Papers

108. Azuma, N., Yokoi, T., Tanaka, T., Matsuzaka, E., Saida, Y., Nishina, S., Terao, M., Takada, S., Fukami, M., Okamura, K., Maehara, K., Yamasaki, T., Hirayama, J., Nishina, H., Handa, H., and Yamaguchi, Y. (2023) Integrator complex subunit 15 controls mRNA splicing and is critical for eye development. Hum. Mol. Genet. ddad034. [Pubmed Citation]

107. Yamamoto, J., Ito, T., Yamaguchi, Y., and Handa, H. (2022) Discovery of CRBN as a target of thalidomide: a breakthrough for progress in the development of protein degraders. Chem. Soc. Rev. 51, 6234-6250. [Pubmed Citation]

106. Suzuki, H., Abe, R., Shimada, M., Hirose, T., Hirose, H., Noguchi, K., Ike, Y., Yasui, N., Furugori, K., Yamaguchi, Y., Toyoda, A., Suzuki, Y., Yamamoto, T., Saitoh, N., Sato, S., Tomomori-Sato, C., Conaway, R., Conaway, J., and Takahashi, H. (2022) The 3′ Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies. Nat. Commun. 13, 2905. [Pubmed Citation]

105. Okuda, M., Suwa, T., Suzuki, H., Yamaguchi, Y., and Nishimura, Y. (2022) Three human RNA polymerases interact with TFIIH via a common RPB6 subunit. Nucleic Acids Res. 50, 1-16. [Pubmed Citation]

104. Shimizu, N., Asatsuma-Okumura, T., Yamamoto, J., Yamaguchi, Y., Handa, H., Ito, T. (2021) PLZF and its fusion proteins are pomalidomide-dependent CRBN neosubstrates. Commun. Biol. 4, 1277. [Pubmed Citation]

103. Ito, T., Yamaguchi, Y., and Handa, H. (2021) Exploiting ubiquitin ligase cereblon as a target for small-molecule compounds in medicine and chemical biology. Cell Chem. Biol. 28, 987-999. [Pubmed Citation]

102. Yamamoto, J., Suwa, T., Murase, Y., Tateno, S., Mizutome, H., Asatsuma-Okumura, T., Shimizu, N., Kishi, T., Momose, S., Kizaki, M., Ito, T., Yamaguchi, Y., and Handa, H. (2020) ARID2 is a pomalidomide-dependent CRL4CRBN substrate in multiple myeloma cells. Nat. Chem. Biol. 16, 1208-1217. [Pubmed Citation]

101. Tateno, S., Iida, M., Fujii, S., Suwa, T., Katayama, M., Tokuyama, H., Yamamoto, J., Ito, T., Sakamoto, S., Handa, H., and Yamaguchi, Y. (2020) Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide. Sci. Rep. 10, 4012. [Pubmed Citation]

100. Takahashi, H., Ranjan, A., Chen, S., Suzuki, H., Shibata, M., Hirose, T., Hirose, H., Sasaki, K., Abe, R., Chen, K., He, Y., Zhang, Y., Takigawa, I., Tsukiyama, T., Watanabe, M., Fujii, S., Iida, M., Yamamoto, J., Yamaguchi, Y., Suzuki, Y., Matsumoto, M., Nakayama, K., Washburn, M., Saraf, A., Florens, L., Sato, S., Tomomori-Sato, C., Conaway, R., Conaway, J., and Hatakeyama, S. (2020) The role of Mediator and Little Elongation Complex in transcription termination. Nat. Commun. 11, 1063. [Pubmed Citation]

99. Asatsuma-Okumura, T., Ando, H., De Simone, M., Yamamoto, J., Sato, T., Shimizu, N., Asakawa, K., Yamaguchi, Y., Ito, T., Guerrini, L., and Handa, H. (2019) p63 is a cereblon substrate involved in thalidomide teratogenicity. Nat. Chem. Biol. 15, 1077-1084. [Pubmed Citation]

98. Ando, H., Sato, T., Ito, T., Yamamoto, J., Sakamoto, S., Nitta, N., Asatsuma-Okumura, T., Shimizu, N., Mizushima, R., Aoki, I., Imai, T., Yamaguchi, Y., Berk, A.J., and Handa, H. (2019) Cereblon control of zebrafish brain size by regulation of neural stem cell proliferation. iScience 15, 95-108. [Pubmed Citation]

97. Suzuki, H., Okamoto-Katsuyama, M., Suwa, T., Maeda, R., Tamura, T.-A., and Yamaguchi, Y. (2019) TLP-mediated global transcriptional repression after double-strand DNA breaks slows down DNA repair and induces apoptosis. Sci. Rep. 9, 4868. [Pubmed Citation]

96. Kabe, Y., Sakamoto, S., Hatakeyama, M., Yamaguchi, Y., Suematsu, M., Itonaga, M., and Handa, H. (2019) Application of high-performance magnetic nanobeads to biological sensing devices. Anal. Bioanal. Chem. 411, 1825-1837. [Pubmed Citation]

95. Mori, T., Ito, T., Liu, S., Ando, H., Sakamoto, S., Yamaguchi, Y., Tokunaga, E., Shibata, S., Handa, H., and Hakoshima, T. (2018) Structural basis of thalidomide enantiomer binding to cereblon. Sci. Rep. 8, 1294. [Pubmed Citation]

94. Kabe, Y., Nakane, T., Koike, I., Yamamoto, T., Sugiura, Y., Harada, E., Sugase, K., Shimamura, T., Ohmura, M., Muraoka, K., Yamamoto, A., Uchida, T., Iwata, S., Yamaguchi, Y., Krayukhina, E., Noda, M., Handa, H., Ishimori, K., Uchiyama, S., Kobayashi, T., and Suematsu, M. (2016) Haem-dependent dimerization of PGRMC1/sigma-2 receptor facilitates cancer proliferation and chemoresistance. Nat. Commun. 7, 11030. [Pubmed Citation]

93. Laitem, C., Zaborowska, J., Tellier, M., Yamaguchi, Y., Cao. Q.-F., Egloff, S., Handa, H., and Murphy, S. (2015) CTCF regulates NELF, DSIF and P-TEFb recruitment during transcription. Transcription 6, 79-90. [Pubmed Citation]

92. Cao, Q.-F., Yamamoto, J., Isobe, T., Tateno, S., Murase, Y., Chen, Y., Handa, H., and Yamaguchi, Y. (2015) Characterization of the human transcription elongation factor Rtf1: evidence for non-overlapping functions of Rtf1 and the Paf1 complex. Mol. Cell. Biol. 35, 3459-3470. [Pubmed Citation]

91. Kawano, M., Doi, K., Fukuda, H., Kita, Y., Imai, K., Inoue, T., Enomoto, T., Matsui, M., Hatakeyama, M., Yamaguchi, Y., and Handa, H. (2014) SV40 VP1 major capsid protein in its self-assembled form allows VP1 pentamers to coat various types of artificial beads in vitro regardless of their sizes and shapes. Biotechnol. Rep. 5, 105-111. [Link to ScienceDirect]

90. Yamamoto, J., Hagiwara, Y., Chiba, K., Isobe, T., Narita, T., Handa, H., and Yamaguchi, Y. (2014) DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes. Nat. Commun. 5, 4263. [Pubmed Citation]

89. Takemoto, M., Kawamura, Y., Hirohama, M., Yamaguchi, Y., Handa, H., Saitoh, H., Nakao, Y., Kawada, M., Khalid, K., Koshino, H., Kimura, K., Ito, A., and Yoshida, M. (2014) Inhibition of protein SUMOylation by davidiin, an ellagitannin from Davidia involucrata. J. Antibiot. 67, 335-338. [Pubmed Citation]

88. Sakamoto, S., Omagari, K., Kita, Y., Mochizuki, Y., Naito, Y., Kawata, S., Matsuda, S., Itano, O., Jinno, H., Takeuchi, H., Yamaguchi, Y., Kitagawa, Y., and Handa, H. (2014) Magnetically-promoted rapid immunoreactions using functionalized fluorescent magnetic beads. Clin. Chem. 60, 610-620. [Pubmed Citation]

87. Gupta, V., Liu, S., Ando, H., Ishii, R., Tateno, S., Kaneko, Y., Yugami, M., Sakamoto, S., Yamaguchi, Y., Nureki, O., and Handa, H. (2013) Salicylic acid induces mitochondrial injury by inhibiting ferrochelatase heme biosynthesis activity. Mol. Pharmacol. 84, 824-833. [Pubmed Citation]

86. Shema-Yaacoby, E., Nikolov, M., Haj-Yahya, M., Siman, P., Allemand, E., Yamaguchi, Y., Muchardt, C., Urlaub, H., Brik, A., Oren, M., and Fischle, W. (2013) Systematic identification of proteins binding to chromatin-embedded ubiquitylated H2B reveals recruitment of SWI/SNF to regulate transcription. Cell Reports 4, 601-608. [Pubmed Citation]

85. Isobe, T., Song, S.-N. J., Tiwari, P., Ito, H., Yamaguchi, Y., and Yoshizaki, K. (2013) Activation-induced cytidine deaminase auto-activates and triggers aberrant gene expression. FEBS Letters 587, 2487-2492. [Pubmed Citation]

84. Enomoto, T., Kawano, M., Fukuda, M., Sawada, W., Inoue, T., Haw, K.C., Kita, Y., Sakamoto, S., Yamaguchi, Y., Imai, T., Hatakeyama, M., Saito, S., Sandhu, A., Matsui, M., Aoki, I., and Handa, H. (2013) Viral protein-coating of magnetic nanoparticles using simian virus 40 VP1. J. Biotechnol. 167, 8-15. [Pubmed Citation]

83. Hotta, K., Nashimoto, A., Yasumura, E., Suzuki, M., Azuma, M., Iizumi, Y., Shima, D., Nabeshima, R., Hiramoto, M., Okada, A., Sakata-Sogawa, K., Tokunaga, M., Ito, T., Ando, H., Sakamoto, S., Kabe, Y., Aizawa, S., Imai, T., Yamaguchi, Y., Watanabe, H., and Handa, H. (2012) Vesnarinone suppresses TNFalpha mRNA expression by inhibiting valosin-containing protein. Mol. Pharmacol. 83, 930-938. [Pubmed Citation]

82. Kershaw, J., Leuze, C., Aoki, I., Obata, T., Kanno, I., Ito, H., Yamaguchi, Y., and Handa, H. (2012) Systematic changes to the apparent diffusion tensor of in vivo rat brain measured with an oscillating-gradient spin-echo sequence. Neuroimage 70C, 10-20. [Pubmed Citation]

81. Karasawa, S., Azuma, M., Kasama, T., Sakamoto, S., Kabe, Y., Imai, T., Yamaguchi, Y., Miyazawa, K., and Handa, H. (2012) Vitamin K2 covalently binds to Bak and induces Bak-mediated apoptosis. Mol. Pharmacol. 83, 613-620. [Pubmed Citation]

80. Yamaguchi, Y., Shibata, H., and Handa, H. (2012) Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond. Biochim. Biophys. Acta 1829, 98-104. (review) [Pubmed Citation]

79. Ito, Y., Ito, T., Karasawa, S., Enomoto, T., Nashimoto, A., Hase, Y., Sakamoto, S., Mimori, T., Matsumoto, Y., Yamaguchi, Y., and Handa, H. (2012) Identification of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) as a novel target of Bisphenol A. PLoS ONE 7, e50481. [Pubmed Citation]

78. Diamant, G., Amir-Zilberstein, L., Yamaguchi, Y., Handa, H., and Dikstein, R. (2012) DSIF restricts NF-kappa B signaling by coordinating elongation with mRNA Processing of negative feedback genes. Cell Reports 2, 722-731. [Pubmed Citation]

77. Enomoto, T., Kukimoto, I., Kawano, M.A., Yamaguchi, Y., Berk, A.J., and Handa, H. (2011) In vitro reconstitution of SV40 particles that are composed of VP1/2/3 capsid proteins and nucleosomal DNA and direct efficient gene transfer. Virology 420, 1-9. [Pubmed Citation]

76. Kawano, A., Hayashi, Y., Noguchi, S., Handa, H., Horikoshi, M., and Yamaguchi, Y. (2011) Global analysis for functional residues of histone variant Htz1 using the comprehensive point mutant library. Genes Cells 16, 590-607. [Pubmed Citation]

75. Taneda, T., Zhu, W., Cao, Q., Watanabe, H., Yamaguchi, Y., Handa, H., and Wada, T. (2011) Erythropoiesis is regulated by the transcription elongation factor Foggy/Spt5 through gata1 gene regulation. Genes Cells 16, 231-242. [Pubmed Citation]

74. Kim, S., Yamamoto, J., Chen, Y., Aida, M., Wada, T., Handa, H., and Yamaguchi, Y. (2010) Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation. Genes Cells 15, 1003-1013. [Pubmed Citation]

73. Chiba, K., Yamamoto, J., Yamaguchi, Y., and Handa, H. (2010) Promoter-proximal pausing and its release: molecular mechanisms and physiological functions. Exp. Cell Res. 316, 2723-2730. (review) [Pubmed Citation]

72. Kume, K., Iizumi, Y., Shimada, M., Ito, Y., Kishi, T., Yamaguchi, Y., and Handa, H. (2010) Role of N-end rule ubiquitin ligases UBR1 and UBR2 in regulating the leucine-mTOR signaling pathway. Genes Cells 15, 339-349. [Pubmed Citation]

71. Ito, T., Ando, H., Suzuki, T., Ogura, T., Hotta, K., Imamura, Y., Yamaguchi, Y., and Handa, H. (2010) Identification of a primary target of thalidomide teratogenicity. Science 327, 1345-1350. [Pubmed Citation]

70. Masaike, Y., Takagi, T., Hirota, M., Yamada, J., Ishihara, S., Yung, T.M.C., Inoue, T., Sawa, C., Sagara, H., Sakamoto, S., Kabe, Y., Takahashi, Y., Yamaguchi, Y., and Handa, H. (2009) Identification of dynamin-2-mediated endocytosis as a new target of osteoporosis drugs, bisphosphonates. Mol. Pharmacol. 77, 262-269. [Pubmed Citation]

69. Chen, Y., Yamaguchi, Y., Tsugeno, Y., Yamamoto, J., Yamada, T., Nakamura, M., Hisatake, K., and Handa, H. (2009) DSIF, the Paf1 complex, and Tat-SF1 have non-redundant, cooperative roles in RNA polymerase II elongation. Genes Dev. 23, 2765-2777. [Pubmed Citation]

68. Chen, H., Contreras, X., Yamaguchi, Y., Handa, H., Peterlin, B.M., and Guo, S. (2009) Repression of RNA Polymerase II elongation in vivo is critically dependent on the C-terminus of Spt5. PLoS ONE 4, e6918. [Pubmed Citation]

67. Kamiya, H., Suzuki, A., Yamaguchi, Y., Handa, H., and Harashima, H. (2009) Incorporation of 8-hydroxyguanosine 5′-triphosphate (8-oxo-7,8-dihydroguanosine 5′-triphosphate) by bacterial and human RNA polymerases. Free Radic. Biol. Med. 46, 1703-1707. [Pubmed Citation]

66. Yung, T.M.C., Narita, T., Komori, T., Yamaguchi, Y., and Handa, H. (2009) Cellular dynamics of the negative transcription elongation factor NELF. Exp. Cell Res. 315, 1693-1705. [Pubmed Citation]

65. Kuramori, C., Hase, Y., Hoshikawa, K., Watanabe, K., Nishi, T., Hishiki, T., Soga, T., Nashimoto, A., Kabe, Y., Yamaguchi, Y., Watanabe, H., Kataoka, K., Suematsu, M., and Handa, H. (2009) Mono-(2-ethylhexyl) phthalate targets glycogen debranching enzyme and affects glycogen metabolism in rat testis. Toxicol. Sci. 109, 143-151. [Pubmed Citation]

64. Sakamoto, S., Kabe, Y., Hatakeyama, M., Yamaguchi, Y., and Handa. H. (2009) Development and application of high-performance affinity beads: toward chemical biology and drug discovery. Chem. Rec. 9, 66-85. (review) [Pubmed Citation]

63. Kuramori, C., Azuma, M., Kume, K., Kaneko, Y., Inoue, A., Yamaguchi, Y., Kabe, Y., Hosoya, T., Kizaki, M., Suematsu, M., and Handa, H. (2009) Capsaicin binds to prohibitin 2 and displaces it from the mitochondria to the nucleus. Biochem. Biophys. Res. Commun. 379, 519-525. [Pubmed Citation]

62. Komori, T., Inukai, N., Yamada, T., Yamaguchi, Y., and Handa, H. (2009) The role of human transcription elongation factor DSIF in the suppression of senescence and apoptosis. Genes Cells 14, 343-354. [Pubmed Citation]

61. Azuma, M., Kabe, Y., Kuramori, C., Kondo, M., Yamaguchi, Y., and Handa, H. (2008) Adenine nucleotide translocator transports haem precursors into mitochondria. PLoS ONE 3, e3070. [Pubmed Citation]

60. Takahashi, R.U., Kanesashi, S.N., Inoue, T., Enomoto, T., Kawano, M.A., Tsukamoto, H., Takeshita, F., Imai, T., Ochiya, T., Kataoka, K., Yamaguchi, Y., and Handa, H. (2008) Presentation of functional foreign peptides on the surface of SV40 virus-like particles. J. Biotechnol. 135, 385-392. [Pubmed Citation]

59. Ando, K., Hirao, S., Kabe, Y., Ogura, Y., Sato, I., Yamaguchi, Y., Wada, T., and Handa, H. (2008) A new APE1/Ref-1-dependent pathway leading to reduction of NF-kappa B and AP-1, and activation of their DNA-binding activity. Nucleic Acids Res. 36, 4327-4336. [Pubmed Citation]

58. Suzuki, M., Furukawa, S., Kuramori, C., Sawa, C., Kabe, Y., Nakamura, M., Sawada, J.I., Yamaguchi, Y., Sakamoto, S., Inouye, S., and Handa, H. (2008) Development of a chemical screening system using aqueorin-fused protein. Biochem. Biophys. Res. Commun. 368, 600-605. [Pubmed Citation]

57. Hase, Y., Tatsuno, M., Nishi, T., Kataoka, K., Kabe, Y., Yamaguchi, Y., Ozawa, N., Natori, M., Handa, H., and Watanabe, H. (2008) Atrazine binds to F1F0-ATP synthase and inhibits mitochondrial function in sperm. Biochem. Biophys. Res. Commun. 366, 66-72. [Pubmed Citation]

56. Tsukamoto, H., Kawano, M., Inoue, T., Enomoto, T., Takahashi, R., Yokoyama, N., Yamamoto, N., Imai, T., Kataoka, K., Yamaguchi, Y., and Handa, H. (2007) Evidence that SV40 VP1-DNA interactions contribute to the assembly of 40-nm spherical viral particles. Genes Cells 12, 1267-1279. [Pubmed Citation]

55. Zhu, W., Wada, T., Okabe, S., Taneda, T., Yamaguchi, Y., and Handa, H. (2007) DSIF contributes to transcriptional activation by DNA-binding activators by preventing pausing during transcription elongation. Nucleic Acids Res. 35, 4064-4075. [Pubmed Citation]

54. Amir-Zilberstein, L., Ainbinder, E., Taube, L., Yamaguchi, Y., Handa, H., and Dikstein, R. (2007) Differential regulation of NF-kappa B by elongation factors is determined by core promoter type. Mol. Cell. Biol. 27, 5246-5259. [Pubmed Citation]

53. Yamaguchi, Y., Mura, T., Chanarat, T., Okamoto, S., and Handa, H. (2007) Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity. Genes Cells 12, 863-875. [Pubmed Citation]

52. Narita, T., Yung, T.M.C., Yamamoto, J., Tsuboi, Y., Tanabe, H., Tanaka, K., Yamaguchi, Y., and Handa, H. (2007) NELF interacts with CBC and participates in 3′-end processing of replication-dependent histone mRNAs. Mol. Cell 26, 349-365. [Pubmed Citation]

51. Yugami, M., Kabe, Y., Yamaguchi, Y., Wada, T., and Handa, H. (2007) hnRNP-U enhances the expression of specific genes by stabilizing mRNA. FEBS Lett. 581, 1-7. [Pubmed Citation]

50. Yamamoto, N., Suzuki, M., Kawano, M., Inoue, T., Takahashi, R., Tsukamoto, H., Enomoto, T., Yamaguchi, Y., Wada, T., and Handa, H. (2007) Adeno-associated virus site-specific integration is regulated by TRP-185. J. Virol. 81, 1990-2001. [Pubmed Citation]

49. Nishio, K., Gokon, N., Hasegawa, M., Ogura, Y., Ikeda, M., Narimatsu, H., Tada, M., Yamaguchi, Y., Sakamoto, S., Abe, M., and Handa, H. (2007) Identification of a chemical substructure that is immobilized to ferrite nanoparticles (FP). Colloids Surf. B. Biointerfaces 54, 249-253. [Pubmed Citation]

48. Kubo, T., Wada, T., Yamaguchi, Y., Shimizu, A., and Handa, H. (2006) Knock-down of 25-kDa subunit of cleavage factor Im in HeLa cells alters alternative polyadenylation within 3′ UTRs. Nucleic Acid Res. 34, 6264-6271. [Pubmed Citation]

47. Uga, H., Kuramori, C., Ohta, A., Tsuboi, Y., Tanaka, H., Hatakeyama, M., Yamaguchi, Y., Takahashi, T., Kizaki, M., and Handa, H. (2006) A new mechanism of methotrexate action revealed by target screening with affinity beads. Mol. Pharmacol. 70, 1832-1839. [Pubmed Citation]

46. Aida, M., Chen, Y., Nakajima, K., Yamaguchi, Y., Wada, T., and Handa, H. (2006) Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene. Mol. Cell. Biol. 26, 6094-6104. [Pubmed Citation]

45. Ogura, Y., Azuma, M., Tsuboi, Y., Kabe, Y., Yamaguchi, Y., Wada, T., Watanabe, H., and Handa, H. (2006) TFII-I down-regulates a subset of estrogen-responsive genes through its interaction with an initiator element and estrogen receptor alpha. Genes Cells 11, 373-381. [Pubmed Citation]

44. Yamada, T., Yamaguchi, Y., Inukai, N., Okamoto, S., Mura, T., and Handa, H. (2006) P-TEFb-mediated phosphorylation of the hSpt5 C-terminal repeats is critical for processive transcription elongation. Mol. Cell 21, 227-237. [Pubmed Citation]

43. Delehouzee, S., Yoshikawa, T., Sawa, C., Sawada, J., Ito, T., Omori, M., Wada, T., Yamaguchi, Y., Kabe, Y., and Handa, H. (2005) GABP, HCF-1 and YY1 are involved in Rb gene expression during myogenesis. Genes Cells 10, 717-731. [Pubmed Citation]

42. Azuma, N., Tadokoro, K., Asaka, A., Yamada, M., Yamaguchi, Y., Handa, H., Matsushima, S., Watanabe, T., Kida, Y., Ogura, T., Shimamura, K., and Nakafuku, M. (2005) Transdifferentiation of the retinal pigment epithelia to the neural retina by transfer of the Pax6 transcriptional factor. Hum. Mol. Genet. 14, 1059-1068. [Pubmed Citation]

41. Wu, C.-H., Lee, C., Fan, R., Smith, M.J., Yamaguchi, Y., Handa, H., and Gilmour, D.S. (2005) Molecular characterization of Drosophila NELF. Nucleic Acids Res. 33, 1269-1279. [Pubmed Citation]

40. Ohtsu, Y., Ohba, R., Imamura, Y., Kobayashi, M., Hatori, H., Zenkoh, T., Hatakeyama, M., Manabe, T., Hino, M., Yamaguchi, Y., Kataoka, K., Kawaguchi, H., Watanabe, H., and Handa, H. (2005) Selective ligand purification using high-performance affinity beads. Anal. Biochem. 338, 245-252. [Pubmed Citation]

39. Wang, G., Balamotis, M.A., Stevens, J.L., Yamaguchi, Y., Handa, H., and Berk, A. (2005) Mediator requirement for both recruitment and post-recruitment steps in transcription initiation. Mol. Cell 17, 683-694. [Pubmed Citation]

38. Azuma, N., Tadokoro, K., Asaka, A., Yamada, M., Yamaguchi, Y., Handa, H., Matsushima, S., Watanabe, T., Kohsaka, S., Kida, Y., Shiraishi, T., Ogura, T., Shimamura, K., and Nakafuku, M. (2005) The Pax6 isoform bearing an alternative spliced exon promotes the development of the neural retinal structure. Hum. Mol. Genet. 14, 735-745. [Pubmed Citation]

37. Kabe, Y., Yamada, J., Uga, H., Yamaguchi, Y., Wada, T., and Handa, H. (2005) NF-Y is essential for the recruitment of RNA polymerase II and inducible transcription of several CCAAT box-containing genes. Mol. Cell. Biol. 25, 512-522. [Pubmed Citation]

36. Jennings, B.H., Shah, S., Yamaguchi, Y., Seki, M., Phillips, R.G., Handa, H., and Ish-Horowicz, D. (2004) Locus-specific requirements for Spt5 in transcriptional activation and repression in Drosophila. Curr. Biol. 14, 1680-1684. [Pubmed Citation]

35. Aiyar, S.E., Sun, J.-L., Blair, A.L., Moskaluk, C.A., Lv, Y., Ye, Q.-N., Yamaguchi, Y., Mukherjee, A., Ren, D.-M., Handa, H., and Li, R. (2004) Attenuation of estrogen receptor alpha-mediated transcription through estrogen-stimulated recruitment of a negative elongation factor. Genes Dev. 18, 2134-2146. [Pubmed Citation]

34. Oshima, S., Nakamura, T., Namiki, S., Okada, E., Tsuchiya, K., Okamoto, R., Yamazaki, M., Yokota, T., Aida, M., Yamaguchi, Y., Kanai, T., Handa, H., and Watanabe, M. (2004) Interferon regulatory factor 1 (IRF-1) and IRF-2 distinctively up-regulate gene expression and production of interleukin-7 in human intestinal epithelial cells. Mol. Cell. Biol. 24, 6298-6310. [Pubmed Citation]

33. Endoh, M., Zhu, W., Hasegawa, J., Watanabe, H., Kim, D.-K., Aida, M., Inukai, N., Narita, T., Yamada, T., Furuya, A., Sato, H., Yamaguchi, Y., Mandal, S.S., Reinberg, D., Wada, T., and Handa, H. (2004) Human Spt6 stimulates transcription elongation by RNA polymerase II in vitro. Mol. Cell. Biol. 24, 3324-3336. [Pubmed Citation]

32. Ainbinder, E., Amir-Zilberstein, L., Yamaguchi, Y., Handa, H., and Dikstein, R. (2004) Elongation inhibition by DRB sensitivity-inducing factor is regulated by the A20 promoter via a novel negative element and NF-kappa B. Mol. Cell. Biol. 24, 2444-2454. [Pubmed Citation]

31. Inukai, N., Yamaguchi, Y., Kuraoka, I., Yamada, T., Kamijo, S., Kato, J., Tanaka, K., and Handa, H. (2004) A novel hydrogen peroxide-induced phosphorylation and ubiquitination pathway leading to RNA polymerase II proteolysis. J. Biol. Chem. 279, 8190-8195. [Pubmed Citation]

30. Nedialkov, Y.A., Gong, X.Q., Yamaguchi, Y., Handa, H., and Burton, Z.F. (2003) Assay of transient state kinetics of RNA polymerase II elongation. Methods Enzymol. 371, 252-264. (review) [Pubmed Citation]

29. Wu, C.-H., Yamaguchi, Y., Benjamin, L.R., Horvat-Gordon, M., Washinski, J., Enerly, E., Larsson, J., Lambertsson, A., Handa, H., and Gilmour, D.S. (2003) NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev. 17, 1402-1414. [Pubmed Citation]

28. Hasegawa, J., Endou, M., Narita, T., Yamada, T., Yamaguchi, Y., Wada, T., and Handa, H. (2003) A rapid purification method for human RNA polymerase II by two-step affinity chromatography. J. Biochem. 133, 133-138. [Pubmed Citation]

27. Azuma, N., Yamaguchi, Y., Handa, H., Tadokoro, K., Asaka, A., Kawase, E., and Yamada, M. (2003) Mutations of the PAX6 gene detected in patients with a variety of optic nerve malformations. Am. J. Hum. Genet. 72, 1565-1570. [Pubmed Citation]

26. Nedialkov, Y.A., Gong, X.Q., Hovde, S.L., Yamaguchi, Y., Handa, H., Geiger, J.H., Yan, H., and Burton, Z.F. (2003) NTP-driven translocation by human RNA polymerase II. J. Biol. Chem. 278, 18303-18312. [Pubmed Citation]

25. Narita, T., Yamaguchi, Y., Yano, K., Sugimoto, S., Chanarat, S., Wada, T., Kim, D., Hasegawa, J., Omori, M., Inukai, N., Endoh, M., Yamada, T., and Handa, H. (2003) Human transcription elongation factor NELF: Identification of novel subunits and reconstitution of the functionally active complex. Mol. Cell. Biol. 23, 1863-1873. [Pubmed Citation]

24. Kim, D.K., Inukai, N., Yamada, T., Furuya, A., Sato, H., Yamaguchi, Y., Wada, T., and Handa, H. (2003) Structure-function analysis of human Spt4: evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex. Genes Cells 8, 371-378. [Pubmed Citation]

23. Shima, D., Yugami, M., Tatsuno, M., Wada, T., Yamaguchi, Y., and Handa, H. (2003) Mechanism of H-8 inhibition of Cyclin-dependent kinase 9: study using inhibitor-immobilized matrices. Genes Cells 8, 215-223. [Pubmed Citation]

22. Kuraoka, I., Endou, M., Yamaguchi, Y., Wada, T., Handa, H., and Tanaka, K. (2003) Effects of endogeneous DNA base lesions on transcription elongation by mammalian RNA polymerase II: Implications for transcription-coupled DNA repair and transcriptional mutagenesis. J. Biol. Chem. 278, 7294-7299. [Pubmed Citation]

21. Nishi, T., Shimizu, N., Hiramoto, M., Sato, I., Yamaguchi, Y., Hasegawa, M., Aizawa, S., Tanaka, H., Kataoka, K., Watanabe, H., and Handa, H. (2002) Spatial redox regulation of a critical cysteine residue of NF-kappa B in vivo. J. Biol. Chem. 277, 44548-44556. [Pubmed Citation]

20. Yamaguchi, Y., Delehouzee, S., and Handa, H. (2002) HIV and HDV: evolution takes different paths to relieve blocks in transcriptional elongation. Microbes Infect. 4, 1169-1175. (review) [Pubmed Citation]

19. Yamaguchi, Y., Inukai, N., Narita, T., Wada, T., and Handa, H. (2002) Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol. Cell. Biol. 22, 2918-2927. [Pubmed Citation]

18. Renner, D.B., Yamaguchi, Y., Wada, T., Handa, H., and Price, D.H. (2001) A highly purified RNA polymerase II elongation control system. J. Biol. Chem. 276, 42601-42609. [Pubmed Citation]

17. Yamaguchi, Y., Filipovska, J., Yano, K., Furuya, A., Inukai, N., Narita, T., Wada, T., Sugimoto, S., Konarska, M.M., and Handa, H. (2001) Stimulation of RNA polymerase II elongation by hepatitis delta antigen. Science 293, 124-127. [Pubmed Citation]

16. Kim, D.K., Yamaguchi Y., Wada, T., and Handa, H. (2001) The regulation of elongation by eukaryotic RNA polymerase II: A recent view. Mol. Cells 11, 267-274. (review) [Pubmed Citation]

15. Shiba, K., Hamaguchi, T., Kataoka, K., Yamaguchi, Y., Handa, H., and Adachi, K. (2001) Cloning of the hamstar androgen receptor gene. J. Dermatol. Sci. 26, 163-168. [Pubmed Citation]

14. Yamaguchi, Y., Narita, T., Inukai, N., Wada, T., and Handa, H. (2001) SPT genes: Key players in the regulation of transcription, chromatin structure and other cellular processes. J. Biochem. 129, 185-191. (review) [Pubmed Citation]

13. Guo, S., Yamaguchi, Y., Schilbach, S., Wada, T., Lee, J., Goddard, A., French, D., Handa, H., and Rosenthal, A. (2000) A regulator of transcriptional elongation controls vertebrate neuronal development. Nature 408, 366-369. [Pubmed Citation]

12. Wada, T., Orphanides, G., Hasegawa, J., Kim, D.-K., Shima, D., Yamaguchi, Y., Fukuda, A., Hisatake, K., Oh, S., Reinberg, D., and Handa, H. (2000) FACT relieves DSIF/NELF-mediated inhibition of transcriptional elongation and reveals functional differences between P-TEFb and TFIIH. Mol. Cell 5, 1067-1072. [Pubmed Citation]

11. Kim, J.B., Yamaguchi, Y., Wada, T., Handa, H., and Sharp, P.A. (1999) Tat-SF1 protein associates with RAP30 and human SPT5 proteins. Mol. Cell. Biol. 19, 5960-5968. [Pubmed Citation]

10. Yamaguchi, Y., Wada, T., Watanabe, D., Takagi, T., Hasegawa, J., and Handa, H. (1999) Structure and function of the human transcription elongation factor DSIF. J. Biol. Chem. 274, 8085-8092. [Pubmed Citation]

9. Azuma, N., Yamaguchi, Y., Handa, H., Hayakawa, M., Kanai, A., and Yamada, M. (1999) Missense mutation in the alternative splice region of the PAX6 gene in eye anomalies. Am. J. Hum. Genet. 65, 656-663. [Pubmed Citation]

8. Nishina, S., Kohsaka, S., Yamaguchi, Y., Handa, H., Kawakami, A., Fujisawa, H., and Azuma, N. (1999) PAX6 expression in the developing human eye. Br. J. Ophthalmol. 83, 723-727. [Pubmed Citation]

7. Yamaguchi, Y., Takagi, T., Wada, T., Yano, K., Furuya, A., Sugimoto, S., Hasegawa, J., and Handa, H. (1999) NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97, 41-51. [Pubmed Citation]

6. Wada, T., Takagi, T., Yamaguchi, Y., Watanabe, D., and Handa, H. (1998) Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro. EMBO J. 17, 7395-7403. [Pubmed Citation]

5. Yamaguchi, Y., Wada, T., and Handa, H. (1998) Interplay between positive and negative elongation factors: drawing a new view of DRB. Genes Cells 3, 9-15. (review) [Pubmed Citation]

4. Wada, T., Takagi, T., Yamaguchi, Y., Ferdous, A., Imai, T., Hirose, S., Sugimoto, S., Yano, K., Hartzog, G.A., Winston, F., Buratowski, S., and Handa, H. (1998) DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12, 343-356. [Pubmed Citation]

3. Yamaguchi, Y., Wada, T., Suzuki, F., Takagi, T., Hasegawa, J., and Handa, H. (1998) Casein kinase II interacts with the bZIP domains of several transcription factors. Nucleic Acids Res. 26, 3854-3861. [Pubmed Citation]

2. Yamaguchi, Y., Sawada, J., Yamada, M., Handa, H., and Azuma, N. (1997) Autoregulation of Pax6 transcriptional activation by two distinct DNA-binding subdomains of the paired domain. Genes Cells 2, 255-261. [Pubmed Citation]

1. Wada, T., Takagi, T., Yamaguchi, Y., Kawase, H., Hiramoto, M., Ferdous, A., Takamiya, M., Lee, K.A., Hurst, H.C., and Handa, H. (1996) Copurification of casein kinase II with transcription factor ATF/E4TF3. Nucleic Acids Res. 24, 876-884. [Pubmed Citation]

Books

21. 山口雄輝 (分担執筆)：サリドマイド胎芽症診療ガイド 2020（国立国際医療研究センター編）、厚労科研費 薬品・医療機器等レギュラトリーサイエンス総合研究事業, 2020.

20. 山口雄輝 (分担執筆)：遺伝子発現制御機構 クロマチン，転写制御，エピジェネティクス (田村隆明，浦聖恵編著)：東京化学同人, 2017.

19. 近藤科江，山口雄輝 (監修)：理系英会話アクティブラーニング2 テツヤ、ディスカッションしようか：羊土社, 2014.

18. 近藤科江，山口雄輝 (監修)：理系英会話アクティブラーニング1 テツヤ、国際学会いってらっしゃい：羊土社, 2014.

17. 山口雄輝，成田央：基礎からしっかり学ぶ生化学：羊土社, 2014.

16. 山口雄輝 (分担執筆)：新しい遺伝子工学 新版 (半田宏編著)：朝倉書店, 2014.

15. Yuki Yamaguchi: Transcription elongation, mechanisms他、多数の項執筆 (2013) Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.), Springer Science + Business Media LLC.

14. 山口雄輝，半田宏 (分担執筆)：転写制御とエピジェネティクス—ゲノムデコードに向けて—：南山堂, 2008.

13. 山口雄輝 (分担執筆)：新しい遺伝子工学 (半田宏編著)：昭晃堂, 2006.

12. Hiroshi Handa and Yuki Yamaguchi (2006) Hepatitis Delta Virus, Landes Bioscience, Texas, USA. [Link]

11. 山口雄輝 (分担執筆)：ケミカルバイオロジー・ケミカルゲノミクス (半田宏編)：シュプリンガー・フェアラーク, 2005.

10. 半田宏，和田忠士，山口雄輝：転写研究集中マスター，羊土社，2005．[Link]

9. 山口雄輝：科学英語論文の赤ペン添削講座，羊土社，2005．[Link]

8. 山口雄輝 (分担執筆)：キーワードで理解する転写イラストマップ：羊土社, 2004.

7. 山口雄輝 (分担執筆)：わかる実験医学シリーズ 転写がわかる：羊土社, 2002.

6. 山口雄輝 (分担執筆)：ゲノムからの情報発現 転写因子とその機能：シュプリンガー・フェアラーク, 2000.

5. 山口雄輝 (分担執筆)：BioScience用語ライブラリー新版：羊土社, 1999.

4. Hiroshi Handa, Yuki Yamaguchi, and Tadashi Wada (分担執筆): Purification of DNA binding proteins. in High resolution chromatography: A practical approach (ed. P.A. Miller), pp. 283-302: Oxford University Press, Oxford, UK, 1999.

3. 山口雄輝 (分担執筆)：分子細胞生物学事典：東京化学同人, 1996.

2. 山口雄輝 (分担執筆)：転写のしくみと疾患：羊土社, 1995.

1. 山口雄輝 (分担執筆)：BioScience用語ライブラリー：羊土社, 1995.