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Blocky proline/glutamine patterns in the SFPQ intrinsically disordered region dictate paraspeckle formation as a distinct membraneless organelle
Hiro Takakuwa, Takao Yoda, Tomohiro Yamazaki, Tetsuro Hirose
2025/02/27
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Biophysical aspect of assembly and regulation of nuclear bodies scaffolded by architectural RNA
Tetsuya Yamamoto, Tomohiro Yamazaki, Kensuke Ninomiya, Shinichi Nakagawa, Tetsuro Hirose
Journal of Molecular Biology p. 169016-169016 2025/02 Research paper (scientific journal)
Publisher: Elsevier BV
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Huntingtin is an RNA binding protein and participates in NEAT1-mediated paraspeckles.
Manisha Yadav, Rachel J Harding, Tiantian Li, Xin Xu, Terence Gall-Duncan, Mahreen Khan, Costanza Ferrari Bardile, Glen L Sequiera, Shili Duan, Renu Chandrasekaran, Anni Pan, Jiachuan Bu, Tomohiro Yamazaki, Tetsuro Hirose, Panagiotis Prinos, Lynette Tippett, Clinton Turner, Maurice A Curtis, Richard L M Faull, Mahmoud A Pouladi, Christopher E Pearson, Housheng Hansen He, Cheryl H Arrowsmith
Science advances Vol. 10 No. 29 2024/07/19 Research paper (scientific journal)
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Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export
Ken-ichi Fujita, Tomohiro Yamazaki, Akila Mayeda, Seiji Masuda
Biochemical and Biophysical Research Communications p. 149682-149682 2024/02 Research paper (scientific journal)
Publisher: Elsevier BV
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Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes
Ken-ichi Fujita, Misa Ito, Midori Irie, Kotaro Harada, Naoko Fujiwara, Yuya Ikeda, Hanae Yoshioka, Tomohiro Yamazaki, Masaki Kojima, Bunzo Mikami, Akila Mayeda, Seiji Masuda
Nature Communications 2024/01/15 Research paper (scientific journal)
Publisher: Research Square Platform LLC
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4.5SH RNA counteracts deleterious exonization of SINE B1 in mice.
Rei Yoshimoto, Yuta Nakayama, Ikuko Nomura, Ikuko Yamamoto, Yumeka Nakagawa, Shigeyuki Tanaka, Misuzu Kurihara, Yu Suzuki, Takehiko Kobayashi, Hiroko Kozuka-Hata, Masaaki Oyama, Mari Mito, Shintaro Iwasaki, Tomohiro Yamazaki, Tetsuro Hirose, Kimi Araki, Shinichi Nakagawa
Molecular cell 2023/12/09 Research paper (scientific journal)
Publisher: Elsevier BV
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Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus.
Tetsuya Yamamoto, Tomohiro Yamazaki, Kensuke Ninomiya, Tetsuro Hirose
Communications biology Vol. 6 No. 1 p. 1129-1129 2023/11/07 Research paper (scientific journal)
Publisher: Cold Spring Harbor Laboratory
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Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles.
Hiro Takakuwa, Tomohiro Yamazaki, Sylvie Souquere, Shungo Adachi, Hyura Yoshino, Naoko Fujiwara, Tetsuya Yamamoto, Tohru Natsume, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
Nature cell biology 2023/11/06 Research paper (scientific journal)
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Satellite RNAs: emerging players in subnuclear architecture and gene regulation.
Kensuke Ninomiya, Tomohiro Yamazaki, Tetsuro Hirose
The EMBO journal Vol. 42 2023/08/01 Research paper (scientific journal)
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Editorial: The why of RNA granules: Form, function, and regulation
Tomohiro Yamazaki, Timothy E. Audas, Natalie G. Farny
FRONTIERS IN MOLECULAR BIOSCIENCES Vol. 9 2022/12 Research paper (scientific journal)
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A guide to membraneless organelles and their various roles in gene regulation.
Tetsuro Hirose, Kensuke Ninomiya, Shinichi Nakagawa, Tomohiro Yamazaki
Nature reviews. Molecular cell biology Vol. 24 2022/11/23 Research paper (scientific journal)
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Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing.
Junichi Iwakiri, Kumiko Tanaka, Takeshi Chujo, Hiro Takakuwa, Tomohiro Yamazaki, Goro Terai, Kiyoshi Asai, Tetsuro Hirose
RNA (New York, N.Y.) Vol. 29 2022/11/16 Research paper (scientific journal)
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Statistical Thermodynamics Approach for Intracellular Phase Separation.
Tomohiro Yamazaki, Tetsuya Yamamoto
Methods in molecular biology (Clifton, N.J.) Vol. 2509 p. 361-393 2022/07 Research paper (scientific journal)
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Micellization: A new principle in the formation of biomolecular condensates.
Tomohiro Yamazaki, Tetsuya Yamamoto, Tetsuro Hirose
Frontiers in molecular biosciences Vol. 9 p. 974772-974772 2022 Research paper (scientific journal)
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Triblock copolymer micelle model of spherical paraspeckles.
Tetsuya Yamamoto, Tomohiro Yamazaki, Tetsuro Hirose
Frontiers in molecular biosciences Vol. 9 p. 925058-925058 2022 Research paper (scientific journal)
Publisher: Cold Spring Harbor Laboratory
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Control of condensates dictates nucleolar architecture.
Tomohiro Yamazaki, Tetsuro Hirose
Science (New York, N.Y.) Vol. 373 No. 6554 p. 486-487 2021/07/30 Research paper (scientific journal)
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ArcRNAs and the formation of nuclear bodies.
Shinichi Nakagawa, Tomohiro Yamazaki, Taro Mannen, Tetsuro Hirose
Mammalian genome Vol. 33 No. 2 p. 382-401 2021/06/03 Research paper (scientific journal)
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Paraspeckles are constructed as block copolymer micelles.
Tomohiro Yamazaki, Tetsuya Yamamoto, Hyura Yoshino, Sylvie Souquere, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
The EMBO journal Vol. 40 No. 12 2021/04/22 Research paper (scientific journal)
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CRISPR-Mediated Mutagenesis of Long Noncoding RNAs.
Tomohiro Yamazaki, Tetsuro Hirose
Methods in molecular biology (Clifton, N.J.) Vol. 2254 p. 283-303 2021 Research paper (scientific journal)
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Phase separation driven by production of architectural RNA transcripts.
Tetsuya Yamamoto, Tomohiro Yamazaki, Tetsuro Hirose
Soft matter Vol. 16 No. 19 p. 4692-4698 2020/05/21 Research paper (scientific journal)
Publisher: Royal Society of Chemistry (RSC)
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Detailed analyses of the crucial functions of Zn transporter proteins in alkaline phosphatase activation.
Eisuke Suzuki, Namino Ogawa, Taka-Aki Takeda, Yukina Nishito, Yu-Ki Tanaka, Takashi Fujiwara, Mayu Matsunaga, Sachiko Ueda, Naoya Kubo, Tokuji Tsuji, Ayako Fukunaka, Tomohiro Yamazaki, Kathryn M Taylor, Yasumitsu Ogra, Taiho Kambe
The Journal of biological chemistry Vol. 295 No. 17 p. 5669-5684 2020/04/24 Research paper (scientific journal)
Publisher: American Society for Biochemistry & Molecular Biology (ASBMB)
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URH49 exports mRNA by remodeling complex formation and mediating the NXF1-dependent pathway.
Ken-Ichi Fujita, Tomohiro Yamazaki, Kotaro Harada, Shigeto Seno, Hideo Matsuda, Seiji Masuda
Biochimica et biophysica acta. Gene regulatory mechanisms Vol. 1863 No. 2 p. 194480-194480 2020/02 Research paper (scientific journal)
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Molecular anatomy of the architectural NEAT1 noncoding RNA: The domains, interactors, and biogenesis pathway required to build phase-separated nuclear paraspeckles.
Tetsuro Hirose, Tomohiro Yamazaki, Shinichi Nakagawa
Wiley interdisciplinary reviews. RNA Vol. 10 No. 6 2019/11 Research paper (scientific journal)
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Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.
Miha Modic, Markus Grosch, Gregor Rot, Silvia Schirge, Tjasa Lepko, Tomohiro Yamazaki, Flora C Y Lee, Ejona Rusha, Dmitry Shaposhnikov, Michael Palo, Juliane Merl-Pham, Davide Cacchiarelli, Boris Rogelj, Stefanie M Hauck, Christian von Mering, Alexander Meissner, Heiko Lickert, Tetsuro Hirose, Jernej Ule, Micha Drukker
Molecular cell Vol. 74 No. 5 p. 951-965 2019/06/06 Research paper (scientific journal)
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Architectural RNAs for Membraneless Nuclear Body Formation.
Tomohiro Yamazaki, Shinichi Nakagawa, Tetsuro Hirose
Cold Spring Harbor symposia on quantitative biology Vol. 84 p. 227-237 2019 Research paper (scientific journal)
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Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu.
Shinichi Nakagawa, Tomohiro Yamazaki, Tetsuro Hirose
Open biology Vol. 8 No. 10 2018/10/24 Research paper (scientific journal)
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CRISPRa-mediated NEAT1 lncRNA upregulation induces formation of intact paraspeckles.
Tomohiro Yamazaki, Chikako Fujikawa, Ayaka Kubota, Akinari Takahashi, Tetsuro Hirose
Biochemical and biophysical research communications Vol. 504 No. 1 p. 218-224 2018/09/26 Research paper (scientific journal)
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Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation.
Tomohiro Yamazaki, Sylvie Souquere, Takeshi Chujo, Simon Kobelke, Yee Seng Chong, Archa H Fox, Charles S Bond, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
Molecular cell Vol. 70 No. 6 p. 1038-1053 2018/06/21 Research paper (scientific journal)
Publisher: Cell Press
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Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II machinery and contains multiple ALS/SMA-causative proteins.
Binkai Chi, Jeremy D O'Connell, Tomohiro Yamazaki, Jaya Gangopadhyay, Steven P Gygi, Robin Reed
Scientific reports Vol. 8 No. 1 p. 8755-8755 2018/06/08 Research paper (scientific journal)
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Long Noncoding RNAs and Their Applications: Focus on Architectural RNA (arcRNA), a Class of lncRNA
Tomohiro Yamazaki
Applied RNA Bioscience p. 161-187 2018
Publisher: Springer Singapore
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Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs.
Takeshi Chujo, Tomohiro Yamazaki, Tetsuya Kawaguchi, Satoshi Kurosaka, Toru Takumi, Shinichi Nakagawa, Tetsuro Hirose
The EMBO journal Vol. 36 No. 10 p. 1447-1462 2017/05/15 Research paper (scientific journal)
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Rab5-regulated endocytosis plays a crucial role in apical extrusion of transformed cells.
Sayaka Saitoh, Takeshi Maruyama, Yuta Yako, Mihoko Kajita, Yoichiro Fujioka, Yusuke Ohba, Nobuhiro Kasai, Natsu Sugama, Shunsuke Kon, Susumu Ishikawa, Takashi Hayashi, Tomohiro Yamazaki, Masazumi Tada, Yasuyuki Fujita
Proceedings of the National Academy of Sciences of the United States of America Vol. 114 No. 12 p. E2327-E2336-E2336 2017/03/21 Research paper (scientific journal)
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Direct Comparison of Manganese Detoxification/Efflux Proteins and Molecular Characterization of ZnT10 Protein as a Manganese Transporter.
Yukina Nishito, Natsuko Tsuji, Hitomi Fujishiro, Taka-Aki Takeda, Tomohiro Yamazaki, Fumie Teranishi, Fumiko Okazaki, Ayu Matsunaga, Karin Tuschl, Rajini Rao, Satoshi Kono, Hiroaki Miyajima, Hiroshi Narita, Seiichiro Himeno, Taiho Kambe
The Journal of biological chemistry Vol. 291 No. 28 p. 14773-87 2016/07/08 Research paper (scientific journal)
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Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies
Takeshi Chujo, Tomohiro Yamazaki, Tetsuro Hirose
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS Vol. 1859 No. 1 p. 139-146 2016/01 Research paper (scientific journal)
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Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies.
Takeshi Chujo, Tomohiro Yamazaki, Tetsuro Hirose
Biochimica et biophysica acta Vol. 1859 No. 1 p. 139-46 2016/01 Research paper (scientific journal)
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U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish.
Yong Yu, Binkai Chi, Wei Xia, Jaya Gangopadhyay, Tomohiro Yamazaki, Marlene E Winkelbauer-Hurt, Shanye Yin, Yoan Eliasse, Edward Adams, Christopher E Shaw, Robin Reed
Nucleic acids research Vol. 43 No. 6 p. 3208-18 2015/03/31 Research paper (scientific journal)
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The building process of the functional paraspeckle with long non-coding RNAs.
Tomohiro Yamazaki, Tetsuro Hirose
Frontiers in bioscience (Elite edition) Vol. 7 No. 1 p. 1-41 2015/01/01 Research paper (scientific journal)
Publisher: Frontiers in Bioscience
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Exome sequencing to identify de novo mutations in sporadic ALS trios.
Alessandra Chesi, Brett T Staahl, Ana Jovičić, Julien Couthouis, Maria Fasolino, Alya R Raphael, Tomohiro Yamazaki, Laura Elias, Meraida Polak, Crystal Kelly, Kelly L Williams, Jennifer A Fifita, Nicholas J Maragakis, Garth A Nicholson, Oliver D King, Robin Reed, Gerald R Crabtree, Ian P Blair, Jonathan D Glass, Aaron D Gitler
Nature neuroscience Vol. 16 No. 7 p. 851-5 2013/07 Research paper (scientific journal)
Publisher: 7
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FUS-SMN protein interactions link the motor neuron diseases ALS and SMA.
Tomohiro Yamazaki, Shi Chen, Yong Yu, Biao Yan, Tyler C Haertlein, Monica A Carrasco, Juan C Tapia, Bo Zhai, Rita Das, Melanie Lalancette-Hebert, Aarti Sharma, Siddharthan Chandran, Gareth Sullivan, Agnes Lumi Nishimura, Christopher E Shaw, Steve P Gygi, Neil A Shneider, Tom Maniatis, Robin Reed
Cell reports Vol. 2 No. 4 p. 799-806 2012/10/25 Research paper (scientific journal)
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The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export.
Eric G Folco, Chung-Sheng Lee, Kobina Dufu, Tomohiro Yamazaki, Robin Reed
PloS one Vol. 7 No. 8 2012 Research paper (scientific journal)
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Enhancing recombinant protein production in human cell lines with a constitutive transport element and mRNA export proteins.
Yuki Aihara, Naoko Fujiwara, Tomohiro Yamazaki, Taiho Kambe, Masaya Nagao, Yutaka Hirose, Seiji Masuda
Journal of biotechnology Vol. 153 No. 3-4 p. 86-91 2011/05/20 Research paper (scientific journal)
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The closely related RNA helicases, UAP56 and URH49, preferentially form distinct mRNA export machineries and coordinately regulate mitotic progression.
Tomohiro Yamazaki, Naoko Fujiwara, Hiroko Yukinaga, Miki Ebisuya, Takuya Shiki, Tomoya Kurihara, Noriyuki Kioka, Taiho Kambe, Masaya Nagao, Eisuke Nishida, Seiji Masuda
Molecular biology of the cell Vol. 21 No. 16 p. 2953-65 2010/08/15 Research paper (scientific journal)
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A screening method tuned for mRNA processing factors in human cells by evaluation of the luciferase reporter activity and the subcellular distribution of bulk poly(A)+ RNA.
Naoko Fujiwara, Mayu Yoshikawa, Tomohiro Yamazaki, Taiho Kambe, Masaya Nagao, Seiji Masuda
Bioscience, biotechnology, and biochemistry Vol. 74 No. 7 p. 1512-6 2010 Research paper (scientific journal)
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Demonstration and characterization of the heterodimerization of ZnT5 and ZnT6 in the early secretory pathway.
Ayako Fukunaka, Tomoyuki Suzuki, Yayoi Kurokawa, Tomohiro Yamazaki, Naoko Fujiwara, Kaori Ishihara, Hitoshi Migaki, Katsuzumi Okumura, Seiji Masuda, Yuko Yamaguchi-Iwai, Masaya Nagao, Taiho Kambe
The Journal of biological chemistry Vol. 284 No. 45 p. 30798-806 2009/11/06 Research paper (scientific journal)
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DEAD-box型RNAヘリカーゼUAP56およびURH49による遺伝子発現制御を介した染色体分配機構における異なる役割
山崎 智弘, 藤原 奈央子, 栗原 朋也, 幸長 弘子, 戎家 美紀, 西田 栄介, 木岡 紀幸, 神戸 大朋, 永尾 雅哉, 増田 誠司
日本生化学会大会プログラム・講演要旨集 Vol. 82回 p. 3T18a-2 2009/09
Publisher: (公社)日本生化学会
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SLC39A9 (ZIP9) regulates zinc homeostasis in the secretory pathway: characterization of the ZIP subfamily I protein in vertebrate cells.
Wataru Matsuura, Tomohiro Yamazaki, Yuko Yamaguchi-Iwai, Seiji Masuda, Masaya Nagao, Glen K Andrews, Taiho Kambe
Bioscience, biotechnology, and biochemistry Vol. 73 No. 5 p. 1142-8 2009/05 Research paper (scientific journal)
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Zinc transport complexes contribute to the homeostatic maintenance of secretory pathway function in vertebrate cells.
Kaori Ishihara, Tomohiro Yamazaki, Yoko Ishida, Tomoyuki Suzuki, Kimimitsu Oda, Masaya Nagao, Yuko Yamaguchi-Iwai, Taiho Kambe
The Journal of biological chemistry Vol. 281 No. 26 p. 17743-50 2006/06/30 Research paper (scientific journal)
