Akira R, Konishi, Fumikazu, Kwon, Kyung-Hoon, Labarga, Alberto, Lamprecht, Anna-Lena, Lin, Yu, Lindenbaum, Pierre, McCarthy, Luke, Morita, Hideyuki, Murakami, Katsuhiko, Nagao, Koji, Nishida, Kozo, Nishimura, Kunihiro, Nishizawa, Tatsuya, Ogishima, Soichi, Ono, Keiichiro, Oshita, Kazuki, Park, Keun-Joon, Prins, Pjotr, Saito, Taro L, Samwald, Matthias, Satagopam, Venkata P, Shigemoto, Yasumasa, Smith, Richard, Splendiani, Andrea, Sugawara, Hideaki, Taylor, James, Vos, Rutger A, Withers, David, Yamasaki, Chisato, Zmasek, Christian M, Kawamoto, Shoko, Okubo, Kosaku, Asai, Kiyoshi, and Takagi, Toshihisa

Abstract

Abstract Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Published
2013

8. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

Author

Katayama, Toshiaki, Arakawa, Kazuharu, Nakao, Mitsuteru, Ono, Keiichiro, Aoki-Kinoshita, Kiyoko F, Yamamoto, Yasunori, Yamaguchi, Atsuko, Kawashima, Shuichi, Chun, Hong-Woo, Aerts, Jan, Aranda, Bruno, Barboza, Lord, Bonnal, Raoul JP, Bruskiewich, Richard, Bryne, Jan C, Fernández, José M, Funahashi, Akira, Gordon, Paul MK, Goto, Naohisa, Groscurth, Andreas, Gutteridge, Alex, Holland, Richard, Kano, Yoshinobu, Kawas, Edward A, Kerhornou, Arnaud, Kibukawa, Eri, Kinjo, Akira R, Kuhn, Michael, Lapp, Hilmar, Lehvaslaiho, Heikki, Nakamura, Hiroyuki, Nakamura, Yasukazu, Nishizawa, Tatsuya, Nobata, Chikashi, Noguchi, Tamotsu, Oinn, Thomas M, Okamoto, Shinobu, Owen, Stuart, Pafilis, Evangelos, Pocock, Matthew, Prins, Pjotr, Ranzinger, René, Reisinger, Florian, Salwinski, Lukasz, Schreiber, Mark, Senger, Martin, Shigemoto, Yasumasa, Standley, Daron M, Sugawara, Hideaki, Tashiro, Toshiyuki, Trelles, Oswaldo, Vos, Rutger A, Wilkinson, Mark D, York, William, Zmasek, Christian M, Asai, Kiyoshi, and Takagi, Toshihisa

Abstract

Abstract Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

Published
2010

14. The effect of γ phosphate modified deoxynucleotide substrates on PCR activity and fidelity

Author

Hashiya, Fumitaka, primary, Murase, Hirotaka, additional, Chandela, Akash, additional, Hiraoka, Haruka, additional, Inagaki, Masahito, additional, Nakashima, Yuko, additional, Abe, Naoko, additional, Nakamura, Mayu, additional, Terai, Goro, additional, Kimura, Yasuaki, additional, Ando, Kaori, additional, Oka, Natsuhisa, additional, Asai, Kiyoshi, additional, and Abe, Hiroshi, additional

Published
2023
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16. A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures

Author

Sato, Kengo, Hamada, Michiaki, Mituyama, Toutai, Asai, Kiyoshi, Sakakibara, Yasubumi, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Salzberg, Steven L., editor, and Warnow, Tandy, editor

Published
2009
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17. Stem Kernels for RNA Sequence Analyses

Author

Sakakibara, Yasubumi, Asai, Kiyoshi, Sato, Kengo, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Hochreiter, Sepp, editor, and Wagner, Roland, editor

Published
2007
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20. A New Variational Framework for Rigid-Body Alignment

Author

Kato, Tsuyoshi, Tsuda, Koji, Tomii, Kentaro, Asai, Kiyoshi, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Fred, Ana, editor, Caelli, Terry M., editor, Duin, Robert P. W., editor, Campilho, Aurélio C., editor, and de Ridder, Dick, editor

Published
2004
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21. GA-Based Inference of Euler Angles for Single Particle Analysis

Author

Saeki, Shusuke, Asai, Kiyoshi, Takahashi, Katsutoshi, Ueno, Yutaka, Isono, Katsunori, Iba, Hitoshi, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Cantú-Paz, Erick, editor, Foster, James A., editor, Deb, Kalyanmoy, editor, Davis, Lawrence David, editor, Roy, Rajkumar, editor, O’Reilly, Una-May, editor, Beyer, Hans-Georg, editor, Standish, Russell, editor, Kendall, Graham, editor, Wilson, Stewart, editor, Harman, Mark, editor, Wegener, Joachim, editor, Dasgupta, Dipankar, editor, Potter, Mitch A., editor, Schultz, Alan C., editor, Dowsland, Kathryn A., editor, Jonoska, Natasha, editor, and Miller, Julian, editor

Published
2003
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22. DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells

Author

Shinriki, Satoru, primary, Hirayama, Mayumi, additional, Nagamachi, Akiko, additional, Yokoyama, Akihiko, additional, Kawamura, Takeshi, additional, Kanai, Akinori, additional, Kawai, Hidehiko, additional, Iwakiri, Junichi, additional, Liu, Rin, additional, Maeshiro, Manabu, additional, Tungalag, Saruul, additional, Tasaki, Masayoshi, additional, Ueda, Mitsuharu, additional, Tomizawa, Kazuhito, additional, Kataoka, Naoyuki, additional, Ideue, Takashi, additional, Suzuki, Yutaka, additional, Asai, Kiyoshi, additional, Tani, Tokio, additional, Inaba, Toshiya, additional, and Matsui, Hirotaka, additional

Published
2022
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23. Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters

Author

Sakuraba, Shun, Iwakiri, Junichi, Hamada, Michiaki, Kameda, Tomoshi, Tsuji, Genichiro, Kimura, Yasuaki, Abe, Hiroshi, and Asai, Kiyoshi

Subjects
Quantitative Biology::Biomolecules
Abstract

Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases.

Published
2020

31. A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila

Author

Saito, Kuniaki, Inagaki, Sachi, Mituyama, Toutai, Kawamura, Yoshinori, Ono, Yukiteru, Sakota, Eri, Kotani, Hazuki, Asai, Kiyoshi, Siomi, Haruhiko, and Siomi, Mikiko C.

Subjects
Physiological aspects, Research, Genetic aspects, Retrotransposons -- Physiological aspects -- Genetic aspects -- Research, Drosophila -- Genetic aspects -- Research -- Physiological aspects, Germ cells -- Genetic aspects -- Physiological aspects -- Research, Gene silencing -- Research -- Genetic aspects -- Physiological aspects, Messenger RNA -- Physiological aspects -- Genetic aspects -- Research, Somatic cells -- Genetic aspects -- Research -- Physiological aspects, Genetic regulation -- Research -- Genetic aspects -- Physiological aspects
Abstract

Genetic studies have shown that piwi and aub are essential in germ-line stem-cell self-renewal and pole-cell formation, respectively (11,12). Mutations introduced into piwi and aub cause de-repression of retro-transposons and [...], PIWI-interacting RNAs (piRNAs) silence retrotransposons in Drosophila germ lines by associating with the PIWI proteins Argonaute 3 (AGO3), Aubergine (Aub) and Piwi (1,2). piRNAs in Drosophila are produced from intergenic repetitive genes and piRNA clusters by two systems: the primary processing pathway and the amplification loop (1-7). The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner (3,4,8). However, primary piRNA processing remains elusive. Here we analysed piRNA processing in a Drosophila ovarian somatic cell line where Piwi, but not Aub or AGO3, is expressed; thus, only the primary piRNAs exist. In addition to flamenco, a Piwi-specificpiRNA cluster (3), traffic jam (tj) (9), a large Maf gene, was determined as a new piRNA cluster. piRNAs arising from tj correspond to the untranslated regions of tj messenger RNA and are sense-oriented. piRNA loading on to Piwi may occur in the cytoplasm. Zucchini (10), a gene encoding a putative cytoplasmic nuclease, is required for tj-derived piRNA production. In tj and piwi mutant ovaries, somatic cells fail to intermingle with germ cells and Fasciclin III is overexpressed. Loss of tj abolishes Piwi expression in gonadal somatic cells. Thus, in gonadal somatic cells, tj gives rise simultaneously to two different molecules: the TJ protein, which activates Piwi expression, and piRNAs, which define the Piwi targets for silencing.

Published
2009

33. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

Author

Kawamura, Yoshinori, Saito, Kuniaki, Kin, Taishin, Ono, Yukiteru, Asai, Kiyoshi, Sunohara, Takafumi, Okada, Tomoko N., Siomi, Mikiko C., and Siomi, Haruhiko

Subjects
Chemical properties, Research, Genetic aspects, Gene silencing -- Research -- Genetic aspects -- Chemical properties, Binding proteins -- Chemical properties -- Genetic aspects -- Research, RNA -- Chemical properties -- Research -- Genetic aspects, Somatic cells -- Genetic aspects -- Chemical properties -- Research
Abstract

RNA silencing is a conserved mechanism in which small RNAs trigger various forms of sequence-specific gene silencing by guiding Argonaute complexes to target RNAs by means of base pairing (1,2). [...]

Published
2008

38. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

Author

Galagan, James E., Calvo, Sarah E., Cuomo, Christina, Ma, Li-Jun, Wortman, Jennifer R., Batzoglou, Serafim, Lee, Su-In, Başturkmen, Meray, Spevak, Christina C., Clutterbuck, John, Kapitonov, Vladimir, Jurka, Jerzy, Scazzocchio, Claudio, Farman, Mark, Butler, Jonathan, Purcell, Seth, Harris, Steve, Braus, Gerhard H., Draht, Oliver, Busch, Silke, D'Enfert, Christophe, Bouchier, Christiane, Goldman, Gustavo H., Bell-Pedersen, Deborah, Griffiths-Jones, Sam, Doonan, John H., Yu, Jaehyuk, Vienken, Kay, Pain, Arnab, Freitag, Michael, Selker, Eric U., Archer, David B., Penalva, Miguel A., Oakley, Berl R., Momany, Michelle, Tanaka, Toshihiro, Kumagai, Toshitaka, Asai, Kiyoshi, Machida, Masayuki, Nierman, William C., Denning, David W., Caddick, Mark, Hynes, Michael, Paoletti, Mathieu, Fischer, Reinhard, Miller, Bruce, Dyer, Paul, Sachs, Matthew S., Osmani, Stephen A., and Birren, Bruce W.

Abstract

Author(s): James E. Galagan (corresponding author) [1]; Sarah E. Calvo [1]; Christina Cuomo [1]; Li-Jun Ma [1]; Jennifer R. Wortman [2]; Serafim Batzoglou [3]; Su-In Lee [3]; Meray Baştürkmen [4]; [...]

Published
2005
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39. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., Pain, Arnab, Anderson, Michael J., Wortman, Jennifer R., Kim, H. Stanley, Arroyo, Javier, Berriman, Matthew, Abe, Keietsu, Archer, David B., Bermejo, Clara, Bennett, Joan, Bowyer, Paul, Chen, Dan, Collins, Matthew, Coulsen, Richard, Davies, Robert, Dyer, Paul S., Farman, Mark, Fedorova, Nadia, Fedorova, Natalie, Feldblyum, Tamara V., Fischer, Reinhard, Fosker, Nigel, Fraser, Audrey, Garcia, Jose L., Garcia, Maria J., Goble, Arlette, Goldman, Gustavo H., Gomi, Katsuya, Griffith-Jones, Sam, Gwilliam, Ryan, Haas, Brian, Haas, Hubertus, Harris, David, Horiuchi, H., Huang, Jiaqi, Humphray, Sean, Jimenez, Javier, Keller, Nancy, Khouri, Hoda, Kitamoto, Katsuhiko, Kobayashi, Tetsuo, Konzack, Sven, Kulkarni, Resham, Kumagai, Toshitaka, Lafton, Anne, Latge, Jean-Paul, Li, Weixi, Lord, Angela, Lu, Charles, Majoros, William H., May, Gregory S., Miller, Bruce L., Mohamoud, Yasmin, Molina, Maria, Monod, Michel, Mouyna, Isabelle, Mulligan, Stephanie, Murphy, Lee, O'Neil, Susan, Paulsen, Ian, Penalva, Miguel A., Pertea, Mihaela, Price, Claire, Pritchard, Bethan L., Quail, Michael A., Rabbinowitsch, Ester, Rawlins, Neil, Rajandream, Marie-Adele, Reichard, Utz, Renauld, Hubert, Robson, Geoffrey D., de Cordoba, Santiago Rodriguez, Rodriguez-Pena, Jose M., Ronning, Catherine M., Rutter, Simon, Salzberg, Steven L., Sanchez, Miguel, Sanchez-Ferrero, Juan C., Saunders, David, Seeger, Kathy, Squares, Rob, Squares, Steven, Takeuchi, Michio, Tekaia, Fredj, Turner, Geoffrey, de Aldana, Carlos R. Vazquez, Weidman, Janice, White, Owen, Woodward, John, Yu, Jae-Hyuk, Fraser, Claire, Galagan, James E., Asai, Kiyoshi, Machida, Masayuki, Hall, Neil, Barrell, Bart, and Denning, David W.

Abstract

Author(s): William C. Nierman (corresponding author) [1]; Arnab Pain [2]; Michael J. Anderson [3]; Jennifer R. Wortman [1]; H. Stanley Kim [1]; Javier Arroyo [4]; Matthew Berriman [2]; Keietsu Abe [...]

Published
2005
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40. Genome sequencing and analysis of Aspergillus oryzae

Author

Machida, Masayuki, Asai, Kiyoshi, Sano, Motoaki, Tanaka, Toshihiro, Kumagai, Toshitaka, Terai, Goro, Kusumoto, Ken-Ichi, Arima, Toshihide, Akita, Osamu, Kashiwagi, Yutaka, Abe, Keietsu, Gomi, Katsuya, Horiuchi, Hiroyuki, Kitamoto, Katsuhiko, Kobayashi, Tetsuo, Takeuchi, Michio, Denning, David W., Galagan, James E., Nierman, William C., Yu, Jiujiang, Archer, David B., Bennett, Joan W., Bhatnagar, Deepak, Cleveland, Thomas E., Fedorova, Natalie D., Gotoh, Osamu, Horikawa, Hiroshi, Hosoyama, Akira, Ichinomiya, Masayuki, Igarashi, Rie, Iwashita, Kazuhiro, Juvvadi, Praveen Rao, Kato, Masashi, Kato, Yumiko, Kin, Taishin, Kokubun, Akira, Maeda, Hiroshi, Maeyama, Noriko, Maruyama, Jun-ichi, Nagasaki, Hideki, Nakajima, Tasuku, Oda, Ken, Okada, Kinya, Paulsen, Ian, Sakamoto, Kazutoshi, Sawano, Toshihiko, Takahashi, Mikio, Takase, Kumiko, Terabayashi, Yasunobu, Wortman, Jennifer R., Yamada, Osamu, Yamagata, Youhei, Anazawa, Hideharu, Hata, Yoji, Koide, Yoshinao, Komori, Takashi, Koyama, Yasuji, Minetoki, Toshitaka, Suharnan, Sivasundaram, Tanaka, Akimitsu, Isono, Katsumi, Kuhara, Satoru, Ogasawara, Naotake, and Kikuchi, Hisashi

Abstract

Author(s): Masayuki Machida (corresponding author) [1]; Kiyoshi Asai [2]; Motoaki Sano [1]; Toshihiro Tanaka [3]; Toshitaka Kumagai [2]; Goro Terai [2, 20]; Ken-Ichi Kusumoto [4]; Toshihide Arima [5]; Osamu Akita [...]

Published
2005
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42. Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing

Author

Iwakiri, Junichi, Tanaka, Kumiko, Chujo, Takeshi, Takakuwa, Hiro, Yamazaki, Tomohiro, Terai, Goro, Asai, Kiyoshi, and Hirose, Tetsuro

Abstract

The mammalian cell nucleus contains dozens of membrane-less nuclear bodies that play significant roles in various aspects of gene expression. Several nuclear bodies are nucleated by specific architectural noncoding RNAs (arcRNAs) acting as structural scaffolds. We have reported that a minor population of cellular RNAs exhibits an unusual semi-extractable feature upon using the conventional procedure of RNA preparation and that needle shearing or heating of cell lysates remarkably improves extraction of dozens of RNAs. Because semi-extractable RNAs, including known arcRNAs, commonly localize in nuclear bodies, this feature may be a hallmark of arcRNAs. Using the semi-extractability of RNA, we performed genome-wide screening of semi-extractable long noncoding RNAs to identify new candidate arcRNAs for arcRNA under hyperosmotic and heat stress conditions. After screening stress-inducible and semi-extractable RNAs, hundreds of readthrough downstream-of-gene (DoG) transcripts over several hundreds of kilobases, many of which were not detected among RNAs prepared by the conventional extraction procedure, were found to be stress-inducible and semi-extractable. We further characterized some of the abundant DoGs and found that stress-inducible transient extension of the 3′-UTR made DoGs semi-extractable. Furthermore, they were localized in distinct nuclear foci that were sensitive to 1,6-hexanediol. These data suggest that semi-extractable DoGs exhibit arcRNA-like features and our semi-extractable RNA-seq is a powerful tool to extensively monitor DoGs that are induced under specific physiological conditions.

Published
2023
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50. The voltage-sensitive sodium channel is a bell-shaped molecule with several cavities

Author

Sato, Chikara, Ueno, Yutaka, Asai, Kiyoshi, Takahashi, Katsutoshi, Sato, Masahiko, Engel, Andreas, and Fujiyoshi, Yoshinori

Abstract

Author(s): Chikara Sato (corresponding author) [1]; Yutaka Ueno [1]; Kiyoshi Asai [1]; Katsutoshi Takahashi [2]; Masahiko Sato [3]; Andreas Engel [4]; Yoshinori Fujiyoshi [5] Voltage-sensitive membrane channels, the sodium channel, [...]

Published
2001
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