Toyotaka ISHIBASHI

DSc in Applied Biological Science
Tokyo University of Science, 2005

Associate Professor
Division of Life Science



(852) 3469 2238
toyotaka@ust.hk
Room 5509
Personal Web

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ORCID
0000-0001-8015-2319

Scopus ID
7401772664




Research Interest Publications Projects Teaching Assignment RPG Supervision Space used




Research Interest

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Biophysics
Chromatin structure
Transcription dynamics



Publications

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All Years 70 2022 0 2021 3 2020 5 2019 2 2018 2 2017 7 2016 51

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2021 3

Primate-specific histone variants
Genome, v. 64, (4), April 2021, p. 337-346
Ding, Dongbo; Nguyen, Thi Thuy; Pang, Yu Hin; Ishibashi, Toyotaka Article
RECQL5 KIX domain splicing isoforms have distinct functions in transcription repression and DNA damage response
DNA Repair, v. 97, January 2021, article number 103007
Ding, Dongbo; Sun, Xulun; Pang, Yu Hin; An, Liwei; Huen, Michael S. Y.; Hu, Taobo; Ishibashi, Toyotaka Article
The elevated transcription of ADAM19 by the oncohistone H2BE76K contributes to oncogenic properties in breast cancer
Journal of Biological Chemistry, v. 296, January 2021, article number 100374
Kang, Tze Zhen Evangeline; Zhu, Lina; Yang, Du; Ding, Dongbo; Zhu, Xiaoxuan; Wan, Yi Ching Esther; Liu, Jiaxian; Ramakrishnan, Saravanan; Chan, Landon Long; Chan, Siu Yuen; Wang, Xin; Gan, Haiyun; Han, Junhong; Ishibashi, Toyataka; Li, Qing; Chan, Kui Ming Article

2020 5

Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes
Signal Transduction and Targeted Therapy, v. 5, (1), March 2020, article number 27
Wan, Yi Ching Esther; Leung, Tsz Chui Sophia; Ding, Dongbo; Sun, Xulun; Liu, Jiaxian; Zhu, Lina; Kang, Tze Zhen Evangeline; Yang, Du; Zhang, Yuchen; Zhang, Jitian; Qian, Chengmin; Huen, Michael Shing Yan; Li, Qing; Chow, Maggie Zi Ying; Zheng, Zongli; Han, Junhong; Goel, Ajay; Wang, Xin; Ishibashi, Toyotaka; Chan, Kui Ming Article
Histone H4 variant, H4G, drives ribosomal RNA transcription and breast cancer cell proliferation by loosening nucleolar chromatin structure
Journal of Cellular Physiology, v. 235, (12), 1 December 2020, p. 9601-9608
Pang, Yu Hin; Sun, Xulun; Ausio, Juan; Ishibashi, Toyotaka Article
Screen Identifies DYRK1B Network as Mediator of Transcription Repression on Damaged Chromatin
Proceedings of the National Academy of Sciences of the United States of America, v. 117, (29), July 2020, p. 17019-17030
Dong, Chao; West, Kirk L.; Tan, Xin Yi; Li, Junshi; Ishibashi, Toyotaka; Yu, Cheng-han; Sy, Shirley M. H.; Leung, Justin W. C.; Huen, Michael S. Y. Article
Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility
Nucleic Acids Research, v. 48, (17), 25 September 2020, p. 9538-9549
Jing, Yihang; Ding, Dongbo; Tian, Gaofei; Kwan, Ka Chun Jonathan; Liu, Zheng; Ishibashi, Toyotaka; Li, Xiang David Article
The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma
Signal Transduction and Targeted Therapy, v. 5, (1), December 2020, article number 106
Wan, Yi Ching Esther; Liu, Jiaxian; Zhu, Lina; Kang, Tze Evangeline Zhen; Zhu, Xiaoxuan; Lis, John; Ishibashi, Toyotaka; Danko, G Charles; Wang, Xin; Chan, Kui Ming Article

2019 2

A Novel Histone H4 Variant H4G Regulates rDNA Transcription in Breast Cancer
Nucleic Acids Research, v. 47, (16), September 2019, p. 8399-8409
Long, Mengping; Sun, Xulun; Shi, Wenjin; An, Yanru; Leung, Tsz Chui Sophia; Ding, Dongbo; Cheema, Manjinder S.; MacPherson, Nicol; Nelson, Christopher J.; Ausio, Juan; Yan, Yan; Ishibashi, Toyotaka Article
Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs
Development, v. 146, (18), September 2019, article number dev179754, p. 1-10
Deng, Mingxi; Wang, Ying; Zhang, Lina; Yang, Yang; Huang, Shengshuo; Wang, Jiguang; Ge, H.; Ishibashi, Toyotaka; Yan, Yan Article

2018 2

Site-Specific Installation of Succinyl Lysine Analog into Histones Reveals the Effect of H2BK34 Succinylation on Nucleosome Dynamics
Cell Chemical Biology, v.25, (2), Febrary 2018, p. 166-174.e7
Jing, Yihang; Liu, Zheng; Tian, Gaofei; Bao, Xiucong; Ishibashi, Toyotaka; Li, Xiang David Article
TEFM Enhances Transcription Elongation by Modifying mtRNAP Pausing Dynamics
Biophysical Journal, v. 115, (12), December 2018, p. 2295-2300
Yu, Hongwu; Xue, Cheng; Long, Mengping; Jia, Huiqiang; Xue, Guosheng; Du, Shengwang; Coello, Yves; Ishibashi, Toyotaka Article

2017 7

Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
Development, v. 144, (12), June 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Article
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
Journal of Cell Science, v. 130, (13), 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Article
Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
The 18th International Congress of Developmental Biology, Singapore, 18-22 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Conference paper
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
2017 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, The University of Hong Kong, Hong Kong, 16 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan Conference paper
Characterization of Nucleolar-localized H4 Histone Variant, H4G
Molecular Biology of the Cell, v. 28, 2017
Long, Mengping; Sun, Xulun; Shi, Wenjin; Ishibashi, Toyotaka Conference paper
Effects of TEFM on the Regulation of Transcription Elongation by Human Mitochondrial RNA Polhymerase
2017 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, The University of Hong Kong, Hong Kong, 16 June 2017
Xue, Cheng; Yu, Hongwu; Long, Mengping; Ishibashi, Toyotaka Conference paper
Molecular and cellular basis of Drosophila neuroblast delamination
Mechanisms of Development, v. 145, (Suppl.), July 2017, article number PS5.48, p. S158
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Yan, Yan Conference paper

2016 4

Poly(ADP-ribosyl)ation-dependent Transient Chromatin Decondensation and Histone Displacement following Laser Microirradiation
Journal of biological chemistry, v. 291, (4), January 2016, p. 1789-1802
Strickfaden, Hilmar; McDonald, Darin; Kruhlak, Michael J.; Haince, Jean-Francois; Th'ng, John P.H.; Rouleau, Michele; Ishibashi, Toytaka; Corry, Gareth N.; Ausio, Juan; Underhill, D. Alan; Pokier, Guy G.; Hendzel, Michael J. Article
Histone Variants and Posttranslational Modifications in Spermatogenesis and Infertility
Epigenetic Biomarkers and Diagnostics / José Luis García-Giménez, editors. London : Academic Press, 2016, p. 479-496
Ausio, Juan; Zhang, Yinan; Ishibashi, Toyotaka Book chapter
Quantitative analysis of myosin-driven apical constriction in delaminating neuroblasts
Genetics Society of America (GSA) 57th Annual Drosophila Research Conference, Orlando, FL, US., 13-17 July 2016
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Chris, Doe; Yan, Yan Conference paper
Quantitative analysis of myosin-driven apical constriction in delaminating neuroblasts
2016 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, Chinese University of Hong Kong, 11 June 2016
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Chris, Doe; Yan, Yan Conference paper

2014 3

Molecular Mechanisms of Transcription through Single-Molecule Experiments
Chemical Reviews, v. 114, (6), March 2014, p. 3203-3223
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Bintu, Lacramioara; Bustamante, Carlos Article
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics
Proceedings of the National Academy of Sciences of the United States of America, v. 111, (9), March 2014, p. 3419-3424
Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Coello, Yves; Lionberger, Troy A.; Lubkowska, Lucyna; Ponticelli, Alfred S.; Kashlev, Mikhail; Bustamante, Carlos Article
Complete Dissection of Transcription Elongation Reveals Slow Translocation of RNA Polymerase II in a Linear Ratchet Mechanism
Biophysical Journal, v. 106, (2), January 2014, p. 485a-486a, Supplement 1
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kahlev, Mikhail; Bustamante, Carlos J. Conference paper

2013 3

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
eLife, v. 2013, (2), September 2013, article number e00971
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos J. Article
A Quantitative Kinetic Model of Eukaryotic Transcription Elongation from Single-Molecule Experiments
Biophysical Journal, v. 104, (2), January 2013, p. 364A-364A
Dangkulwanich, Manchuta; Liu, Shixin; Ishibashi, Toyotaka; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos Conference paper
Dissecting the Nucleosomal Barrier to Transcription
Biophysical Journal, v. 102, (3), January 2013, p. 284A-284A
Ishibashi, Toyotaka; Bintu, Lacramioara; Dangkulwanich, Manchuta; Wu, Gloria; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos Conference paper

2012 2

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Proceedings of the National Academy of Sciences of the United States of America, v. 109, (23), 2012, p. 8948-8953
Zamft, B.; Bintu, L.; Ishibashi, Toyotaka; Bustamante, C. Article
Nucleosomal Elements that Control the Topography of the Barrier to Transcription
Cell, v. 151, (4), November 2012, p. 738-749
Bintu, Lacramioara; Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Wu, Yueh-Yi; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos Article

2010 3

H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis
Nucleic acids research, v. 38, (6), April 2010, p. 1780-1789
Ishibashi, Toyotaka; Li, Andra; Eirin-Lopez, Jose M.; Zhao, Ming; Missiaen, Kristal; Abbott, D. Wade; Meistrich, Marvin; Hendzel, Michael J.; Ausio, Juan Article
Phosphorylation of Histone H2A.X by DNA-dependent Protein Kinase Is Not Affected by Core Histone Acetylation, but It Alters Nucleosome Stability and Histone H1 Binding
Journal of biological chemistry, v. 285, (23), June 2010, p. 17778-17788
Li, Andra; Yu, Yaping; Lee, Sheng-Chun; Ishibashi, Toyotaka; Lees-Miller, Susan P.; Ausio, Juan Article
Histone variants. signaling or structural modules
Handbook of Cell Signaling, 2/e / Edited by Ralph A. Bradshaw and Edward A. Dennis. Elsevier Inc., v.3, 2010, p. 2409-2425, Chapter 289
Ishibashi, Tototaka; Li, A.; Ausió, J. Book chapter

2009 6

Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome
Biochemistry, v. 48, (22), 2009, p. 5007-5017
Ishibashi, T.; Dryhurst, D.; Rose, K.L.; Shabanowitz, J.; Hunt, D.F.; Ausió, J. Article
Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates
BMC biology, v. 14, (7), December 2009, p. 86
Dryhurst, Deanna; Ishibashi, Toyotaka; Rose, Kristie L.; Eirin-Lopez, Jose M.; McDonald, Darin; Silva-Moreno, Begonia; Veldhoen, Nik; Helbing, Caren C.; Hendzel, Michael J.; Shabanowitz, Jeffrey; Hunt, Donald F.; Ausio, Juan Article
H2A.Z and H3.3 histone variants affect nucleosome structure: Biochemical and biophysical studies
Biochemistry, v. 48, (46), 2009, p. 10852-10857
Thakar, A.; Gupta, P.; Ishibashi, T.; Finn, R.; Silva-Moreno, B.; Uchiyama, S.; Fukui, K.; Tomschik, M.; Ausio, J.; Zlatanova, J. Article
New developments in post-translational modifications and functions of histone H2A variants
Biochemistry and cell biology, v. 87, (1), 2009, p. 7-17
Thambirajah, A.A.; Li, A.; Ishibashi, T.; Ausió, J. Article
The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues
BMC evolutionary biology, v. 9, (1), 2009, article number 31
EirínLópez, J.M.; González-Romero, R.; Dryhurst, D.; Ishibashi, T.; Ausió, J. Article
The multi-replication protein A (RPA) system - A new perspective
The FEBS journal, v. 276, (4), 2009, p. 943-963
Sakaguchi, K.; Ishibashi, T.; Uchiyama, Y.; Iwabata, K. Article

2008 3

H2A.Bbd: A quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way
The FASEB journal, v. 22, (1), 2008, p. 316-326
EirínLópez, J.M.; Ishibashi, Toyotaka; Ausió, J. Article
MBD4-mediated glycosylase activity on a chromatin template is enhanced by acetylation
Molecular and cellular biology, v. 28, (15), 2008, p. 4734-4744
Ishibashi, T.; So, K.; Cupples, C.G.; Ausió, J. Article
MeCP2 preferentially binds to methylated linker DNA in the absence of the terminal tail of histone H3 and independently of histone acetylation
FEBS letters, v. 582, (7), 2008, p. 1157-1162
Ishibashi, Toyotaka; Thambirajah, A.A.; Ausió, J. Article

2007 1

Probasin promoter assembles into a strongly positioned nucleosome that permits androgen receptor binding
Molecular and Cellular Endocrinology, v. 268, March 2007, p. 10-19
Maffey, Allison H.; Ishibashi, Toyotaka; He, Cheng; Wang, Xiaoying; White, Adrienne R.; Hendy, Stephen C.; Nelson, Colleen C.; Rennie, Paul S.; Ausio, Juan Article

2006 6

A higher plant has three different types of RPA heterotrimeric complex
The Journal of biochemistry, v. 139, (1), 2006, p. 99-104
Ishibashi, Toyotaka; Kimura, S.; Sakaguchi, K. Article
A novel protein refolding method using a zeolite
Analytical biochemistry, v. 348, (2), 2006, p. 307-314
Chiku, H.; Kawai, A.; Ishibashi, Toyotaka; Takehara, M.; Yanai, T.; Mizukami, F.; Sakaguchi, K. Article
Characterization of T-DNA insertion mutants and RNAi silenced plants of Arabidopsis thaliana UV-damaged DNA binding protein 2 (AtUV-DDB2)
Plant molecular biology, v. 61, (1-2), 2006, p. 227-240
Koga, A.; Ishibashi, Toyotaka; Kimura, S.; Uchiyama, Y.; Sakaguchi, K. Article
DNA repair mechanisms in UV-B tolerant plants
JARQ, v. 40, (2), April 2006, p. 107-113
Ishibashi, Toyotaka; Kimura, Seisuke; Furukawa, Tornoyuki; Sakaguchi, Kengo Article
H2A.Z stabilizes chromatin in a way that is dependent on core histone acetylation
Journal of biological chemistry, v. 281, (29), July 2006, p. 20036-20044
Thambirajah, Anita A.; Dryhurst, Deanna; Ishibashi, Toyotaka; Li, Andra; Maffey, Allison H.; Ausio, Juan Article
Higher plant RecA-like protein is homologous to RadA
DNA repair, v. 5, (1), 2006, p. 80-88
Ishibashi, Toyotaka; Isogai, Minako; Kiyohara, Hiroyuki; Hosaka, Masahiro; Chiku, Hiroyuki; Koga, Asami; Yamamoto, Taichi; Uchiyama, Yukinobu; Mori, Yoko; Hashimoto, Junji; Ausió, Juan Thomas; Kimura, Seisuke; Sakaguchi, Kengo Article

2005 5

Characterization of the origin recognition complex (ORC) from a higher plant, rice (Oryza sativa L.)
Gene, v. 353, (1), 2005, p. 23-30
Mori, Y.; Yamamoto, T.; Sakaguchi, N.; Ishibashi, Toyotaka; Furukawa, T.; Kadota, Y.; Kuchitsu, K.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article
DNA repair in higher plants
生化学, v. 77, (2), 2005, p. 113-123
Kimura, S.; Ishibashi, T.; Yamamoto, T.; Sakaguchi, K. Article
Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage
Journal of Plant Research, v. 118, (2), 2005, p. 91-97
Yamamoto, T.; Mori, Y.; Ishibashi, Toyotaka; Uchiyama, Y.; Ueda, T.; Ando, T.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article
Plastid DNA polymerases from higher plants, Arabidopsis thaliana
Biochemical and biophysical research communications, v. 334, (1), 2005, p. 43-50
Mori, Y.; Kimura, S.; Saotome, A.; Kasai, N.; Sakaguchi, N.; Uchiyama, Y.; Ishibashi, Toyotaka; Yamamoto, T.; Chiku, H.; Sakaguchi, K. Article
Two types of replication protein A in seed plants: Characterization of their functions in vitro and in vivo
The FEBS journal, v. 272, (13), 2005, p. 3270-3281
Ishibashi, Toyotaka; Koga, A.; Yamamoto, T.; Uchiyama, Y.; Mori, Y.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article

2004 5

Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes
Genes & development, v. 18, (17), 2004, p. 2172-2181
Yanagawa, Y.; Sullivan, J.A.; Komatsu, S.; Gusmaroli, G.; Suzuki, G.; Yin, J.; Ishibashi, Toyotaka; Saijo, Y.; Rubio, V.; Kimura, S.; Wang, J.; Deng, X.W. Article
Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex
Biochemical and biophysical research communications, v. 314, (2), 2004, p. 434-439
Yamamoto, T.; Mori, Y.; Ishibashi, Toyotaka; Uchiyama, Y.; Sakaguchi, N.; Furukawa, T.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article
Degradation of proliferating cell nuclear antigen by 26S proteasome in rice (Oryza sativa L.)
Planta, v. 218, (4), 2004, p. 640-646
Yamamoto, T.; Kimura, S.; Mori, Y.; Oka, M.; Ishibashi, Toyotaka; Yanagawa, Y.; Nara, T.; Nakagawa, H.; Hashimoto, J.; Sakaguchi, K. Article
DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells
Nucleic acids research, v. 32, (9), 2004, p. 2760-2767
Kimura, S.; Tahira, Y.; Ishibashi, Tototaka; Mori, Y.; Mori, T.; Hashimoto, J.; Sakaguchi, K. Article
Plant DNA polymerase λ, a DNA repair enzyme that functions in plant meristematic and meiotic tissues
European journal of biochemistry, v. 271, (13), 2004, p. 2799-2807
Uchiyama, Y.; Kimura, S.; Yamamoto, T.; Ishibashi, Toyotaka; Sakaguchi, K. Article

2003 5

Characterization of all the subunits of replication factor C from a higher plant, rice (Oryza sativa L.), and their relation to development
Plant molecular biology, v. 53, (1-2), 2003, p. 15-25
Furukawa, T.; Ishibashi, Toyotaka; Kimura, S.; Tanaka, H.; Hashimoto, J.; Sakaguchi, K. Article
Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L.
Planta, v. 217, (2), 2003, p. 175-183
Yamamoto, T.; Kimura, S.; Mori, Y.; Uchiyama, Y.; Ishibashi, Toyotaka; Hashimoto, J.; Sakaguchi, K. Article
OsSEND-1: A new RAD2 nuclease family member in higher plants
Plant molecular biology, v. 51, (1), 2003, p. 59-70
Furukawa, T.; Kimura, S.; Ishibashi, Toyotaka; Mori, Y.; Hashimoto, J.; Sakaguchi, K. Article
Plant-specific regulation of replication protein A2 (OsRPA2) from rice during the cell cycle and in response to ultraviolet light exposure
Planta, v. 217, (3), 2003, p. 457-465
Marwedel, T.; Ishibashi, Toyotaka; Lorbiecke, R.; Jacob, S.; Sakaguchi, K.; Sauter, M. Article
Rice UV-damaged DNA binding protein homologues are most abundant in proliferating tissues
Gene, v. 308, (1-2), 2003, p. 79-87
Ishibashi, Toyotaka; Kimura, S.; Yamamoto, T.; Furukawa, T.; Takata, K.I.; Uchiyama, Y.; Hashimoto, J.; Sakaguchi, K. Article

2002 2

A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.)
Nucleic acids research, v. 30, (7), 2002, p. 1585-1592
Kimura, S.; Uchiyama, Y.; Kasai, N.; Namekawa, S.; Saotome, A.; Ueda, T.; Ando, T.; Ishibashi, Toyotaka; Oshige, M.; Furukawa, T.; Yamamoto, T.; Hashimoto, J.; Sakaguchi, K. Article
Characterization of DNA polymerase δ from a higher plant, rice (Oryza sativa L.)
Gene, v. 295, (1), 2002, p. 19-26
Uchiyama, Y.; Hatanaka, M.; Kimura, S.; Ishibashi, Toyotaka; Ueda, T.; Sakakibara, Y.; Matsumoto, T.; Furukawa, T.; Hashimoto, J.; Sakaguchi, K. Article

2001 2

A plant homologue of 36 kDa subunit of replication factor C: Molecular cloning and characterization
Plant science, v. 161, (1), 2001, p. 99-106
Furukawa, T.; Kimura, S.; Ishibashi, Toyotaka; Hashimoto, J.; Sakaguchi, K. Article
Two types of replication protein A 70 kDa subunit in rice, Oryza sativa: Molecular cloning, characterization, and cellular & tissue distribution
Gene, v. 272, (1-2), 2001, p. 335-343
Ishibashi, Toyotaka; Kimura, S.; Furukawa, T.; Hatanaka, M.; Hashimoto, J.; Sakaguchi, K. Article

2000 1

Molecular cloning and characterization of a plant homologue of the origin recognition complex 1 (ORC1)
Plant science, v. 158, (1-2), 2000, p. 33-39
Kimura, S.; Ishibashi, Toyotaka; Hatanaka, M.; Sakakibara, Y.; Hashimoto, J.; Sakaguchi, K. Article


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Article 3

Primate-specific histone variants
Genome, v. 64, (4), April 2021, p. 337-346
Ding, Dongbo; Nguyen, Thi Thuy; Pang, Yu Hin; Ishibashi, Toyotaka
RECQL5 KIX domain splicing isoforms have distinct functions in transcription repression and DNA damage response
DNA Repair, v. 97, January 2021, article number 103007
Ding, Dongbo; Sun, Xulun; Pang, Yu Hin; An, Liwei; Huen, Michael S. Y.; Hu, Taobo; Ishibashi, Toyotaka
The elevated transcription of ADAM19 by the oncohistone H2BE76K contributes to oncogenic properties in breast cancer
Journal of Biological Chemistry, v. 296, January 2021, article number 100374
Kang, Tze Zhen Evangeline; Zhu, Lina; Yang, Du; Ding, Dongbo; Zhu, Xiaoxuan; Wan, Yi Ching Esther; Liu, Jiaxian; Ramakrishnan, Saravanan; Chan, Landon Long; Chan, Siu Yuen; Wang, Xin; Gan, Haiyun; Han, Junhong; Ishibashi, Toyataka; Li, Qing; Chan, Kui Ming


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Article 5

Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes
Signal Transduction and Targeted Therapy, v. 5, (1), March 2020, article number 27
Wan, Yi Ching Esther; Leung, Tsz Chui Sophia; Ding, Dongbo; Sun, Xulun; Liu, Jiaxian; Zhu, Lina; Kang, Tze Zhen Evangeline; Yang, Du; Zhang, Yuchen; Zhang, Jitian; Qian, Chengmin; Huen, Michael Shing Yan; Li, Qing; Chow, Maggie Zi Ying; Zheng, Zongli; Han, Junhong; Goel, Ajay; Wang, Xin; Ishibashi, Toyotaka; Chan, Kui Ming
Histone H4 variant, H4G, drives ribosomal RNA transcription and breast cancer cell proliferation by loosening nucleolar chromatin structure
Journal of Cellular Physiology, v. 235, (12), 1 December 2020, p. 9601-9608
Pang, Yu Hin; Sun, Xulun; Ausio, Juan; Ishibashi, Toyotaka
Screen Identifies DYRK1B Network as Mediator of Transcription Repression on Damaged Chromatin
Proceedings of the National Academy of Sciences of the United States of America, v. 117, (29), July 2020, p. 17019-17030
Dong, Chao; West, Kirk L.; Tan, Xin Yi; Li, Junshi; Ishibashi, Toyotaka; Yu, Cheng-han; Sy, Shirley M. H.; Leung, Justin W. C.; Huen, Michael S. Y.
Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility
Nucleic Acids Research, v. 48, (17), 25 September 2020, p. 9538-9549
Jing, Yihang; Ding, Dongbo; Tian, Gaofei; Kwan, Ka Chun Jonathan; Liu, Zheng; Ishibashi, Toyotaka; Li, Xiang David
The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma
Signal Transduction and Targeted Therapy, v. 5, (1), December 2020, article number 106
Wan, Yi Ching Esther; Liu, Jiaxian; Zhu, Lina; Kang, Tze Evangeline Zhen; Zhu, Xiaoxuan; Lis, John; Ishibashi, Toyotaka; Danko, G Charles; Wang, Xin; Chan, Kui Ming


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Article 2

A Novel Histone H4 Variant H4G Regulates rDNA Transcription in Breast Cancer
Nucleic Acids Research, v. 47, (16), September 2019, p. 8399-8409
Long, Mengping; Sun, Xulun; Shi, Wenjin; An, Yanru; Leung, Tsz Chui Sophia; Ding, Dongbo; Cheema, Manjinder S.; MacPherson, Nicol; Nelson, Christopher J.; Ausio, Juan; Yan, Yan; Ishibashi, Toyotaka
Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs
Development, v. 146, (18), September 2019, article number dev179754, p. 1-10
Deng, Mingxi; Wang, Ying; Zhang, Lina; Yang, Yang; Huang, Shengshuo; Wang, Jiguang; Ge, H.; Ishibashi, Toyotaka; Yan, Yan


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Article 2

Site-Specific Installation of Succinyl Lysine Analog into Histones Reveals the Effect of H2BK34 Succinylation on Nucleosome Dynamics
Cell Chemical Biology, v.25, (2), Febrary 2018, p. 166-174.e7
Jing, Yihang; Liu, Zheng; Tian, Gaofei; Bao, Xiucong; Ishibashi, Toyotaka; Li, Xiang David
TEFM Enhances Transcription Elongation by Modifying mtRNAP Pausing Dynamics
Biophysical Journal, v. 115, (12), December 2018, p. 2295-2300
Yu, Hongwu; Xue, Cheng; Long, Mengping; Jia, Huiqiang; Xue, Guosheng; Du, Shengwang; Coello, Yves; Ishibashi, Toyotaka


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Article 2

Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
Development, v. 144, (12), June 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
Journal of Cell Science, v. 130, (13), 2017, p. 2153-2164
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan

Conference paper 5

Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts
The 18th International Congress of Developmental Biology, Singapore, 18-22 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
Apical Constriction is Driven by a Pulsatile Apical Myosin Network in Delaminating Drosophila Neuroblasts
2017 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, The University of Hong Kong, Hong Kong, 16 June 2017
An, Yanru; Xue, Guosheng; Yang, Shaobo; Deng, Mingxi; Zhou, Xiaowei; Yu, Weichuan; Ishibashi, Toyotaka; Zhang, Lei; Yan, Yan
Characterization of Nucleolar-localized H4 Histone Variant, H4G
Molecular Biology of the Cell, v. 28, 2017
Long, Mengping; Sun, Xulun; Shi, Wenjin; Ishibashi, Toyotaka
Effects of TEFM on the Regulation of Transcription Elongation by Human Mitochondrial RNA Polhymerase
2017 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, The University of Hong Kong, Hong Kong, 16 June 2017
Xue, Cheng; Yu, Hongwu; Long, Mengping; Ishibashi, Toyotaka
Molecular and cellular basis of Drosophila neuroblast delamination
Mechanisms of Development, v. 145, (Suppl.), July 2017, article number PS5.48, p. S158
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Yan, Yan


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Article 1

Poly(ADP-ribosyl)ation-dependent Transient Chromatin Decondensation and Histone Displacement following Laser Microirradiation
Journal of biological chemistry, v. 291, (4), January 2016, p. 1789-1802
Strickfaden, Hilmar; McDonald, Darin; Kruhlak, Michael J.; Haince, Jean-Francois; Th'ng, John P.H.; Rouleau, Michele; Ishibashi, Toytaka; Corry, Gareth N.; Ausio, Juan; Underhill, D. Alan; Pokier, Guy G.; Hendzel, Michael J.

Book chapter 1

Histone Variants and Posttranslational Modifications in Spermatogenesis and Infertility
Epigenetic Biomarkers and Diagnostics / José Luis García-Giménez, editors. London : Academic Press, 2016, p. 479-496
Ausio, Juan; Zhang, Yinan; Ishibashi, Toyotaka

Conference paper 2

Quantitative analysis of myosin-driven apical constriction in delaminating neuroblasts
Genetics Society of America (GSA) 57th Annual Drosophila Research Conference, Orlando, FL, US., 13-17 July 2016
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Chris, Doe; Yan, Yan
Quantitative analysis of myosin-driven apical constriction in delaminating neuroblasts
2016 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, Chinese University of Hong Kong, 11 June 2016
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Chris, Doe; Yan, Yan


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Article 2

Molecular Mechanisms of Transcription through Single-Molecule Experiments
Chemical Reviews, v. 114, (6), March 2014, p. 3203-3223
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Bintu, Lacramioara; Bustamante, Carlos
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics
Proceedings of the National Academy of Sciences of the United States of America, v. 111, (9), March 2014, p. 3419-3424
Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Coello, Yves; Lionberger, Troy A.; Lubkowska, Lucyna; Ponticelli, Alfred S.; Kashlev, Mikhail; Bustamante, Carlos

Conference paper 1

Complete Dissection of Transcription Elongation Reveals Slow Translocation of RNA Polymerase II in a Linear Ratchet Mechanism
Biophysical Journal, v. 106, (2), January 2014, p. 485a-486a, Supplement 1
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kahlev, Mikhail; Bustamante, Carlos J.


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Article 1

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
eLife, v. 2013, (2), September 2013, article number e00971
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos J.

Conference paper 2

A Quantitative Kinetic Model of Eukaryotic Transcription Elongation from Single-Molecule Experiments
Biophysical Journal, v. 104, (2), January 2013, p. 364A-364A
Dangkulwanich, Manchuta; Liu, Shixin; Ishibashi, Toyotaka; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos
Dissecting the Nucleosomal Barrier to Transcription
Biophysical Journal, v. 102, (3), January 2013, p. 284A-284A
Ishibashi, Toyotaka; Bintu, Lacramioara; Dangkulwanich, Manchuta; Wu, Gloria; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos


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Article 2

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Proceedings of the National Academy of Sciences of the United States of America, v. 109, (23), 2012, p. 8948-8953
Zamft, B.; Bintu, L.; Ishibashi, Toyotaka; Bustamante, C.
Nucleosomal Elements that Control the Topography of the Barrier to Transcription
Cell, v. 151, (4), November 2012, p. 738-749
Bintu, Lacramioara; Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Wu, Yueh-Yi; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos


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Article 2

H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis
Nucleic acids research, v. 38, (6), April 2010, p. 1780-1789
Ishibashi, Toyotaka; Li, Andra; Eirin-Lopez, Jose M.; Zhao, Ming; Missiaen, Kristal; Abbott, D. Wade; Meistrich, Marvin; Hendzel, Michael J.; Ausio, Juan
Phosphorylation of Histone H2A.X by DNA-dependent Protein Kinase Is Not Affected by Core Histone Acetylation, but It Alters Nucleosome Stability and Histone H1 Binding
Journal of biological chemistry, v. 285, (23), June 2010, p. 17778-17788
Li, Andra; Yu, Yaping; Lee, Sheng-Chun; Ishibashi, Toyotaka; Lees-Miller, Susan P.; Ausio, Juan

Book chapter 1

Histone variants. signaling or structural modules
Handbook of Cell Signaling, 2/e / Edited by Ralph A. Bradshaw and Edward A. Dennis. Elsevier Inc., v.3, 2010, p. 2409-2425, Chapter 289
Ishibashi, Tototaka; Li, A.; Ausió, J.


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Article 6

Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome
Biochemistry, v. 48, (22), 2009, p. 5007-5017
Ishibashi, T.; Dryhurst, D.; Rose, K.L.; Shabanowitz, J.; Hunt, D.F.; Ausió, J.
Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates
BMC biology, v. 14, (7), December 2009, p. 86
Dryhurst, Deanna; Ishibashi, Toyotaka; Rose, Kristie L.; Eirin-Lopez, Jose M.; McDonald, Darin; Silva-Moreno, Begonia; Veldhoen, Nik; Helbing, Caren C.; Hendzel, Michael J.; Shabanowitz, Jeffrey; Hunt, Donald F.; Ausio, Juan
H2A.Z and H3.3 histone variants affect nucleosome structure: Biochemical and biophysical studies
Biochemistry, v. 48, (46), 2009, p. 10852-10857
Thakar, A.; Gupta, P.; Ishibashi, T.; Finn, R.; Silva-Moreno, B.; Uchiyama, S.; Fukui, K.; Tomschik, M.; Ausio, J.; Zlatanova, J.
New developments in post-translational modifications and functions of histone H2A variants
Biochemistry and cell biology, v. 87, (1), 2009, p. 7-17
Thambirajah, A.A.; Li, A.; Ishibashi, T.; Ausió, J.
The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues
BMC evolutionary biology, v. 9, (1), 2009, article number 31
EirínLópez, J.M.; González-Romero, R.; Dryhurst, D.; Ishibashi, T.; Ausió, J.
The multi-replication protein A (RPA) system - A new perspective
The FEBS journal, v. 276, (4), 2009, p. 943-963
Sakaguchi, K.; Ishibashi, T.; Uchiyama, Y.; Iwabata, K.


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Article 3

H2A.Bbd: A quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way
The FASEB journal, v. 22, (1), 2008, p. 316-326
EirínLópez, J.M.; Ishibashi, Toyotaka; Ausió, J.
MBD4-mediated glycosylase activity on a chromatin template is enhanced by acetylation
Molecular and cellular biology, v. 28, (15), 2008, p. 4734-4744
Ishibashi, T.; So, K.; Cupples, C.G.; Ausió, J.
MeCP2 preferentially binds to methylated linker DNA in the absence of the terminal tail of histone H3 and independently of histone acetylation
FEBS letters, v. 582, (7), 2008, p. 1157-1162
Ishibashi, Toyotaka; Thambirajah, A.A.; Ausió, J.


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Article 1

Probasin promoter assembles into a strongly positioned nucleosome that permits androgen receptor binding
Molecular and Cellular Endocrinology, v. 268, March 2007, p. 10-19
Maffey, Allison H.; Ishibashi, Toyotaka; He, Cheng; Wang, Xiaoying; White, Adrienne R.; Hendy, Stephen C.; Nelson, Colleen C.; Rennie, Paul S.; Ausio, Juan


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Article 6

A higher plant has three different types of RPA heterotrimeric complex
The Journal of biochemistry, v. 139, (1), 2006, p. 99-104
Ishibashi, Toyotaka; Kimura, S.; Sakaguchi, K.
A novel protein refolding method using a zeolite
Analytical biochemistry, v. 348, (2), 2006, p. 307-314
Chiku, H.; Kawai, A.; Ishibashi, Toyotaka; Takehara, M.; Yanai, T.; Mizukami, F.; Sakaguchi, K.
Characterization of T-DNA insertion mutants and RNAi silenced plants of Arabidopsis thaliana UV-damaged DNA binding protein 2 (AtUV-DDB2)
Plant molecular biology, v. 61, (1-2), 2006, p. 227-240
Koga, A.; Ishibashi, Toyotaka; Kimura, S.; Uchiyama, Y.; Sakaguchi, K.
DNA repair mechanisms in UV-B tolerant plants
JARQ, v. 40, (2), April 2006, p. 107-113
Ishibashi, Toyotaka; Kimura, Seisuke; Furukawa, Tornoyuki; Sakaguchi, Kengo
H2A.Z stabilizes chromatin in a way that is dependent on core histone acetylation
Journal of biological chemistry, v. 281, (29), July 2006, p. 20036-20044
Thambirajah, Anita A.; Dryhurst, Deanna; Ishibashi, Toyotaka; Li, Andra; Maffey, Allison H.; Ausio, Juan
Higher plant RecA-like protein is homologous to RadA
DNA repair, v. 5, (1), 2006, p. 80-88
Ishibashi, Toyotaka; Isogai, Minako; Kiyohara, Hiroyuki; Hosaka, Masahiro; Chiku, Hiroyuki; Koga, Asami; Yamamoto, Taichi; Uchiyama, Yukinobu; Mori, Yoko; Hashimoto, Junji; Ausió, Juan Thomas; Kimura, Seisuke; Sakaguchi, Kengo


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Article 5

Characterization of the origin recognition complex (ORC) from a higher plant, rice (Oryza sativa L.)
Gene, v. 353, (1), 2005, p. 23-30
Mori, Y.; Yamamoto, T.; Sakaguchi, N.; Ishibashi, Toyotaka; Furukawa, T.; Kadota, Y.; Kuchitsu, K.; Hashimoto, J.; Kimura, S.; Sakaguchi, K.
DNA repair in higher plants
生化学, v. 77, (2), 2005, p. 113-123
Kimura, S.; Ishibashi, T.; Yamamoto, T.; Sakaguchi, K.
Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage
Journal of Plant Research, v. 118, (2), 2005, p. 91-97
Yamamoto, T.; Mori, Y.; Ishibashi, Toyotaka; Uchiyama, Y.; Ueda, T.; Ando, T.; Hashimoto, J.; Kimura, S.; Sakaguchi, K.
Plastid DNA polymerases from higher plants, Arabidopsis thaliana
Biochemical and biophysical research communications, v. 334, (1), 2005, p. 43-50
Mori, Y.; Kimura, S.; Saotome, A.; Kasai, N.; Sakaguchi, N.; Uchiyama, Y.; Ishibashi, Toyotaka; Yamamoto, T.; Chiku, H.; Sakaguchi, K.
Two types of replication protein A in seed plants: Characterization of their functions in vitro and in vivo
The FEBS journal, v. 272, (13), 2005, p. 3270-3281
Ishibashi, Toyotaka; Koga, A.; Yamamoto, T.; Uchiyama, Y.; Mori, Y.; Hashimoto, J.; Kimura, S.; Sakaguchi, K.


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Article 5

Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes
Genes & development, v. 18, (17), 2004, p. 2172-2181
Yanagawa, Y.; Sullivan, J.A.; Komatsu, S.; Gusmaroli, G.; Suzuki, G.; Yin, J.; Ishibashi, Toyotaka; Saijo, Y.; Rubio, V.; Kimura, S.; Wang, J.; Deng, X.W.
Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex
Biochemical and biophysical research communications, v. 314, (2), 2004, p. 434-439
Yamamoto, T.; Mori, Y.; Ishibashi, Toyotaka; Uchiyama, Y.; Sakaguchi, N.; Furukawa, T.; Hashimoto, J.; Kimura, S.; Sakaguchi, K.
Degradation of proliferating cell nuclear antigen by 26S proteasome in rice (Oryza sativa L.)
Planta, v. 218, (4), 2004, p. 640-646
Yamamoto, T.; Kimura, S.; Mori, Y.; Oka, M.; Ishibashi, Toyotaka; Yanagawa, Y.; Nara, T.; Nakagawa, H.; Hashimoto, J.; Sakaguchi, K.
DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells
Nucleic acids research, v. 32, (9), 2004, p. 2760-2767
Kimura, S.; Tahira, Y.; Ishibashi, Tototaka; Mori, Y.; Mori, T.; Hashimoto, J.; Sakaguchi, K.
Plant DNA polymerase λ, a DNA repair enzyme that functions in plant meristematic and meiotic tissues
European journal of biochemistry, v. 271, (13), 2004, p. 2799-2807
Uchiyama, Y.; Kimura, S.; Yamamoto, T.; Ishibashi, Toyotaka; Sakaguchi, K.


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Article 5

Characterization of all the subunits of replication factor C from a higher plant, rice (Oryza sativa L.), and their relation to development
Plant molecular biology, v. 53, (1-2), 2003, p. 15-25
Furukawa, T.; Ishibashi, Toyotaka; Kimura, S.; Tanaka, H.; Hashimoto, J.; Sakaguchi, K.
Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L.
Planta, v. 217, (2), 2003, p. 175-183
Yamamoto, T.; Kimura, S.; Mori, Y.; Uchiyama, Y.; Ishibashi, Toyotaka; Hashimoto, J.; Sakaguchi, K.
OsSEND-1: A new RAD2 nuclease family member in higher plants
Plant molecular biology, v. 51, (1), 2003, p. 59-70
Furukawa, T.; Kimura, S.; Ishibashi, Toyotaka; Mori, Y.; Hashimoto, J.; Sakaguchi, K.
Plant-specific regulation of replication protein A2 (OsRPA2) from rice during the cell cycle and in response to ultraviolet light exposure
Planta, v. 217, (3), 2003, p. 457-465
Marwedel, T.; Ishibashi, Toyotaka; Lorbiecke, R.; Jacob, S.; Sakaguchi, K.; Sauter, M.
Rice UV-damaged DNA binding protein homologues are most abundant in proliferating tissues
Gene, v. 308, (1-2), 2003, p. 79-87
Ishibashi, Toyotaka; Kimura, S.; Yamamoto, T.; Furukawa, T.; Takata, K.I.; Uchiyama, Y.; Hashimoto, J.; Sakaguchi, K.


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Article 2

A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.)
Nucleic acids research, v. 30, (7), 2002, p. 1585-1592
Kimura, S.; Uchiyama, Y.; Kasai, N.; Namekawa, S.; Saotome, A.; Ueda, T.; Ando, T.; Ishibashi, Toyotaka; Oshige, M.; Furukawa, T.; Yamamoto, T.; Hashimoto, J.; Sakaguchi, K.
Characterization of DNA polymerase δ from a higher plant, rice (Oryza sativa L.)
Gene, v. 295, (1), 2002, p. 19-26
Uchiyama, Y.; Hatanaka, M.; Kimura, S.; Ishibashi, Toyotaka; Ueda, T.; Sakakibara, Y.; Matsumoto, T.; Furukawa, T.; Hashimoto, J.; Sakaguchi, K.


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Article 2

A plant homologue of 36 kDa subunit of replication factor C: Molecular cloning and characterization
Plant science, v. 161, (1), 2001, p. 99-106
Furukawa, T.; Kimura, S.; Ishibashi, Toyotaka; Hashimoto, J.; Sakaguchi, K.
Two types of replication protein A 70 kDa subunit in rice, Oryza sativa: Molecular cloning, characterization, and cellular & tissue distribution
Gene, v. 272, (1-2), 2001, p. 335-343
Ishibashi, Toyotaka; Kimura, S.; Furukawa, T.; Hatanaka, M.; Hashimoto, J.; Sakaguchi, K.


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Article 1

Molecular cloning and characterization of a plant homologue of the origin recognition complex 1 (ORC1)
Plant science, v. 158, (1-2), 2000, p. 33-39
Kimura, S.; Ishibashi, Toyotaka; Hatanaka, M.; Sakakibara, Y.; Hashimoto, J.; Sakaguchi, K.


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2016 4

Poly(ADP-ribosyl)ation-dependent Transient Chromatin Decondensation and Histone Displacement following Laser Microirradiation
Journal of biological chemistry, v. 291, (4), January 2016, p. 1789-1802
Strickfaden, Hilmar; McDonald, Darin; Kruhlak, Michael J.; Haince, Jean-Francois; Th'ng, John P.H.; Rouleau, Michele; Ishibashi, Toytaka; Corry, Gareth N.; Ausio, Juan; Underhill, D. Alan; Pokier, Guy G.; Hendzel, Michael J. Article
Histone Variants and Posttranslational Modifications in Spermatogenesis and Infertility
Epigenetic Biomarkers and Diagnostics / José Luis García-Giménez, editors. London : Academic Press, 2016, p. 479-496
Ausio, Juan; Zhang, Yinan; Ishibashi, Toyotaka Book chapter
Quantitative analysis of myosin-driven apical constriction in delaminating neuroblasts
Genetics Society of America (GSA) 57th Annual Drosophila Research Conference, Orlando, FL, US., 13-17 July 2016
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Chris, Doe; Yan, Yan Conference paper
Quantitative analysis of myosin-driven apical constriction in delaminating neuroblasts
2016 Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, Chinese University of Hong Kong, 11 June 2016
An, Yanru; Xue, Guosheng; Ishibashi, Toyotaka; Chris, Doe; Yan, Yan Conference paper

2014 3

Molecular Mechanisms of Transcription through Single-Molecule Experiments
Chemical Reviews, v. 114, (6), March 2014, p. 3203-3223
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Bintu, Lacramioara; Bustamante, Carlos Article
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics
Proceedings of the National Academy of Sciences of the United States of America, v. 111, (9), March 2014, p. 3419-3424
Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Coello, Yves; Lionberger, Troy A.; Lubkowska, Lucyna; Ponticelli, Alfred S.; Kashlev, Mikhail; Bustamante, Carlos Article
Complete Dissection of Transcription Elongation Reveals Slow Translocation of RNA Polymerase II in a Linear Ratchet Mechanism
Biophysical Journal, v. 106, (2), January 2014, p. 485a-486a, Supplement 1
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kahlev, Mikhail; Bustamante, Carlos J. Conference paper

2013 3

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
eLife, v. 2013, (2), September 2013, article number e00971
Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos J. Article
A Quantitative Kinetic Model of Eukaryotic Transcription Elongation from Single-Molecule Experiments
Biophysical Journal, v. 104, (2), January 2013, p. 364A-364A
Dangkulwanich, Manchuta; Liu, Shixin; Ishibashi, Toyotaka; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos Conference paper
Dissecting the Nucleosomal Barrier to Transcription
Biophysical Journal, v. 102, (3), January 2013, p. 284A-284A
Ishibashi, Toyotaka; Bintu, Lacramioara; Dangkulwanich, Manchuta; Wu, Gloria; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos Conference paper

2012 2

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Proceedings of the National Academy of Sciences of the United States of America, v. 109, (23), 2012, p. 8948-8953
Zamft, B.; Bintu, L.; Ishibashi, Toyotaka; Bustamante, C. Article
Nucleosomal Elements that Control the Topography of the Barrier to Transcription
Cell, v. 151, (4), November 2012, p. 738-749
Bintu, Lacramioara; Ishibashi, Toyotaka; Dangkulwanich, Manchuta; Wu, Yueh-Yi; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos Article

2010 3

H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis
Nucleic acids research, v. 38, (6), April 2010, p. 1780-1789
Ishibashi, Toyotaka; Li, Andra; Eirin-Lopez, Jose M.; Zhao, Ming; Missiaen, Kristal; Abbott, D. Wade; Meistrich, Marvin; Hendzel, Michael J.; Ausio, Juan Article
Phosphorylation of Histone H2A.X by DNA-dependent Protein Kinase Is Not Affected by Core Histone Acetylation, but It Alters Nucleosome Stability and Histone H1 Binding
Journal of biological chemistry, v. 285, (23), June 2010, p. 17778-17788
Li, Andra; Yu, Yaping; Lee, Sheng-Chun; Ishibashi, Toyotaka; Lees-Miller, Susan P.; Ausio, Juan Article
Histone variants. signaling or structural modules
Handbook of Cell Signaling, 2/e / Edited by Ralph A. Bradshaw and Edward A. Dennis. Elsevier Inc., v.3, 2010, p. 2409-2425, Chapter 289
Ishibashi, Tototaka; Li, A.; Ausió, J. Book chapter

2009 6

Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome
Biochemistry, v. 48, (22), 2009, p. 5007-5017
Ishibashi, T.; Dryhurst, D.; Rose, K.L.; Shabanowitz, J.; Hunt, D.F.; Ausió, J. Article
Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates
BMC biology, v. 14, (7), December 2009, p. 86
Dryhurst, Deanna; Ishibashi, Toyotaka; Rose, Kristie L.; Eirin-Lopez, Jose M.; McDonald, Darin; Silva-Moreno, Begonia; Veldhoen, Nik; Helbing, Caren C.; Hendzel, Michael J.; Shabanowitz, Jeffrey; Hunt, Donald F.; Ausio, Juan Article
H2A.Z and H3.3 histone variants affect nucleosome structure: Biochemical and biophysical studies
Biochemistry, v. 48, (46), 2009, p. 10852-10857
Thakar, A.; Gupta, P.; Ishibashi, T.; Finn, R.; Silva-Moreno, B.; Uchiyama, S.; Fukui, K.; Tomschik, M.; Ausio, J.; Zlatanova, J. Article
New developments in post-translational modifications and functions of histone H2A variants
Biochemistry and cell biology, v. 87, (1), 2009, p. 7-17
Thambirajah, A.A.; Li, A.; Ishibashi, T.; Ausió, J. Article
The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues
BMC evolutionary biology, v. 9, (1), 2009, article number 31
EirínLópez, J.M.; González-Romero, R.; Dryhurst, D.; Ishibashi, T.; Ausió, J. Article
The multi-replication protein A (RPA) system - A new perspective
The FEBS journal, v. 276, (4), 2009, p. 943-963
Sakaguchi, K.; Ishibashi, T.; Uchiyama, Y.; Iwabata, K. Article

2008 3

H2A.Bbd: A quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way
The FASEB journal, v. 22, (1), 2008, p. 316-326
EirínLópez, J.M.; Ishibashi, Toyotaka; Ausió, J. Article
MBD4-mediated glycosylase activity on a chromatin template is enhanced by acetylation
Molecular and cellular biology, v. 28, (15), 2008, p. 4734-4744
Ishibashi, T.; So, K.; Cupples, C.G.; Ausió, J. Article
MeCP2 preferentially binds to methylated linker DNA in the absence of the terminal tail of histone H3 and independently of histone acetylation
FEBS letters, v. 582, (7), 2008, p. 1157-1162
Ishibashi, Toyotaka; Thambirajah, A.A.; Ausió, J. Article

2007 1

Probasin promoter assembles into a strongly positioned nucleosome that permits androgen receptor binding
Molecular and Cellular Endocrinology, v. 268, March 2007, p. 10-19
Maffey, Allison H.; Ishibashi, Toyotaka; He, Cheng; Wang, Xiaoying; White, Adrienne R.; Hendy, Stephen C.; Nelson, Colleen C.; Rennie, Paul S.; Ausio, Juan Article

2006 6

A higher plant has three different types of RPA heterotrimeric complex
The Journal of biochemistry, v. 139, (1), 2006, p. 99-104
Ishibashi, Toyotaka; Kimura, S.; Sakaguchi, K. Article
A novel protein refolding method using a zeolite
Analytical biochemistry, v. 348, (2), 2006, p. 307-314
Chiku, H.; Kawai, A.; Ishibashi, Toyotaka; Takehara, M.; Yanai, T.; Mizukami, F.; Sakaguchi, K. Article
Characterization of T-DNA insertion mutants and RNAi silenced plants of Arabidopsis thaliana UV-damaged DNA binding protein 2 (AtUV-DDB2)
Plant molecular biology, v. 61, (1-2), 2006, p. 227-240
Koga, A.; Ishibashi, Toyotaka; Kimura, S.; Uchiyama, Y.; Sakaguchi, K. Article
DNA repair mechanisms in UV-B tolerant plants
JARQ, v. 40, (2), April 2006, p. 107-113
Ishibashi, Toyotaka; Kimura, Seisuke; Furukawa, Tornoyuki; Sakaguchi, Kengo Article
H2A.Z stabilizes chromatin in a way that is dependent on core histone acetylation
Journal of biological chemistry, v. 281, (29), July 2006, p. 20036-20044
Thambirajah, Anita A.; Dryhurst, Deanna; Ishibashi, Toyotaka; Li, Andra; Maffey, Allison H.; Ausio, Juan Article
Higher plant RecA-like protein is homologous to RadA
DNA repair, v. 5, (1), 2006, p. 80-88
Ishibashi, Toyotaka; Isogai, Minako; Kiyohara, Hiroyuki; Hosaka, Masahiro; Chiku, Hiroyuki; Koga, Asami; Yamamoto, Taichi; Uchiyama, Yukinobu; Mori, Yoko; Hashimoto, Junji; Ausió, Juan Thomas; Kimura, Seisuke; Sakaguchi, Kengo Article

2005 5

Characterization of the origin recognition complex (ORC) from a higher plant, rice (Oryza sativa L.)
Gene, v. 353, (1), 2005, p. 23-30
Mori, Y.; Yamamoto, T.; Sakaguchi, N.; Ishibashi, Toyotaka; Furukawa, T.; Kadota, Y.; Kuchitsu, K.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article
DNA repair in higher plants
生化学, v. 77, (2), 2005, p. 113-123
Kimura, S.; Ishibashi, T.; Yamamoto, T.; Sakaguchi, K. Article
Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage
Journal of Plant Research, v. 118, (2), 2005, p. 91-97
Yamamoto, T.; Mori, Y.; Ishibashi, Toyotaka; Uchiyama, Y.; Ueda, T.; Ando, T.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article
Plastid DNA polymerases from higher plants, Arabidopsis thaliana
Biochemical and biophysical research communications, v. 334, (1), 2005, p. 43-50
Mori, Y.; Kimura, S.; Saotome, A.; Kasai, N.; Sakaguchi, N.; Uchiyama, Y.; Ishibashi, Toyotaka; Yamamoto, T.; Chiku, H.; Sakaguchi, K. Article
Two types of replication protein A in seed plants: Characterization of their functions in vitro and in vivo
The FEBS journal, v. 272, (13), 2005, p. 3270-3281
Ishibashi, Toyotaka; Koga, A.; Yamamoto, T.; Uchiyama, Y.; Mori, Y.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article

2004 5

Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes
Genes & development, v. 18, (17), 2004, p. 2172-2181
Yanagawa, Y.; Sullivan, J.A.; Komatsu, S.; Gusmaroli, G.; Suzuki, G.; Yin, J.; Ishibashi, Toyotaka; Saijo, Y.; Rubio, V.; Kimura, S.; Wang, J.; Deng, X.W. Article
Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex
Biochemical and biophysical research communications, v. 314, (2), 2004, p. 434-439
Yamamoto, T.; Mori, Y.; Ishibashi, Toyotaka; Uchiyama, Y.; Sakaguchi, N.; Furukawa, T.; Hashimoto, J.; Kimura, S.; Sakaguchi, K. Article
Degradation of proliferating cell nuclear antigen by 26S proteasome in rice (Oryza sativa L.)
Planta, v. 218, (4), 2004, p. 640-646
Yamamoto, T.; Kimura, S.; Mori, Y.; Oka, M.; Ishibashi, Toyotaka; Yanagawa, Y.; Nara, T.; Nakagawa, H.; Hashimoto, J.; Sakaguchi, K. Article
DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells
Nucleic acids research, v. 32, (9), 2004, p. 2760-2767
Kimura, S.; Tahira, Y.; Ishibashi, Tototaka; Mori, Y.; Mori, T.; Hashimoto, J.; Sakaguchi, K. Article
Plant DNA polymerase λ, a DNA repair enzyme that functions in plant meristematic and meiotic tissues
European journal of biochemistry, v. 271, (13), 2004, p. 2799-2807
Uchiyama, Y.; Kimura, S.; Yamamoto, T.; Ishibashi, Toyotaka; Sakaguchi, K. Article

2003 5

Characterization of all the subunits of replication factor C from a higher plant, rice (Oryza sativa L.), and their relation to development
Plant molecular biology, v. 53, (1-2), 2003, p. 15-25
Furukawa, T.; Ishibashi, Toyotaka; Kimura, S.; Tanaka, H.; Hashimoto, J.; Sakaguchi, K. Article
Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L.
Planta, v. 217, (2), 2003, p. 175-183
Yamamoto, T.; Kimura, S.; Mori, Y.; Uchiyama, Y.; Ishibashi, Toyotaka; Hashimoto, J.; Sakaguchi, K. Article
OsSEND-1: A new RAD2 nuclease family member in higher plants
Plant molecular biology, v. 51, (1), 2003, p. 59-70
Furukawa, T.; Kimura, S.; Ishibashi, Toyotaka; Mori, Y.; Hashimoto, J.; Sakaguchi, K. Article
Plant-specific regulation of replication protein A2 (OsRPA2) from rice during the cell cycle and in response to ultraviolet light exposure
Planta, v. 217, (3), 2003, p. 457-465
Marwedel, T.; Ishibashi, Toyotaka; Lorbiecke, R.; Jacob, S.; Sakaguchi, K.; Sauter, M. Article
Rice UV-damaged DNA binding protein homologues are most abundant in proliferating tissues
Gene, v. 308, (1-2), 2003, p. 79-87
Ishibashi, Toyotaka; Kimura, S.; Yamamoto, T.; Furukawa, T.; Takata, K.I.; Uchiyama, Y.; Hashimoto, J.; Sakaguchi, K. Article

2002 2

A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.)
Nucleic acids research, v. 30, (7), 2002, p. 1585-1592
Kimura, S.; Uchiyama, Y.; Kasai, N.; Namekawa, S.; Saotome, A.; Ueda, T.; Ando, T.; Ishibashi, Toyotaka; Oshige, M.; Furukawa, T.; Yamamoto, T.; Hashimoto, J.; Sakaguchi, K. Article
Characterization of DNA polymerase δ from a higher plant, rice (Oryza sativa L.)
Gene, v. 295, (1), 2002, p. 19-26
Uchiyama, Y.; Hatanaka, M.; Kimura, S.; Ishibashi, Toyotaka; Ueda, T.; Sakakibara, Y.; Matsumoto, T.; Furukawa, T.; Hashimoto, J.; Sakaguchi, K. Article

2001 2

A plant homologue of 36 kDa subunit of replication factor C: Molecular cloning and characterization
Plant science, v. 161, (1), 2001, p. 99-106
Furukawa, T.; Kimura, S.; Ishibashi, Toyotaka; Hashimoto, J.; Sakaguchi, K. Article
Two types of replication protein A 70 kDa subunit in rice, Oryza sativa: Molecular cloning, characterization, and cellular & tissue distribution
Gene, v. 272, (1-2), 2001, p. 335-343
Ishibashi, Toyotaka; Kimura, S.; Furukawa, T.; Hatanaka, M.; Hashimoto, J.; Sakaguchi, K. Article

2000 1

Molecular cloning and characterization of a plant homologue of the origin recognition complex 1 (ORC1)
Plant science, v. 158, (1-2), 2000, p. 33-39
Kimura, S.; Ishibashi, Toyotaka; Hatanaka, M.; Sakakibara, Y.; Hashimoto, J.; Sakaguchi, K. Article


No Publications






Teaching Assignment

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2021-22 Winter 0 2021-22 Fall 1 2020-21 Summer 1 2020-21 Spring 5 2020-21 Winter 0 2020-21 Fall 7

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LIFS6113E Current Topics in Biochemistry and Biophysics


UROP1000 Undergraduate Research Opportunities


BIBU4850 Biotechnology and Business Project Research
LIFS4800 Epigenetics and Chromosome Biology
LIFS4961 Biochemistry and Cell Biology Capstone Project
LIFS4963 Biotechnology Capstone Project
LIFS4981 Biochemistry and Cell Biology Project Research II


BIBU4850 Biotechnology and Business Project Research
LIFS4960 Biological Science Capstone Project
LIFS4961 Biochemistry and Cell Biology Capstone Project
LIFS4971 Biochemistry and Cell Biology Project Research I
LIFS5070 Workshops in Biosciences
LIFS5710 Cellular Regulation
LIFS6113D Current Topics in Biochemistry and Biophysics


No Teaching Assignments


No Teaching Assignments






Research Postgraduate (RPG) Supervision From January 2019 to December 2022 (As of 30 January 2022)

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All Supervisions Current RPGs Graduated RPGs

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Current RPGs

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Doctor of Philosophy NGUYEN, Thi Thuy
Life Science( 2020 - )

PANG, Yu Hin
Life Science( 2020 - )

MA, Xiaohui
Life Science( 2018 - )

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Graduated RPGs

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Doctor of Philosophy DING, Dongbo
Life Science( Completed in 2020 )

LONG, Mengping
Life Science( Completed in 2019 )

SUN, Xulun
Life Science( Completed in 2019 )

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Master of Philosophy LEE, Min-hsun
Life Science( Completed in 2021 )

NGUYEN, Thi Thuy
Life Science( Completed in 2020 )

PANG, Yu Hin
Life Science( Completed in 2020 )









ProjectsFrom January 2020 to December 2022

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All Projects 5 Leading Projects 2 Participating Projects 3

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Detection and Functional Study of Genetic Structure Variations in Familial Breast Cancer Using the Third Generation Sequencing Technology


应用第三代测序技术对家族性乳腺癌基因结构变异的检测及功能研究 Participating


Innovation and Technology Fund


Project Team (HKUST)
YU Weichuan (Lead)
ISHIBASHI Toyotaka


2022 -




Structure and molecular mechanisms of the eukaryotic replisome


真核生物复制机器的结构和分子机制研究 Participating


RGC - Collaborative Research Fund


Project Team (HKUST)
ISHIBASHI Toyotaka


2021 -




A Study of Self-Restraining Mechanisms of DNA Damage Surveillance and Repair


DNA损伤监测和修复: 自我约束机制的研究 Participating


RGC - Collaborative Research Fund


Project Team (HKUST)
ISHIBASHI Toyotaka


2018 - 2021




Biochemical and functional studies of a novel histone H4 variant H4G


乳腺癌细胞特异性组蛋白变体H4G的生化学和功能研究 Leading


RGC - General Research Fund


Project Team (HKUST)
ISHIBASHI Toyotaka (Lead)


2017 - 2021




Elucidating the role of chromatin dynamics during spermatogenesis and its impact on transcription at the single-molecule level.


在单分子水准上阐明染色质组分与结构动态特性对精子发生和转录的影响 Leading


RGC - Early Career Scheme


Project Team (HKUST)
ISHIBASHI Toyotaka (Lead)


2014 - 2020