Publications

Plant DNA replication

  • Dresselhaus, T., Srilunchang, K. O., Leljak-Levanic, D., Schreiber, D. N., and Garg, P. (2006) The fertilization induced DNA replication Factor MCM6 of maize shuttles between cytoplasm and nucleus, and is essential for plant growth and development. Plant Physiol., 140, 512-527.
  • de Jager, S. M., Maughan, S., Dewitte, W., Scofield, S., and Murray, J. A. (2005) The developmental context of cell-cycle control in plants. Semin. Cell. Dev. Biol. 16, 385-396.
  • Diaz-Trivino, S., del Mar Castellano, M., de la Paz Sanchez, M., Ramirez-Parra, E., Desvoyes, B., and Gutierrez, C. (2005). The genes encoding Arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells. Nucleic Acids Res 33, 5404-5414.
  • Mori, Y., Yamamoto, T., Sakaguchi, N., Ishibashi, T., Furukawa, T., Kadota, Y., Kuchitsu, K., Hashimoto, J., Kimura, S., and Sakaguchi, K. (2005) Characterization of the origin recognition complex (ORC) from a higher plant, rice (Oryza sativa L.). Gene 353, 23-30.
  • Castellano Mdel , M., Boniotti, M. B., Caro, E., Schnittger, A., and Gutierrez, C. (2004). DNA replication licensing affects cell proliferation or endoreplication in a cell type-specific manner. Plant Cell 16, 2380-2393.
  • Collinge, M. A., Spillane, C., Kohler, C., Gheyselinck, J., and Grossniklaus, U. (2004). Genetic interaction of an origin recognition complex subunit and the Polycomb group gene MEDEA during seed development. Plant Cell 16, 1035-1046.
  • Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471-476.
  • Masuda, H. P., Ramos, G. B., de Almeida-Engler, J., Cabral, L. M., Coqueiro, V. M., Macrini, C. M., Ferreira, P. C., and Hemerly, A. S. (2004) Genome based identification and analysis of the pre-replicative complex of Arabidopsis thaliana. FEBS Lett. 574, 192-202.
  • Rudd, S., Frisch, M., Grote, K., Meyers, B.C., Mayer, K., and Werner, T. (2004) Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol. 135, 715-722.
  • Witmer, X., Alvarez-Venegas, R., San-Miguel, P., Danilevskaya, O., and Avramova, Z. (2003). Putative subunits of the maize origin of replication recognition complex ZmORC1-ZmORC5. Nucleic Acids Res. 31, 619-628.
  • Michalowski, S.M., Allen, G.C., Hall, G.E., Thompson, W.F., and Spiker, S. (1999) Characterization of randomly obtained matrix attachment regions (MARs) from higher plants. Biochemistry 38, 12795-12804.
  • Doelling, J.H., Gaudino, R.J., and Pikaard, C.S. (1993) Functional analysis of Arabidopsis thaliana rRNA gene and spacer promoters in vivo and by transient expression. Proc. Natl. Acad. Sci. USA 90, 7528-7532.
  • Van’t Hof, J. and Lamm, S.S. (1991). Single-stranded replication intermediates of ribosomal DNA replicons of pea. EMBO J. 10, 1949-1953.

Origins and replication initation complex proteins

  • Karnani, N., Taylor1, C., Malhotra1, A., and Dutta1, A. (2007) Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res., 17, 865-876.
  • Marinsek, N., Barry, E. R., Makarova, K. S., Dionne, I., Koonin, E. V., and Bell, S. D. (2006) GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep., 7, 539-545.
  • Marheineke, K., Hyrien, O., and Krude, T. (2005) Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system. Nucleic Acids Res. 33, 6931-6941.
  • McNairn, A. J., and Gilbert, D. M. (2005) Overexpression of ORC subunits and increased ORC-chromatin association in transformed mammalian cells. J. Cell. Biochem. 96, 879-887.
  • Takeda, D. Y., Shibata, Y., Parvin, J. D., and Dutta, A. (2005) Recruitment of ORC or CDC6 to DNA is sufficient to create an artificial origin of replication in mammalian cells. Genes Dev. 19, 2827-2836.
  • Remus, D., Beall, E. L., and Botchan, M. R. (2004) DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J. 23, 897-907.
  • Abdurashidova, G., Danailov, M. B., Ochem, A., Triolo, G., Djeliova, V., Radulescu, S., Vindigni, A., Riva, S., and Falaschi, A. (2003) Localization of proteins bound to a replication origin of human DNA along the cell cycle. EMBO J. 22, 4294-4303.
  • Harvey, K. J., and Newport, J. (2003) Metazoan origin selection - Origin recognition complex chromatin binding is regulated by Cdc6 recruitment and ATP hydrolysis. J. Bio. Chem. 278, 48524-48528.
  • Bell, S. P., and Dutta, A. (2002) DNA replication in eukaryotic cells. Ann. Rev. Biochem. 71, 333-374.
  • Bell, S. P., and Stillman, B. (1992). ATP-dependent recognition of eukaryotic origins of DNA-replication by a multiprotein complex. Nature 357, 128-134.

Replication through chromatin and development

  • Falbo, K. B., and Shen, X. T. (2006) Chromatin remodeling in DNA replication. J. Cell. Biochem. 97, 684-689.
  • Fu, H., Wang, L., Lin, C.-M., Singhania, S., Bouhassira, E.E., and Aladjem, M.I. (2006) Preventing gene silencing with human replicators. Nat. Biotech. 24, 572-576.
  • Gilbert, N., Gilchrist, S., and Bickmore, W.A. (2005) Chromatin organization in the mammalian nucleus. Int. Rev. Cytol. 242, 283-336.
  • Kohzaki, H., and Murakami, Y. (2005) Transcription factors and DNA replication origin selection. Bioessays 27, 1107-1116.
  • Lemaitre, J. M., Danis, E., Pasero, P., Vassetzky, Y., and Mechali, M. (2005) Mitotic remodeling of the replicon and chromosome structure. Cell 123, 787-801.
  • Norio, P., Kosiyatrakul, S., Yang, Q., Guan, Z., Brown, N. M., Thomas, S., Riblet, R., and Schildkraut, C. L. (2005) Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. Mol. Cell 20, 575-587.
  • Pliss, A., Koberna, K., Vecerova, J., Malinsky, J., Masata, M., Fialova, M., Raska, I., and Berezney, R. (2005) Spatio-temporal dynamics at rDNA foci: global switching between DNA replication and transcription. J. Cell. Biochem. 94, 554-565.
  • Wallace, J. A., and Orr-Weaver, T. L. (2005) Replication of heterochromatin: Insights into mechanisms of epigenetic inheritance. Chromosoma 114, 389-402.
  • Danis, E., Brodolin, K., Menut, S., Maiorano, D., Girard-Reydet, C., and Mechali, M. (2004) Specification of a DNA replication origin by a transcription complex. Nat. Cell Biol. 6, 721-730.
  • Gilbert, N., Boyle, S., Fiegler, H., Woodfine, K., Carter, N. P., and Bickmore, W. A. (2004) Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118, 555-566.
  • MacAlpine, D. M., Rodriguez, H. K., and Bell, S. P. (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev. 18, 3094-3105.
  • Sadoni, N., Cardoso, M. C., Stelzer, E. H., Leonhardt, H., and Zink, D. (2004) Stable chromosomal units determine the spatial and temporal organization of DNA replication. J. Cell Sci. 117, 5353-5365.
  • Weinreich, M., Palacios DeBeer, M. A. P., and Fox, C. A. (2004) The activities of eukaryotic replication origins in chromatin. BBA-Gene Struc. Exp. 1677, 142-157.
  • Shareef, M. M., Badugu, R., and Kellum, R. (2003) HP1/ORC complex and heterochromatin assembly. Genetica 117, 127-134.

Origin Mapping Techniques

  • Feng, W., Collingwood, D., Boeck, M. E., Fox, L. A., Alvino, G. M., Fangman, W. L., Raghuraman, M. K., and Brewer, B. J. (2006) Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nat. Cell Biol., 8, 148-155.
  • Mesner, L. D., Crawford, E. L., and Hamlin, J. L. (2006) Isolating apparently pure libraries of replication origins from complex genomes. Mol. Cell 21, 719-726.
  • Patel, P. K., Arcangioli, B., Baker, S. P., Bensimon, A., and Rhind, N. (2006) DNA replication origins fire stochastically in fission yeast. Mol. Biol. Cell. 17, 308-316.
  • Urban , A. E., Korbel, J. O., Selzer, R., Richmond, T., Hacker, A., Popescu, G. V., Cubells, J. F., Green, R., Emanuel, B. S., Gerstein, M. B., et al. (2006) High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 103, 4534-4539.
  • Dai, J. L., Chuang, R. Y., and Kelly, T. J. (2005) DNA replication origins in the Schizosaccharomyces pombe genome. Proc. Nat. Acad. Sci. USA 102, 337-342.
  • Todorovic,V., Giadrossi, S., Pelizon, C., Mendoza-Maldonado, R., Masai., and Giacca, M. (2005). Human origins of DNA replication selected from a library of nascent DNA. Mol. Cell 19, 567-575.
  • Barrett, M. T., Scheffer, A., Ben-Dor, A., Sampas, N., Lipson, D., Kincaid, R., Tsang, P., Curry, B., Baird, K., Meltzer, P. S., et al. (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. USA 101, 17765-17770.
  • Breier, A. M., Chatterji, S., and Cozzarelli, N. R. (2004) Prediction of Saccharomyces cerevisiae replication origins. Genome Biol. 5.
  • Woodfine, K., Fiegler, H., Beare, D. M., Collins, J. E., McCann, O. T., Young, B. D., Debernardi, S., Mott, R., Dunham, I., and Carter, N. P. (2004) Replication timing of the human genome. Hum. Mol. Genet. 13, 191-202.
  • Fiegler, H., Carr, P., Douglas, E. J., Burford, D. C., Hunt, S., Scott, C. E., Smith, J., Vetrie, D., Gorman, P., Tomlinson, I. P., and Carter, N. P. (2003) DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromos, Cancer 36, 361-374.
  • Wyrick, J. J., Aparicio, J. G., Chen, T., Barnett, J. D., Jennings, E. G., Young, R. A., Bell, S. P., and Aparicio, O. M. (2001) Genome-wide distribution of ORC and MCM proteins in S-cerevisiae: High-resolution mapping of replication origins. Science 294, 2357-2360.
  • Orlando, V. (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25, 99-104.
  • Giacca, M., Pelizon, C., and Falaschi, A. (1997). Mapping replication origins by quantifying relative abundance of nascent DNA strands using competitive polymerase chain reaction. Methods 13, 301-312.
  • Gencheva, M., Anachkova, B., and Sussev, G. (1996) Mapping the sites of initiation of DNA replication in rat and human rRNA genes. J. Biol. Chem. 271, 2608-2614.
 
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Last updated July 09, 2007