eIMBL

DNA Replication

Systems Biology

Genomic Medicine

Molecular Oriental Medicine

Infectious Disease

DNA Replication

Hiroyuki ARAKI, Ph.D.
Tak, Y-S., Tanaka, Y., Endo, S., Kamimura, Y. and Araki, H. (2006) A CDK-catalysed regulatory phosphorylation for formation of the DNA replication complex Sld2-Dpb11.
EMBO J. 25, 1987-1996.

Arturo FALASCHI, M.D. Ph.D.
Cui, S., Arosio, D., Doherty. K.M., Brosh, R.M. JR., Falaschi, A. and Vindignt, A. (2004) Analysis of the unwinding activity of the dimeric RecQ1 helicase in the presence of human replication protein A.
Nucl. Acids Res. 32, 1-13.

Sonia, P., Colaluca, I. N., Cubells, M. Peverali, F.A., Destro, A.,Giadrossi, S., Giacca, M., Falaschi, A., Riva, S. and Biamonti, G. (2004) Modular Structure of the Human Lamin B2 Replicator.
Mol. Cell. Biol. 24, 2958-2967.

Falaschi, A., Biamonti, G., and Riva, S. (2006) DNA replication origins. In: Encyclopedic reference of genomic and proteomics in Molecular Medicine. Springer Verlag

Aladjem, M. I., Falaschi, A. and Kowalski, D. (2006) Eukaryotic DNA replication origins. In: DNA replication in eukaryotic cells (2nd edition). Cold Spring Harbor Press.

Masatoshi FUJITA, M.D. Ph.D.
Kudoh, A., Fujita, M., Zhan, L., Shirata, N., Daikoku, T., Sugaya, Y., Isomura, H., Nishiyama, Y. and Tsurumi, T. (2005) Epstein-Barr virus lytic replication elicits ATM checkpoint signal transduction while providing an S-phase-like cellular environment.
J. Biol. Chem. 280, 8156-8163.

Daikoku, T., Kudoh, A., Fujita, M., Sugaya, Y., Isomura, H. Shirata, N. and Tsurumi, T. (2005) Architecture of replication compartments formed during Epstein-Barr Virus lytic replication.
J. Virol. 79, 3409-3418.

Shirata, N., Kudoh, A., Daikoku, T., Tatsumi, Y., Fujita, M., Kiyono, T., Sugaya, Y., Isomura, H., Ishizaki, K. and Tsurumi, T. (2005) Activation of ATM DNA damage checkpoint signal transduction elicited by Herpes simplex virus infection.
J. Biol. Chem. 280, 30336-30341.

Nishitani, H., Sugimoto, N., Roukos, V., Nakanishi, Y., Saijo, M., Obuse,C., Tsurimoto, T., Nakayama, K-I., Nakayama, K., Fujita, M., Lygerous, Z. and Nishimoto, T. (2006) Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis.
EMBO J. 25, 1126-1136.

Tatsumi, Y., Sugimoto, N., Yugawa, T., Narisawa-Saito, M., Kiyono, T. and Fujita, M. (2006) Deregulation of Cdt1 induces chromosomal damage without rereplication and leads to chromosomal instability.
J. Cell Sci. 119, 3128-3140.

Fujita, M. (2006) DNA Replication Initiation. In Encyclopedic Reference of
Genomics and Proteomics in Molecular Medicine (edited by Ganten, D. and
Ruckpaul, K.). Springer, Berlin Heidelberg & New York, pp446-449.

Fujita, M. (2006) Cdt1 revisited: complex and tight regulation during the cell cycle and consequences of deregulation in mammalian cells.
Cell Div. 1, 22.

Tsutomu KATAYAMA, Ph.D.
Kawakami, H., Ozaki , S. (Equal contributors), Suzuki, S., Nakamura, K., Senriuchi, T., Su’etsugu, M., Fujimitsu, K., and Katayama, T. (2006) The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif.
Mol. Microbiol. (in press)

Kawakami, H., Su’etsugu, M. and Katayama, T. (2006) An isolated Hda-clamp complex is functional in the regulatory inactivation of DnaA and DNA replication
J. Struct. Biol. 156, 220-229

Ozaki, S., Fujimitsu, K., Kurumizaka, H., and Katayama, T. (2006) The DnaA homolog of the hyperthermophilic eubacterium Thermotoga maritima forms an open complex with a minimal 149-bp origin region in an ATP-dependent manner.
Genes Cells 11, 425-438

Ote, T., Hashimoto, M., Ikeuchi, Y., Su'etsugu, M., Suzuki, T., Katayama, T., and Kato, J. (2006) Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation.
Mol. Microbiol. 59, 265-274

Kawakami, H., Keyamura, K., and Katayama, T. (2005) Formation of an ATP-DnaA-specific initiation complex requires DnaA arginine-285, a conserved motif in the AAA+ protein family.
J. Biol. Chem. 280, 27420-27430

Su’etsugu, M, Shimuta, T., Ishida, T., Kawakami, H. and Katayama, T. (2005) Protein associations in DnaA-ATP hydrolysis mediated by the replicase clamp-Hda complex.
J. Biol. Chem. 280, 6528-6536

Shioi, S., Ose, T., Maenaka, K., Shiroishi, M., Abe, Y., Kohda, D., Katayama, T., and Ueda, T. (2005) Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site.
Biochem. Biophys. Res. Commun. 326, 766-776

Hishimoto, M., Ichimura, Y., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., Ote, T., Yamakawa, T., Yamazaki, Y., Mori, H., Katayama, T., and Kato, J. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome.
Mol. Microbiol. 55, 137-149

Joon Kyu LEE, Ph.D.
Cho, W.H., Lee, Y.J., Kong, S.I., Hurwitz, J., and Lee, J.K. (2006) Cdc7 kinase phosphorylates serine residues adjacent to acidic amino acids in the minichromosome maintenance 2 protein.
Proc. Natl. Acad. Sci. U.S.A. 103,11521-11526.

Kim, S.M., Yang, J.W., Park, M.J., Lee, J.K., Kim, S.U., Lee, Y.S., and Lee, M.A. Regulation of human tyrosine hydroxylase gene by neuron-restrictive silencer factor.
Biochem. Biophys. Res. Commun. 346, 426-435.

Chun LIANG, Ph.D.

Hisao MASAI, Ph. D.
Fujii-Yamamoto, H., Kim, J-M., Arai, K. and Masai, H. (2005) Cell cycle and developmental regulations of replication factors in mouse embryonic stem cells.
J. Biol. Chem. 280, 12976-12987.

Yoshizawa, N.,Ishii, A., Taniyama, C., Matsui, E., Arai, K., and Masai, H. (2005) A second human Dbf4/ASK-related protein, Drf1/ASKL1 is required for efficient completion of S and M phases."
J. Biol. Chem. 280, 13062-13070.

Yamashita, N., Kim, J-M., Koiwai, O., Arai, K. and Masai, H. (2005) Functional analyses of mouse ASK, an activator subunit for Cdc7 kinase, using conditional ASK knockout ES cells.
Genes to Cells 50, 551-563.

You, Z. and Masai, H. (2005) DNA binding and helicase actions of mouse Mcm4/6/7 helicase.
Nucl. Acids Res. 33, 3033-3047.

Todorovic, V., Giadrossi, S., Pelizon, C., Masai, H. and Giacca, M. (2005) Novel human origins of DNA replication selected from a library of nascent DNA.
Mol. Cell 19, 567-575.

Matsumoto, S., Ogino, K., Noguchi, E., Russell, P. and Masai, H. (2005) Hsk1-Dfp1/Him1, the Cdc7-Dbf4 Kinase in Schizosaccharomyces pombe, associates with Swi1, a component of the replication fork protection complex.
J. Biol. Chem. 280, 42536-42542.

Ogino, K., and Masai, H. (2006) Rad3-Cds1 mediates coupling of initiation of meiotic recombination with DNA replication: Mei4-dependent transcription as a potential target of meiotic checkpoint.
J. Biol. Chem. 281,1338-1344.

Tanaka, T. and Masai, H. (2006) Stabilization of a stalled replication fork by concerted actions of two helicases.
J. Biol. Chem. 281, 3484-3493.

Sasaki, K., Ose, T., Tanaka, T., Mizukoshi, T., Ishigaki, T., Maenaka,K., Masai, H. and Kohda, D. (2006) Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli.
Biochim. Biophys. Acta. 1764, 157-160.

Kitamura, R., Sekimoto, T., Ito, S., Harada, S., Yamagata, H., Masai, H., Yoneda, H. and Yanagi, K. (2006) Nuclear import of Epstein-Barr Virus Nuclear Antigen 1 mediated by NPI-1 (Importin ?5) is up- and down-regulated by phosphorylation of the nuclear localization signal for which Lys379 and Arg380 are essential.
J. Virol., 80, 1979-1991.

Ogino, K., Hirota, K., Matsumoto, S., Takeda, T., Ohta, K., Arai, K. and Masai, H. (2006) Hsk1 kinase is required for induction of meiotic double-stranded DNA breaks without involving checkpoint kinases in fission yeast.
Proc. Natl. Acad. Sci. U.S.A. 103, 8131-8136.

Hayashida,T., Oda , M., Ohsawa K.,Yamaguchi A., Giacca, M., Locksley, R.M., Masai H.*, and Miyatake, S.* (2006) Replication initiation from a novel origin identified in the Th2 cytokine cluster locus requires a distant conserved non-coding sequence. (*cocommunicating authors)
J. Immunol. 176, 5446-5454.

Masai, H., Taniyama, C., Ogino, K., Matsui, E., Kakusho, N., Matsumoto, M., Kim, J-M., Ishii, A., Tanaka, T., Kobayashi, T., Tamai, K., Ohtani, K., and Arai, K. Phosphorylation of MCM4 by Cdc7 kinase facilitates its interaction with Cdc45 on the chromatin.
J. Biol. Chem. in press

Hisao MASUKATA, Ph.D.
Yabuuchi, H., Yamada, Y., Uchida, T., Sunathvanichkul, T., Nakagawa, T. and Masukata, H. (2006) Ordered assembly of Sld3, GINS and Cdc45 is distinctly regulated by DDK and CDK for activation of replication origins.
EMBO J. 25, 4663-4674.

Nitani, N., Nakamura, K., Nakagawa, C., Masukata, H. and Nakagawa, T. (2006) Regulation of DNA replication machinery by mrc1 in fission yeast.
Genetics 174, 155-165.

Yeon-Soo SEO, Ph.D.

Kim, J.H., Kim, H.D., Ryu, G.H., Kim, D.H., Hurwitz, J. and Seo, Y.S. (2006) Isolation of human Dna2 endonuclease and characterization of its enzymatic properties.
Nucleic Acids Res. 34,1854-1864.

Kim, J.H., Kang, Y.H., Kang, H.J., Kim, D.H., Ryu, G.H., Kang, M.J. and Seo, Y.S. (2005) In vivo and in vitro studies of Mgs1 suggest a link between genome instability and Okazaki fragment processing.
Nucleic Acids Res. 33, 6137-6150.

Katsuhiko SHIRAHIGE, Ph.D.
Tamaki, H., Yun, C.W., Mizutani, T., Tsuzuki, T., Takagi, Y., Shinozaki, M., Kodama, Y., Shirahige, K., and Kumagai, H. (2005) Glucose-dependent cell size is regulated by a G protein-coupled receptor system in yeast Saccharomyces cerevisiae.
Genes Cells 10, 193-206

Tonami, Y., Murakami, H., Shirahige, K. and Nakanishi. M. (2005) A checkpoint control linking meiotic S phase and recombination initiation in fission yeast.
Proc. Natl. Acad. Sci. U.S.A. 102, 5797-5801.

Unno, K., Juvvadi, P.R., Nakajima, H., Shirahige, K. and Kitamoto, K. (2005) Identification and characterization of rns4/vps32 mutation in the RNase T1 expression-sensitive strain of Saccharomyces cerevisiae: Evidence for altered ambient response resulting in transportation of the secretory protein to vacuoles.
FEMS Yeast Res. 5, 801-812.

Riedel, C.G., Katis, V.L., Katou, Y., Mori, S., Helmhart, W., Galova, M., Petronczki, M., Gregan, J., Cetin, B., Mudrak, I., Ogris, E., Mechtler, K., Pelletier, L., Buchholz, F., Shirahige, K. and Nasmyth, K. (2006) Protein Phosphatase 2A protects centromeric sister chromatid cohesion.
Nature (article) 441,53-61.

Kanoh, Y., Tamai, K., and Shirahige, K. (2006) Different requirements for the association of ATR-ATRIP and 9-1-1 to the stalled replication forks.
Gene 377, 88-95.

Matsui, K., Hirayama, T., Kuroda, K., Shirahige, K., Ashikari, T. and Ueda, M. (2006) Screening for candidate genes involved in tolerance to organic solvents in yeast.
Appl. Microbiol. Biotechnol. 71, 75-79.

Lindroos, H.B., Strom, L., Itoh, T., Katou, Y., Shirahige, K.* and Sjogren, C.* (*shared corresponding author). (2006) Chromosomal Association of the Smc5/6 Complex Reveals that It Functions in Differently Regulated Pathways.
Mol. Cell 22, 755-767

Ding, D.Q., Sakurai, N., Katou, Y., Itoh, T., Shirahige, K., Haraguchi, T., and Hiraoka, Y. (2006) Meiotic cohesins modulate chromosome compaction during meiotic prophase in fission yeast.
J. Cell. Biol. 174, 499-508

Lengronne, A., McIntyre, J., Katou, Y., Kanoh, Y., Hopfner, K.P., Shirahige, K., and Uhlmann, F. (2006) Establishment of Sister Chromatid Cohesion at the S. cerevisiae Replication Fork.
Mol. Cell 23, 787-799

Petronczki, M., Matos, J., Mori, S., Gregan, J., Bogdanova, A., Schwickart, M., Mechtler, K., Shirahige, K., Zachariae, W., and Nasmyth, K. (2006) Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1.
Cell 126, 1049-1064.

Kaneshiro, K., Tsutsumi, S., Tsuji, S., Shirahige, K. and Aburatani, H. (2006) An integrated map of p53-binding sites and histone modification in the human ENCODE regions.
Genomics in press

Katou, Y., Kaneshiro, K., Aburatani, H., and Shirahige, K. (2006) Genomic Approach for the Understanding of Dynamic Aspect of Chromosome Behavior.
Methods in Enzymology, Elsevier Life Sciences (CA), Vol.409, chapter 23, 389-410 in “DNA Repair” (edited by J.Campbell)

Haruhiko TAKISAWA, Ph.D.
Hashimoto, Y., Tsujimura, T., Sugino, A., and Takisawa, H. (2006) The phosphorylated C-terminal domain of Xenopus Cut5 directly mediates ATR-dependent activation of Chk1.
Genes Cells 11, 993-1007.

Matsuno, K., Kumano, M., Kubota, Y., Hashimoto, Y., and Takisawa, H. (2006) The N-terminal noncatalytic region of Xenopus RecQ4 is required for chromatin binding of DNA polymerase alpha in the initiation of DNA replication.
Mol. Cell. Biol. 26, 4843-4852.

Pacek, M., Tutter, A.V., Kubota,Y., Takisawa, H., and Walter, J.C. (2006) Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication.
Mol Cell 21, 581-587.

Iizuka, M., Matsui, T., Takisawa, H., and Smith, M.M. (2006) Regulation of replication licensing by acetyltransferase Hbo1.
Mol. Cell. Biol. 26,1098-1108.

Yoshida, K., Takisawa, H., and Kubota, Y. (2005) Intrinsic nuclear import activity of geminin is essential to prevent re-initiation of DNA replication in Xenopus eggs.
Genes Cells 10, 63-73.

Haruhiko TAKISAWA, Ph.D.
Nishitani, H., Sugimoto, N., Roukos, V., Nakanishi, Y., Saijo, M., Obuse, C., Tsurimoto, T., Nakayama, KI., Nakayama, K., Fujita, M., Lygerou, Z. and Nishimoto, T. (2006) Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis.
EMBO J. 25,1126-1136.

Tsurimoto, T., Shinozaki, A., Yano, M., Seki, M. and Enomoto, T. (2005) Human Werner helicase interacting protein 1 (WRNIP1) functions as a novel modulator for DNA polymerase delta.
Genes Cells 10, 13-22.