Publication

Nguyen TT*, Ding D*, Bai X, Pang MYH, Deng M, Liu Y, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T#. The novel H2B variant, H2BW2, destabilizes nucleosomes​ and enhances the expression of TERRA non-coding RNA​,  in submission (* co-first author)

Hao J, Shi J, Lian S, Zhang Z, Hu T, Ishibashi T, Wang D, Wang S, Fan X, Yu W. ​gSV: a general structural variant detector using long-read sequencing data, in submission

Deng M, Chen Z, Zhang X, Li C, Nguyen TT, Wang J, Dou K, Ishibashi T, Yan Y. Metabolic stress-induced epigenetic reprogramming is an evolutionarily ancient path to malignant growth,  in submission

Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T. (2024) Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions, Nucl. Acids Res., 52(19), 11612-11625

Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y. (2023) Synergism between CMG helicase and leading strand DNA polymerase at replication fork, Nat.Commun.,14(1),5849

Hu T, Li J, Long M, Wu J, Zhang Z, Xie F, Zhao J, Yang H, Song Q, Lian S, Shi J, Guo X, Yuan D, Lang D, Yu G, Liang B, Zhou X, Ishibashi T, Fan X, Yu W, Wang D, Wang Y, Peng IF, Wang S. (2022) Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing, Front. Cell Dev. Biol. 10, 854640

Kang TZE, Zhu L, Yang D, Ding D, Zhu X, Wan YCE, Liu L, Ramakrishnan S, Han J, Chan SY, Wang X, Ishibashi T, Li Q, Chan KM. (2021) The elevated transcription of ADAM19 by the oncohistone H2BE76K contributes to oncogenic properties in breast cancer, J. Biol. Chem., 296, 100374

Ding D, Sun X, Pang MYH, An L, Huen MSY, Hu T, Ishibashi T (2021) RecQl5 KIX domain splicing isoforms have distinct functions in transcription repression and DNA damage response, DNA repair, 97,103007

Ding D, Nguyen TT, Pang MYH, Ishibashi T. (2021) Primate-specific histone variants, Genome. 64(4), 337-346.

Jing Y, Ding D, Tian G, Kwan KCJ, Liu Z, Ishibashi T#, Li XD#. (2020) Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility, Nucl. Acids Res. 48(17), 9538-49. #co-corresponding author

Dong C, West KL, Tan XY, Li J, Ishibashi T, Yu CH, Sy SMH, Leung JWC, Huen MSY. (2020) Screen identifies DYRK1B network as mediator of transcription repression on damaged chromatin, Proc. Natl. Acad. Sci. USA, 117(29), 17019-30.

Wan YCE, Liu J, Zhu L, Kang TZE, Zhu X, Lis J, Ishibashi T, Danko CG, Wang X and Chan KM. (2020) The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma, Signal Transduct. Target Ther., 5(1), 106.

Pang YHP, Sun X, Ausio J, Ishibashi T#. (2020) Histone H4 variant, H4G, drives ribosomal RNA transcription and breast cancer cell proliferation by loosing nucleolar chromatin structure, J. Cell Physiol. 235(12), 9601-8. #corresponding author 

Wang Y.C.E., Leung T.C.S., Ding D., Sun X., Liu J., Kang T.Z.E., Yang D., Zhang Y., Zhang J., Qian C., Huen M.S.Y., Li Q., Chow M.Z.Y., Han J., Goel A., Wang X., Ishibashi T.#, Chan K.M.#. (2020) Cancer-associated histone mutation H2BG53D disrupts DNA-histone octamer interaction and promotes oncogenic phenotypes, Signal Transduct. Target Ther., 5, 27. 

Deng M., Wang, Y., Zhang L., Yang Y., Haung S., Wang J., Ge H., Ishibashi T., Yan Y. (2019) Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs, Development, 146(18). 

Long M.*, Sun X.*, Shi W., Yanru A., Leung T.C.S., Ding D., Cheema M.S., MacPherson N., Nelson C., Ausio J., Yan Y., Ishibashi T#. (2019) Novel histone variant H4G regulates rDNA transcription in breast cancer, Nucl. Acids Res., 47(16), 8399-8409 (* co-first author)

Yu H., Xue C., Long M., Jia H., Xue G., Du S., Coello Y., Ishibashi T.# (2018) TEFM enhances transcription elongation by modifying mtRNAP pausing dynamics, Biophys.  J., 15(12), 2259-2300 

Jing Y., Liu Z., Tian G., Bao X., Ishibashi T., Li X.D. (2018) Site-specific installation of succinyl lysine analog into histones the effect of H2BK34 succinylation on nucleosome dynamics, Cell Chem. Biol., 25(2), 166-174. 

Yanru A, Xue G, Yang S, Deng M, Zhou X, Yu W, Ishibashi T, Zhang L, Yan Y. (2017) Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts, Develpment, 144(12), 2153-64.

Strickfaden H, McDonald D, Kruhlak MJ, Haince JF, Th’ng JP, Rouluau M, Ishibashi T, Corry GN, Ausio J, Underhill DA, Poirier GG, Hendzel MJ. (2016)  Poly(ADP)-ribosylation-dependent transient chromation decondensation and histone displacement following laser micro-irradiation, J. Biol. Chem., 291(4), 1789-802.

Ishibashi T*#, Dangkulwanich M*, Coello Y*, Lionberger TA, Lubkowska L, Ponticelli AS, Kashlev M, Bustamante C#. (2014) Complete dissection of transcription elongation reveals slow translocation of Pol II in a linear ratchet mechanism, PNAS, 111(9), 3419-24. (*co-first author) 

Dangkulwanich M, Ishibashi T., Bintu L, Bustamante C. (2014) Molecular mechanisms of transcription through single-molecule experiments, Chem. Rev., Review, 114(6), 3203-23.

Dangkulwanich M, Ishibashi T#, Liu S, Kireeva ML, Lubkowska L, Kashlev M, Bustamante C. (2013) Complete dissection of transcription elongation reveals slow translocation of Pol II in a linear ratchet mechanism, Elife, 2, e00971. #co-first author

Bintu L, Ishibashi T#, Dangkulwanich M, Wu Y, Lubkowska L, Kashlev M, Bustamante C. (2012) Nucleosomal elements that control the topography of the barrier to transcription, Cell, 151(4), 738-49. #co-first author

Zamft B, Bintu L, Ishibashi T, Bustamante C. (2012) Nascent RNA structure modulate of the transcriptional dynamics of RNA Polymerases, Proc. Natl. Acad. Sci. USA, 109(23), 8948-53.

Ishibashi T#, Li A, Eirín-López JM, Ming M, Abbott DW, Meistrich ML, Ausió J. (2010) H2A.Bbd: An X-chromosome-encoded histone involved in mammalian spermiogenesis, Nucl. Acids Res., 38(6), 1780-9. #co-first author

Li A, Yu Y, Lee SC, Ishibashi T, Lees-Miller SP, Ausió J. (2010) Phosphorylation of histone H2A.X by DNA-dependent Protein Kinase (DNA-PK) is not affected by core histone acetylation but it alters nucleosome stability and histone H1 binding, J. Biol. Chem., 285(23), 17778-88.

Dryhurst D, Ishibashi T, Rose KL, Eirín-López JM, McDonald D, Silva-Moreno B, Veldhoen N, Helbing CC, Hendzel MJ, Shabanowitz J, Hunt DF, Ausió J. (2009) Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates, BMC Biol., 14(7), 86.

Thakar A, Gupta P, Ishibashi T, Finn R, Silva-Moreno B, Uchiyama S, Fukui K, Tomoschik M, Ausió J, Zlatanova J. (2009) H2A.Z and H3.3 histone variants affect nucleosome structure: biochemical and biophysical studies, Biochemistry, 48(46), 10852-7.

Ishibashi T#, Dryhurst D, Rose KL, Shabanowitz J, Hunt DF, Ausió J. (2009) Acetylation of Vertebrate H2A.Z and its effect on the structure of the nucleosome, Biochemistry, 48(22), 5007-17. #first author

Eirín-López JM, Gonzalez-Romelo R, Dryhurst D, Ishibashi T, Ausió J. (2009) The evolutionary and functional 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 acids, BMC Evol. Biol., 9(31), 9-31.

Sakaguchi K, Ishibashi T, Uchiyama Y, Iwabata K. (2009) The Multi-Replication Protein A (RPA) System; A New Perspective, FEBS J., Review, 276(4), 943-63.

Thambirajah AA, Li A, Ishibashi T, Ausió J. (2009) Post-translational modifications of H2A variants, Biochem. Cell Biol., Review, 87(1), 7-17.

Eirin-Lopez JM, Ishibashi T#, Ausió J. (2008) H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way, FASEB J., 22(1), 316-26. #co-first author

Ishibashi T#, So K, Cupples GC, Ausió J. (2008) MBD4-mediated glycosylase activity on a chromatin template is enhanced by acetylation, Mol. Cell. Biol., 28(15), 4734-44. #first author

Ishibashi T#, Thambirajah AA, Ausió J. (2008) MeCP2 preferentially binds to methylated linker DNA in the absence of the terminal tail of histone H3 and independently of histone acetylation, FEBS Lett., 582(7), 1157-62. #first author

Maffey AH, Ishibashi T, He C, Wang X, White AR, Hendy SC, Nelson CC, Rennis PS, Ausió J. (2007) Probasin promoter assembles into a strongly positioned nucleosome that permits androgen receptor binding, Mol. Cell. Endocrinol., 268(1-2), 10-9.

Koga A, Ishibashi T, Kimura S, Uchiyama Y, Sakaguchi K. (2006) Characterization of T-DNA insertion mutants and RNAi silenced plants of Arabidopsis thaliana UV-damaged DNA binding protein 2 (AtUV-DDB2), Plant Mol. Biol., 61(1-2), 227-40.

Thambirajah AA, Dryhurst D, Ishibashi T, Li A, Maffey AH, Ausió J. (2006) H2A.Z stabilizes chromatin in a way that is dependent on core histone acetylation, J. Biol. Chem., 281(29), 20036-44.

Ishibashi T, Kimura S, Furukawa T, Sakaguchi K. (2006) DNA repair mechanisms in UV-B tolerant plants, JARQ, 40, 107-13. 

Ishibashi T, Kimura S, Sakaguchi K. (2006) A higher plant has three different types of RPA heterotrimeric complex, J. Biochem., 139(1), 99-104.

Chiku H, Kawai A, Ishibashi T, Takehara M, Yanai T, Mizukami F, Sakaguchi K. (2006) A novel protein refolding method using a zeolite, Anal. Biochem., 348(2), 307-14.

Ishibashi T#, Isogai M, Chiku H, Hosaka M, Koga A, Yamamoto T, Uchiyama Y, Mori Y, Kiyohara H, Hashimoto J, Ausió J, Kimura S, Sakaguchi K. (2006) Higher plant RecA-like protein is homologous to RadA, DNA Repair, 5(1), 80-8. #first author

Mori Y, Kimura S, Saotome A, Kasai N, Sakaguchi N, Uchiyama Y, Ishibashi T, Yamamoto T, Chiku H, Sakaguchi K. (2005) Plastid DNA polymerases from higher plants, Arabidopsis thaliana, Biochem. Biophys. Res. Commun., 334(1), 43-50.

Ishibashi T#, Koga A, Yamamoto T, Uchiyama Y, Mori Y, Hashimoto J, Kimura S, Sakaguchi K. (2005) Two types of Replication Protein A in seed plants, FEBS J., 272(13), 3270-81. #first author

Yamamoto T, Mori Y, Ishibashi T, Uchiyama Y, Ueda T, Ando T, Hashimoto J, Kimura S, Sakaguchi K. (2005) Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage. J. Plant Res., 118(2), 91-7.

Yanagawa Y, Sullivan JA, Komatsu S, Gusmarioli G, Suzuki G, Yin J, Ishibashi T, Saijo Y, Rubio V, Kimura S, Wang J, Deng XW. (2004) Arabidopsis COP10 forms a complex with DDB1a and DET1 and enhances the activity of ubiquitin conjugating enzymes. Genes Dev., 18, 2172-81.

Uchiyama Y, Kimura S, Yamamoto T, Ishibashi T, Sakaguchi K. (2004) Plant DNA polymerase lamda, a DNA repair enzyme which functions in plant meristematic and meiotic tissues, Eur. J. Biochem., 271(13), 2799-807.

Kimura S, Tahira Y, Ishibashi T, Mori Y, Mori T, Hashimoto J, Sakaguchi K. (2004) DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while dark repair is active in proliferating cells, Nucl. Acids Res., 32(9), 2760-7.

Yamamoto T, Mori Y, Ishibashi T, Uchiyama Y, Sakaguchi N, Furukawa T, Hashimoto J, Kimura S, Sakaguchi K. (2004) Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex, Biochem. Biophys. Res. Commun., 314(2), 434-9.

Yamamoto T, Kimura S, Mori Y, Oka M, Ishibashi T, Yanagawa Y, Nara T, Nakagawa H, Hashimoto J, Sakaguchi K. (2004) Degradation of proliferating cell nuclear antigen by 26S proteasome in rice (Oryza sativa L.) Planta, 218(4), 640-6.

Furukawa T, Ishibashi T, Kimura S, Tanaka H, Hashimoto J, Sakaguchi K. (2003) Characterization of all the subunits of replication factor C from a higher plant, rice (Oryza sativa L.), and their relation to development, Plant Mol. Biol., 53(1-2), 15-25.

Marwedel T, Ishibashi T, Lorbiecke R, Jacob S, Sakaguchi K, Sauter M. (2003) Plant-specific regulation of replication protein A2 (OsRPA2) from rice during the cell cycle and in response to ultraviolet light exposure, Planta, 217(3), 457-65.

Yamamoto T, Kimura S, Mori Y, Uchiyama Y, Ishibashi T, Hashimoto J, Sakaguchi K. (2003) Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L., Planta, 217(2), 175-83.

Ishibashi T#, Kimura S, Yamamoto T, Furukawa T, Takata K, Uchiyama Y, Hashimoto J, Sakaguchi K. (2003) Rice UV-damaged DNA binding protein homologues are most abundant in proliferating tissues, Gene, 308, 79-87. #first author

Furukawa T, Kimura S, Ishibashi T, Mori Y, Hashimoto J, Sakaguchi K. (2003) OsSEND-1: a new RAD2 nuclease family member in higher plants, Plant Mol. Biol., 51, 59-70.

Uchiyama Y, Hatanaka M, Kimura S, Ishibashi T, Ueda T, Sakakibara Y, Matsumoto T, Furukawa T, Hashimoto J, Sakaguchi K. (2002) Characterization of DNA polymerase delta from a higher plant, rice (Oryza sativa L.), Gene, 295(1), 19-26.

Kimura S, Uchiyama Y, Kasai N, Namekawa S, Saotome A, Ueda T, Ando T, Ishibashi T, Oshige M, Furukawa T, Yamamoto T, Hashimoto J, Sakaguchi K. (2002) A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.), Nucl. Acids Res., 30(7), 1585-92.

Ishibashi T#, Kimura S, Furukawa T, Hatanaka M, Hashimoto J, Sakaguchi K. (2001) Two types of replication protein A 70 kDa subunit in rice, Oryza sativa: molecular cloning, characterization, and cellular & tissue distribution, Gene, 272(1-2), 335-43. #first author

Furukawa T, Kimura S, Ishibashi T, Hashimoto J, Sakaguchi K. (2001) Plant homologue of 36 kDa subunit of replication factor C: molecular cloning and characterization, Plant Sci., 161, 99-106.

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