![Transcription factories in a Hela cell [from Cook PR (1999) Science 284, 1790]](../images/pombo.png)
Kimura, H., and Cook, P.R. (2001). Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153, 1341-1353. [PubMed] [pdf]
Cook, P.R. (2001). 'Principles of nuclear structure and function'. 376 pp. 147 fig. J. Wiley and Sons, New York. ISBN: 0-471-41538-3. [Home page] [Local page]
Robinson, J.M., Takizawa, T., Pombo, A., and Cook, P.R. (2001). Correlative fluorescence and electron microscopy on ultrathin cryosections: bridging the resolution gap. J. Histochem. Cytochem. 49, 803-808. [PubMed] [pdf]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2001). Coupled transcription and translation within nuclei of mammalian cells. Science 293, 1139-1142. [PubMed] [Supplementary material] [pdf]
Sugaya, K., Sasanuma, S., Cook, P.R., and Mita, K. (2001). A mutation in the largest (catalytic) subunit of RNA polymerase II and its relation to the arrest of the cell cycle in G(1) phase. Gene 274, 77-81. [PubMed] [pdf]
Blow, J.J., Gillespie, P.J., Francis, D., and Jackson, D.A. (2001). Replication origins in Xenopus egg extracts are 5-15 kilobases apart and are activated in clusters that fire at different times. J. Cell Biol. 152, 15-25. [PubMed]
Takebayashi, S., Manders, E.M.M., Kimura, H., Taguchi, H., and Okumura, K. (2001). Mapping sites where replication initiates in mammalian cells using DNA fibers. Exp. Cell Res. 271, 263-268. [PubMed]
Takemura, M., Ohoka, F., Perpelescu, M., Ogawa, M., Matsushita, H., Takaba, T., Akiyama, T., Umekawa, H., Furuichi, Y., Cook, P.R., and Yoshida, S. (2002). Phosphorylation-dependent migration of retinoblastoma protein into the nucleolus triggered by binding to nucleophosmin/B23. Exp. Cell Res. 276, 233-241. [PubMed] [pdf]
Kimura, H., Sugaya, K., and Cook, P.R. (2002). The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159, 777-782. [PubMed] [pdf]
Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nature Genetics 32, 347-352. [PubMed] [pdf]
Iborra, F.J., and Cook, P.R. (2002). The interdependence of nuclear structure and function. Curr. Opin. Cell Biol. 14, 780-785. [PubMed] [pdf]
Kwek, K.Y., Murphy, S., Furger, A., Thomas, B., O'Gorman, W., Kimura, H., Proudfoot, N.J., and Akoulitchev, A. (2002). U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat. Struct. Biol. 9, 800-805. [PubMed]
Iborra, F.J. (2002). The path that RNA takes from the nucleus to the cytoplasm: a trip with some surprises. Histochem. Cell. Biol. 118, 95-103. [PubMed]
Rodríguez-López, A.M., Jackson, D.A., Iborra, F., and Cox, L.S. (2002). Asymmetry of DNA replication fork progression in Werner's syndrome. Aging Cell 1, 30-39. [PubMed]
Iborra, F.J., Cook, P.R., and Jackson, D.A. (2003). Applying microscopy to the analysis of nuclear structure and function. Methods 29, 131-141. [PubMed] [pdf]
Kudo, Y., Boyd, C.A., Kimura, H., Cook, P.R., Redman, C.W. and Sargent, I.L. (2003). Quantifying the syncytialisation of human placental trophoblast BeWo cells grown in vitro. Biochim. Biophys. Acta. 1640, 25-31. [PubMed] [pdf]
Cook, P.R. (2003). Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483-4491. [PubMed] [pdf]
Rodríguez-López, A.M., Jackson, D.A., Nehlin, J.O., Iborra, F., Warren, A.V., and Cox, L.S. (2003). Characterisation of the interaction between WRN, the helicase/exonuclease defective in progeroid Werner's syndrome, and an essential replication factor, PCNA. Mech. Ageing Dev. 124, 167-174. [PubMed]
Iborra, F.J., Escargueil, A.E., Kwek, K.Y., Akoulitchev, A. and Cook, P.R. (2004). Molecular cross-talk between the transcription, translation, and nonsense-mediated decay machineries. J. Cell Sci. 117, 899-906. [PubMed] [pdf]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). Approaches for monitoring nuclear translation. Meth. Molec. Biol. 257, 103-113. [PubMed] [pdf]
Kimura, H., Hieda, M., and Cook, P.R. (2004). Measuring histone and polymerase dynamics in living cells. Methods Enzymol. 375, 381-393. [PubMed] [pdf]
Iborra, F.J., Kimura, H., and Cook, P.R. (2004). The functional organization of mitochondrial genomes in human cells. BMC Biology 2, 9. [PubMed] [pdf]
Bernas, T., Zarebski, M., Cook, P.R., and Dobrucki, J.W. (2004). Minimizing photobleaching during confocal microscopy of fluorescent probes bound to chromatin: role of anoxia and photon flux. J. Microsc. 215, 281-296. [PubMed] [pdf]
Philimonenko, A.A., Jackson, D.A., Hodny, Z., Janacek, J., Cook, P.R., and Hozak, P. (2004). Dynamics of DNA replication: an ultrastructural study. J. Struct. Biol. 148, 279-289. [PubMed] [pdf]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). The case for nuclear translation. J. Cell Sci. 117, 5713-5720. [PubMed] [pdf]
Hieda, M., Winstanley, H., Maini, P., Iborra, F.J., and Cook, P.R. (2005). Different populations of RNA polymerase II in living mammalian cells. Chromosome Res. 13, 135-144. [PubMed] [pdf]
Bartlett, J., Blagojevic, J., Carter, D., Eskiw, C., Fromaget, M., Job, C., Shamsher, M., Faro Trindade, I, Xu, M., and Cook, P.R. (2006). Specialized transcription factories. Biochem. Soc. Symp. 73, 67-75. [PubMed] [pdf]
Bon, M., Marenduzzo, D., Cook, P.R. (2006). Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context. Structure 14, 197–204. [PubMed] [pdf]
Marenduzzo, D., Micheletti, C., and Cook, P.R. (2006). Entropy-driven genome organization. Biophys. J. 90, 3712-3721. [PubMed] [pdf]
Bon, M., McGowan, S., and Cook, P.R. (2006). Many expressed genes in bacteria and yeast are transcribed only once per cell cycle. FASEB J. 20, 1721-1723. [PubMed] [Supporting on-line information; search for a gene of interest; downloads] [pdf]
Faro-Trindade, I., and Cook, P.R. (2006). A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol. Biol. Cell 17, 2910-2920. [PubMed] [pdf]
Toan, N.M., Marenduzzo, D., Cook, P.R., and Micheletti, C. (2006). Depletion effects and loop formation in self-avoiding polymers. Phys. Rev. Lett. 97, 178302. [PubMed] [pdf]
Faro-Trindade, I., and Cook, P.R. (2006). Transcription factories: structures conserved during differentiation and evolution. Biochem. Soc. Trans. 34, 1133-1137. [PubMed] [pdf]
Marenduzzo, D., Finan, K., and Cook, P.R. (2006). The depletion attraction: an underappreciated force driving cellular organization. J. Cell Biol. 175, 681-686. [PubMed] [pdf]
Kimura, H., and Cook, P.R. (2007). Dynamic chromatin loops and the regulation of gene expression. In ‘Nuclear dynamics: molecular biology and visualization of the nucleus’; K. Nagata, and T. Takeyasu, Eds; Springer, Japan. [pdf]
Marenduzzo, D., Faro-Trindade, I., and Cook, P.R. (2007). What are the molecular ties that maintain genomic loops? Trends Genet. 23, 126-133. [PubMed] [pdf]
Fromaget, M., and Cook, P.R. (2007). Photobleaching reveals complex effects of inhibitors on transcribing RNA polymerase II in living cells. Exp. Cell Res. 313, 3026-3033. [PubMed] [pdf]
Escargueil A.E., Poindessous, V., Soares, D.G., Sarasin, A., Cook, P.R., and Larsen, A.K. (2008). Influence of irofulven, a transcription-coupled repair-specific antitumor agent, on RNA polymerase activity: stability and dynamics in living mammalian cells. J. Cell Sci. 121, 1275-1283. [PubMed] [pdf]
Xu, M., and Cook, P.R. (2008). Similar active genes cluster in specialized transcription factories. J. Cell Biol. 181, 615-623. [PubMed] [pdf]
Eskiw, C.H., Rapp, A., Carter, D.R.F., and Cook, P.R. (2008). RNA polymerase II activity is located on the surface of ~87 nm protein-rich transcription factories. J. Cell Sci. 121, 1999-2007. [PubMed] [pdf]
Carter, D.R.F., Eskiw, C., and Cook, P.R. (2008). Transcription factories. Biochem. Soc. Trans. 36, 585-589. [PubMed] [pdf]
Xu, M., and Cook, P.R. (2008). The role of specialized transcription factories in chromosome pairing. Biochem. Biophys. Acta 1783, 2155-2160. [PubMed] [pdf]
Cook, P.R., and Marenduzzo, D. (2009). Entropic organization of interphase chromosomes. J. Cell Biol. 186, 825-834. [PubMed] [pdf]
Wada, Y., Ohta, Y., Xu, M., Tsutsumi, S., Minami, T., Inoue, K., Komura, D., Kitakami, J., Oshida, N., Papantonis, A., Izumi, A., Kobayashi, M., Meguro, H., Kanki, Y., Mimura, I., Yamamoto, K., Mataki, C., Hamakubo, T., Shirahige, K., Aburatani, H., Kimura, H., Kodama, T., Cook. P.R., and Ihara, S. (2009). Visualizing a wave of transcription as it sweeps along activated human genes. Proc. Natl. Acad. Sci. USA, 106, 18357-18361. [PubMed] [pdf]
Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1-10. [PubMed] [pdf]
Papantonis, A., and Cook, P.R. (2010). Genome architecture and the role of transcription. Curr. Opin. Cell. Biol. 22, 1-6. [PubMed] [pdf]
Papantonis, A., Larkin, J.D., Wada, Y., Ohta, Y., Ihara, S., Kodama, T., and Cook, P.R. (2010). Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol. 8, e1000419. [PubMed] [pdf]