Papers: 1969-2020
Peter Cook thanks all those that helped make these papers
[Notes highlighting properties of loops and transcription factories]
Harris, H., and Cook, P.R. (1969). Synthesis of an enzyme determined by an erythrocyte nucleus in a hybrid cell. J. Cell Sci. 5, 121-134. [PubMed]
Cook, P.R. (1970). Species specificity of an enzyme determined by an erythrocyte nucleus in an interspecific hybrid cell. J. Cell Sci. 7, 1-3. [PubMed]
Cook, P.R. (1970). ‘Studies on differentiation in vertebrate cells’. A thesis presented for the degree of Doctor of Philosophy in the University of Oxford.
Schwartz, A.G., Cook, P.R., and Harris, H. (1971). Correction of a genetic defect in a mammalian cell. Nature, New Biol. 230, 5-8. [PubMed]
Miller, O.J., Cook, P.R., Khan, P. M., Shin, S., and Siniscalco, M. (1971). Mitotic separation of two human X-linked genes in man-mouse somatic cell hybrids. Proc. Natl. Acad. Sci. U.S.A. 68, 116-120. [PubMed]
Cook, P.R. (1971). Insertion of small pieces of foreign genetic material into somatic cells. Biochem. J. 124, 35P-37P. [PubMed]
Shin, S., Khan, P. M., and Cook, P.R. (1971). Characterisation of hypoxanthine-guanine phosphoribosyl transferase in man-mouse somatic cell hybrids by an improved electrophoretic method. Biochem. Genet. 5, 91-99. [PubMed]
Cook, P.R. (1973). Hypothesis on differentiation and the inheritance of gene superstructure. Nature 245, 23-25. [PubMed]
Cook, P.R. (1974). On the inheritance of differentiated traits. Biol. Rev. 49, 51-84.
Cook, P.R. (1975). Linkage of the loci for glucose-6-phosphate dehydrogenase and for inosinic acid pyrophosphorylase to the X chromosome of the field-vole Microtus agrestis. J. Cell Sci. 17, 95-112. [PubMed]
Cook, P.R. and Brazell, I.A. (1975). Supercoils in human DNA. J. Cell Sci. 19, 261-279. [PubMed] [Demonstration of loops in linear human chromosomes]
Cook, P.R., and Brazell, I.A. (1976). Conformational constraints in nuclear DNA. J. Cell Sci. 22, 287-302. [PubMed]
Cook, P.R., Brazell, I.A., and Jost, E. (1976). Characterization of nuclear structures containing superhelical DNA. J. Cell Sci. 22, 303-324. [PubMed]
Cook, P.R., and Brazell, I.A. (1976). Detection and repair of single-strand breaks in nuclear DNA. Nature 263, 679-682. [PubMed]
Cook, P.R., and Brazell, I.A. (1977). The superhelical density of nuclear DNA from human cells. Eur. J. Biochem. 74, 527-531. [PubMed]
Cook, P.R., and Brazell, I.A. (1977). Supercoils in nuclear DNA and the repair of radiation damage. Mut. Res. 46, 111-112.
Colman, A., and Cook, P.R. (1977). Transcription of superhelical DNA from cell nuclei. Eur. J. Biochem. 76, 63-78. [PubMed]
Levin, J.M., Jost, E., and Cook, P.R. (1978). The dissociation of nuclear proteins from superhelical DNA. J. Cell Sci. 29, 103-116. [PubMed]
Cook, P.R., Brazell, I.A., Pawsey, S.A., and Giannelli, F. (1978). Changes induced by ultraviolet light in the superhelical DNA of lymphocytes from subjects with xeroderma pigmentosum and normal controls. J. Cell Sci. 29, 117-127. [PubMed]
Cook, P.R., and Brazell, I.A. (1978). Spectrofluorometric measurement of the binding of ethidium to superhelical DNA from cell nuclei. Eur. J. Biochem. 84, 465-477. [PubMed]
Warren, A.C., and Cook, P.R. (1978). Supercoiling of DNA and nuclear conformation during the cell cycle. J. Cell Sci. 30, 211-226. [PubMed]
McCready, S.J., Akrigg, A., and Cook, P.R. (1979). Electron microscopy of intact nuclear DNA from human cells. J. Cell Sci. 39, 53-62. [PubMed]
Akrigg, A., and Cook, P.R. (1980). DNA gyrase stimulates transcription. Nucl. Acids Res. 8, 845-854. [PubMed]
Cook, P.R., and Brazell, I.A. (1980). Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage. Nucl. Acids Res. 8, 2895-2906. [PubMed]
McCready, S.J., Godwin, J., Mason, D.W., Brazell, I.A., and Cook, P.R. (1980). DNA is replicated at the nuclear cage. J. Cell Sci. 46, 365-386. [PubMed]
Levin, J.M., and Cook, P.R. (1981). Conformational changes induced by salt in complexes of histones and superhelical nuclear DNA. J. Cell Sci. 50, 199-208. [PubMed]
Levin, J.M., and Cook, P.R. (1981). Reconstruction of complexes of histones and superhelical nuclear DNA. J. Cell Sci. 50, 209-224. [PubMed]
Jackson, D.A., McCready, S.J., and Cook, P.R. (1981). RNA is synthesised at the nuclear cage. Nature 292, 552-555. [PubMed] [RNA polymerases are attached to the nuclear sub-structure when active]
McCready, S.J., Jackson, D.A., and Cook, P.R. (1982). Attachment of superhelical DNA to the nuclear cage during replication and transcription. Prog. Mut. Res. 4, 113-130.
Jackson, D.A., Caton, A.J., McCready S.J., and Cook, P.R. (1982). Influenza virus RNA is synthesised at fixed sites in the nucleus. Nature 296, 366-368. [PubMed] [Active flu RNA polymerases are transiently immobile when active]
Cook, P.R. Lang, J., Hayday, A., Lania, L., Fried, M., Chiswell, D.J., and Wyke, J.A. (1982). Active viral genes in transformed cells lie close to the nuclear cage. EMBO J. 1, 447-452. [PubMed] [Genes become active by attaching to the nuclear sub-structure]
Patel, S.B., and Cook, P.R. (1983). The DNA-protein cross: a method for detecting specific DNA-protein complexes in crude mixtures. EMBO J. 2, 137-142. [PubMed]
Cook, P.R., and Lang, J. (1984). The spatial organization of sequences involved in initiation and termination of eukaryotic DNA replication. Nucl. Acids Res. 12, 1069-1075. [PubMed]
Cook, P.R. (1984). A general method for isolating intact nuclear DNA. EMBO J. 3, 1837-1842. [PubMed]
McCready, S.J., and Cook, P.R. (1984). Lesions induced in DNA by ultra-violet light are repaired at the nuclear cage. J. Cell Sci. 70, 189-196. [PubMed] [Active DNA polymerases repairing DNA damage are attached to the nuclear sub-structure]
Jackson, D.A., Patel, S.B., and Cook, P.R. (1984). Attachment of repeated sequences to the nuclear cage. Nucl. Acids Res. 12, 6709-6726. [PubMed]
Jackson, D.A., McCready, S.J. and Cook, P.R. (1984). Replication and transcription depend on attachment of DNA to the nuclear cage. J. Cell Sci. Suppl. 1, 59-79. [PubMed]
Cook, P.R., and Laskey, R.A. (editors), (1984). ‘Higher order structure in the nucleus’. Proceedings of the First British Society for Cell Biology - Company of Biologists Symposium held in Manchester, April, 1984. J. Cell Sci. Suppl. 1.
Dyson, P.J., Cook, P.R., Searle, S., and Wyke, J.A. (1985). The chromatin structure of Rous sarcoma proviruses is changed by factors that act in trans in cell hybrids. EMBO J. 4, 413-420. [PubMed]
McCready, S.J., and Cook, P.R. (1985). Unscheduled DNA synthesis takes place at the nuclear cage. Br. J. Cancer 51, 604.
Jackson, D.A., and Cook, P.R. (1985). A general method for preparing chromatin containing intact DNA. EMBO J. 4, 913-918. [PubMed]
Jackson, D.A., and Cook, P.R. (1985). Transcription occurs at a nucleoskeleton. EMBO J. 4, 919-925. [PubMed]
Jackson, D.A., and Cook, P.R. (1986). Replication occurs at a nucleoskeleton. EMBO J. 5, 1403-1410. [PubMed]
Whittaker, J., Lang, J., Cook, P.R., Aspinall, S., McCready, S.J., and Cox, B.S. (1986). Part of the human ribosomal RNA locus stabilizes a plasmid in yeast. Nucl. Acids Res. 14, 5683-5692. [PubMed]
Jackson, D.A., and Cook, P.R. (1986). A cell-cycle dependent DNA polymerase activity that replicates intact DNA in chromatin. J. Mol. Biol. 192, 65-76. [PubMed]
Jackson, D.A., and Cook, P.R. (1986). Different populations of DNA polymerase α in Hela cells. J. Mol. Biol. 192, 77-86. [PubMed]
Jackson, D.A., and Cook, P.R. (1987). The nucleoskeleton: active site of transcription and replication. In ‘Modern Trends in Human Leukemia VII’, edited by Neth, R., Gallo, R.C., Greaves, M.F., and Kabisch, H., pp 299-303, Springer-Verlag, Berlin. Also published as Jackson, D.A., and Cook, P.R. (1987). The nucleoskeleton: active site of transcription and replication. Haematol. Blood Transfus. 31, 299-303.
Cook, P.R., and Jackson, D.A. (1988). The nucleoskeleton: active site of transcription or artifact? In ‘Chromosomes and Chromatin’ Vol. III, edited by Adolph, K.W., pp 97-118, CRC Press, Baton Rouge, Florida.
Cook, P.R. (1988). The nucleoskeleton: artefact, passive framework or active site? J. Cell Sci. 90, 1-6. [PubMed]
Jackson, D.A., Yuan, J., and Cook, P.R. (1988). A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. J. Cell Sci. 90, 365-378. [PubMed]
Jackson, D.A., and Cook, P.R. (1988). Visualization of a filamentous nucleoskeleton with a 23 nm axial repeat. EMBO J. 7, 3667-3677. [PubMed] [Lamin-like proteins form an internal nucleoskeleton]
Dear, P.H., and Cook, P.R. (1989). Happy mapping: a proposal for linkage mapping the human genome. Nucl. Acids Res. 17, 6795-6807. [PubMed]
Cook, P.R. (1989). The nucleoskeleton and the topology of transcription. Eur. J. Biochem. 185, 487-501. [PubMed]
Jackson, D.A., Dickinson, P., and Cook, P.R. (1990). The size of chromatin loops in HeLa cells. EMBO J. 9, 567-571. [PubMed] [Still the most accurate estimate of the size of chromatin loops in man?]
Cook, P.R. (1990). How mobile are active RNA polymerases? J. Cell Sci. 96, 189-192. [PubMed]
Dickinson, P., Cook, P.R., and Jackson, D.A. (1990). Active RNA polymerase I is fixed within the nucleus of HeLa cells. EMBO J. 9, 2207-2214. [PubMed]
Jackson, D.A., Dickinson, P., and Cook, P.R. (1990). Attachment of DNA to the nucleoskeleton of HeLa cells examined using physiological conditions. Nucl. Acids Res. 18, 4385-4393. [PubMed]
Dear, P.H., and Cook, P.R. (1991). Cellular gels: purifying and mapping long DNA molecules. Biochem. J. 273, 695-699. [PubMed]
Cook, P.R. (1991). The nucleoskeleton and the topology of replication. Cell 66, 627-635. [PubMed]
Mullins, S.T., Annan, N.K., Cook, P.R., and Lowe, G. (1992). Bis-intercalators of DNA with a rigid linker in an extended configuration. Biochemistry 31, 842-849. [PubMed]
Annan, N.K., Cook, P.R., Mullins, S.T., and Lowe, G. (1992). Evidence for cross-linking DNA by bis-intercalators with rigid and extended linkers is provided by knotting and catenation. Nucl. Acids Res. 20, 983-990. [PubMed]
Cook, P.R., and Gove, F. (1992). Transcription by an immobilized RNA polymerase from bacteriophage T7 and the topology of transcription. Nucl. Acids Res. 20, 3591-3598. [PubMed]
Jackson, D.A., Dolle, A., Robertson, G., and Cook, P.R. (1992). The attachments of chromatin loops to the nucleoskeleton. Cell Biol. Int. Rep. 16, 687-696. [PubMed]
Cook, P.R. (1993). A model for reverse transcription by a dimeric enzyme. J. Gen. Virol. 74, 691-697. Corrigendum 74, 3037. [PubMed]
Dear, P.H., and Cook, P.R. (1993). Happy mapping: linkage mapping using a physical analogue of meiosis. Nucl. Acids Res. 21, 13-20. [PubMed]
Hozák, P., Hassan, A.B., Jackson, D.A., and Cook, P.R. (1993). Visualization of replication factories attached to a nucleoskeleton. Cell 73, 361-373. [PubMed] [Replication factories were discovered before transcription factories]
Jackson, D.A., Hassan, A.B., Errington, R.J., and Cook, P.R. (1993). Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065. [PubMed] [Demonstration that active polymerases cluster in factories]
Cook, P.R., Dolle, A., Hassan, A.B., Hozák, P., and Jackson, D.A. (1993). The role of the nucleoskeleton in RNA metabolism. Nucl. Acids Mol. Biol. 7, 226-237.
Hassan, A.B., and Cook, P.R. (1993). Visualization of replication sites in unfixed human cells. J. Cell Sci. 105, 541-550. [PubMed]
Jackson, D.A., and Cook, P.R. (1993). Transcriptionally-active minichromosomes are attached transiently in nuclei through transcription units. J. Cell Sci. 105, 1143-1150. [PubMed]
Hozák, P., and Cook, P.R. (1994). Replication factories. Trends Cell Biol. 4, 48-52. [PubMed]
Cook, P.R. (1994). Transcription by immobile RNA polymerases. In ‘The legacy of cell fusion’. Ed. S. Gordon. Oxford University Press, Oxford. pp 84-100.
Hassan, A.B., Errington, R.J., White, N.S., Jackson, D.A., and Cook. P.R. (1994). Replication and transcription sites are colocalized in human cells. J. Cell Sci. 107, 425-434. [PubMed]
Hozák, P., Cook, P.R., Schöfer, C., Mosgöller, W., and Wachtler, F. (1994). Site of transcription of ribosomal RNA and intra-nucleolar structure in HeLa cells. J. Cell Sci. 107, 639-648. [PubMed] [Ribosomal RNA is made on the surface of nucleolar factories]
Hassan, A.B., and Cook, P.R. (1994). Does transcription by RNA polymerase play a direct role in the initiation of replication? J. Cell Sci. 107, 1381-1387. [PubMed]
Cook, P.R. (1994). RNA polymerase: structural determinant of the chromatin loop and the chromosome. BioEssays 16, 425-430. [PubMed] [How enhancers work]
Jackson, D.A., Balajee, A.S., Mullenders, L., and Cook, P.R. (1994). Sites in human nuclei where DNA damaged by ultra-violet light is repaired: visualization and localization relative to the nucleoskeleton. J. Cell Sci. 107, 1745-1752. [PubMed]
Jackson, D.A., Hassan, A.B., Errington, R.J., and Cook, P.R. (1994). Sites in human nuclei where damage induced by ultra-violet light is repaired: localization relative to transcription sites and concentrations of proliferating cell nuclear antigen and the tumour suppressor protein, p53. J. Cell Sci. 107, 1753-1760. [PubMed]
Hozák, P., Jackson, D.A., and Cook, P.R. (1994). Replication factories and nuclear bodies: the ultrastructural characterization of replication sites during the cell cycle. J. Cell Sci. 107, 2191-2202. [PubMed]
Hozák, P., Sasseville, A. M-J., Raymond, R., and Cook. P.R. (1995). Lamin proteins form an internal nucleoskeleton as well as a peripheral lamina in human cells. J. Cell Sci. 108, 635-644. [PubMed]
Jackson, D.A., and Cook, P.R. (1995). The structural basis of nuclear function. Int. Rev. Cytol. 162A, 125-149. [PubMed]
Cook, P.R. (1995). A chromomeric model for nuclear and chromosome structure. J. Cell Sci. 108, 2927-2935. [PubMed] [Still the most plausible model?]
Hughes, T.A., Pombo, A., McManus, J., Hozák, P., Jackson, D.A., and Cook, P.R. (1995). On the structure of replication and transcription factories. J. Cell Sci., Suppl. 19, 59-65. [PubMed]
McManus, J., Hughes, T.A., Pombo, A., Jones, E.., Iborra, F.J., Jackson, D.A., and Cook, P.R. (1995). ‘Nuclear factories for replication, transcription and repair.’ In Proceedings of the 10th International Congress of Radiation Research. Radiation Research 1985-1995, Congress Proceedings 2, 352-361.
Hozák, P., Jackson, D.A., and Cook. P.R. (1996). The role of nuclear structure in DNA replication. In ‘Eukaryotic DNA replication: frontiers in molecular biology’ (Ed. J.J. Blow), pp124-142. Oxford University Press, Oxford.
Iborra, F.J., Pombo, A., Jackson, D.A., and Cook, P.R. (1996). Active RNA polymerases are localized within discrete transcription ‘factories’ in human nuclei. J. Cell Sci. 109, 1427-1436. [PubMed] Corrigendum published in Iborra, F.J., Jackson, D.A., and Cook, P.R. (1998). J. Cell Sci. 111, 2269-2282. [Early estimate of number and size of factories containing RNA polymerase II]
Hughes, T.A., and Cook, P.R. (1996). Mimosine arrests the cell cycle after cells enter S-phase. Exp. Cell Res. 222, 275-280. [PubMed]
Jackson, D.A., Bartlett, J., and Cook, P.R. (1996). Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units. Nucl. Acids Res. 24, 1212-1219. [PubMed]
Carpenter, M.L., Lowe, G., and Cook, P.R. (1996). The structure of 4-way DNA junctions: specific binding of bis-intercalators with rigid linkers. Nucl. Acids Res. 24, 1594-1601. [PubMed]
McCoubrey, A., Latham, H.C., Cook, P.R., Rodger, A., and Lowe, G. (1996). 4-Picoline-2,2':6',2"-terpyridine-platinum (II) - a potent intercalator of DNA. FEBS Letters 380, 73-78. [PubMed]
Iborra, F.J., Pombo, A., McManus, J., Jackson, D.A., and Cook, P.R. (1996). The topology of transcription by immobilized polymerases. Exp. Cell Res. 229, 167-173. [PubMed] [How the β-globin gene becomes active]
Pombo, A., and Cook, P.R. (1996). The localization of sites containing nascent RNA and splicing factors. Exp. Cell Res. 229, 201-203. [PubMed]
Pombo, A., McManus, J., Hughes, T.A., Iborra, F.J., Jackson, D.A., and Cook, P.R. (1996). Transcription factories and chromosome structure. Chromosomes Today 12, 147-160.
Cook, P.R. (1997). The transcriptional basis of chromosome pairing. J. Cell Sci. 110, 1033-1040. [PubMed] [Still the most plausible explanation?]
Pombo, A., Cuello, P., Schul, W., Yoon, J.-B., Roeder, R.G., Cook, P.R., and Murphy, S. (1998). Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle. EMBO J. 17, 1768-1778. [PubMed] [Evidence that different factories specialize in transcribing different sets of genes]
Jackson, D.A., and Cook, P.R. (1998). Analyzing DNA replication: non-isotopic labeling. In ‘Cells: a laboratory manual’, pp 109.1-109.13. Edited by D.L. Spector, R.D. Goldman and L.A. Leinwand. Cold Spring Harbor Laboratory Press, NY.
Jackson, D.A., and Cook, P.R. (1998). Analyzing RNA synthesis: non-isotopic labeling. In ‘Cells: a laboratory manual’, pp 110.1-110.10. Edited by D.L. Spector, R.D. Goldman and L.A. Leinwand. Cold Spring Harbor Laboratory Press, NY.
Jackson, D.A., Iborra, F.J., Manders, E.M.M., and Cook, P.R. (1998). Numbers and organization of RNA polymerases, nascent transcripts and transcription units in HeLa nuclei. Mol. Biol. Cell 9, 1523-1536. [PubMed] Erratum published in Mol. Biol. Cell 9, 2698. [Early estimates of numbers]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (1998). The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins. J. Cell Sci. 111, 2269-2282. [PubMed]
Iborra, F.J., and Cook, P.R. (1998). The size of sites containing SR proteins in human nuclei: problems associated with characterizing small structures by immunogold labelling. J. Histochem. Cytochem. 46, 985-992. [PubMed]
Pombo, A., Hollinshead, M., and Cook, P.R. (1999). Bridging the resolution gap: imaging the same transcription factories in cryosections by light and electron microscopy. J. Histochem. Cytochem. 47, 471-480. [PubMed]
Manders, E.M.M., Kimura, H., and Cook, P.R. (1999). Direct imaging of DNA in living cells reveals the dynamics of chromosome formation. J. Cell Biol. 144, 813-822. [PubMed]
Pombo, A., Jackson, D.A., Hollinshead, M., Wang, Z., Roeder, R.G., and Cook, P.R. (1999). Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241-2253. [PubMed] [RNA polymerases II and III are active in different factories]
Kimura, H., Tao, Y., Roeder, R.G., and Cook, P.R. (1999). Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol. Cell. Biol. 19, 5383-5392. [PubMed] [Early estimates of numbers]
Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed] [Widely-cited review]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2000). The path of mRNA through nuclear pores: apparent entry from the sides into specialized pores. J. Cell Sci. 113, 291-302. [PubMed]
Jones, E., Kimura, H., Vigneron, M., Wang, Z., Roeder, R.G., and Cook, P.R. (2000). Isolation and characterization of monoclonal antibodies directed against subunits of human RNA polymerases I, II, and III. Exp. Cell Res. 254, 163-172. [PubMed]
Pombo, A., Jones, E., Iborra, F.J., Kimura, H., Sugaya, K., Cook, P.R., and Jackson, D.A. (2000). Specialized transcription factories within mammalian nuclei. Crit. Rev. Eukaryotic Gene Exp. 10, 21-29. [PubMed]
Sugaya, K., Vigneron, M., and Cook, P.R. (2000). Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J. Cell Sci. 113, 2679-2683. [PubMed] [Early visualization of factories in living cells using a gfp-tagged polymerase]
Wade-Martins, R., White, R.E., Kimura, H., Cook, P.R., and James, M.R. (2000). Stable correction of a genetic deficiency in human cells by an episome carrying a 115 kbp genomic transgene. Nature Biotechnology 18, 1311-1314. [PubMed]
Cook, P.R. (2001). Hot nuclei at the Cold Spring. EMBO Reports 2, 14-16. [PubMed]
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. [A text-book for undergraduates]
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]
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]
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] [Another heresy I still believe to be true: ribosomes in nuclear factories translate – and proof-read – nascent RNAs!]
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]
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]
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] [About 25% RNA polymerase is active in HeLa cells]
Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nature Genetics 32, 347-352. [PubMed]
Iborra, F.J., and Cook, P.R. (2002). The interdependence of nuclear structure and function. Curr. Opin. Cell Biol. 14, 780-785. [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]
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]
Cook, P.R. (2003). Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483-4491. [PubMed]
Kimura, H., Hieda, M., and Cook, P.R. (2004). Measuring histone and polymerase dynamics in living cells. Methods Enzymol. 375, 381-393. [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]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). Approaches for monitoring nuclear translation. Meth. Molec. Biol. 257, 103-113. [PubMed]
Iborra, F.J., Kimura, H., and Cook, P.R. (2004). The functional organization of mitochondrial genomes in human cells. BMC Biology 2, 9. [PubMed]
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]
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]
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). The case for nuclear translation. J. Cell Sci. 117, 5713-5720. [PubMed]
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]
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]
Bon, M., Marenduzzo, D., and 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] [Modeling provides insights into various biological mysteries associated with loops]
Marenduzzo, D., Micheletti, C., and Cook, P.R. (2006). Entropy-driven genome organization. Biophys. J. 90, 3712-3721. [PubMed] [Powerful entropic forces drive chromosome organization]
Bon, M., McGowan, S.J., 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]
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] [Estimates of changing numbers of active polymerases and factories as embryonic cells differentiate]
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]
Faro-Trindade, I., and Cook, P.R. (2006). Transcription factories: structures conserved during differentiation and evolution. Biochem. Soc. Trans. 34, 1133-1137. [PubMed]
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] [Introducing a powerful force almost unknown to biologists that drives particle clustering, including factory formation]
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.
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]
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]
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]
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] [High-resolution EM images of factories]
Xu, M., and Cook, P.R. (2008). Similar active genes cluster in specialized transcription factories. J. Cell Biol. 181, 615-623. [PubMed] [Different promoters direct genes to different factories]
Carter, D.R.F., Eskiw, C., and Cook, P.R. (2008). Transcription factories. Biochem. Soc. Trans. 36, 585-589. [PubMed]
Xu, M., and Cook, P.R. (2008). The role of specialized transcription factories in chromosome pairing. Biochem. Biophys. Acta 1783, 2155-2160. [PubMed] [Updating our model for chromosome pairing]
Cook, P.R., and Marenduzzo, D. (2009). Entropic organization of interphase chromosomes. J. Cell Biol. 186, 825-834. [PubMed] [Illustrates the power of entropic forces]
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]
Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1–10. [PubMed]
Papantonis, A., and Cook, P.R. (2010). Genome architecture and the role of transcription. Curr. Opin. Cell. Biol. 22, 1–6. [PubMed]
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] [Decisive (but indirect) evidence that RNA polymerases are immobile while active]
Papantonis, A., and Cook, P.R. (2011). Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2, 41-44. [PubMed]
Finan, K., Cook, P.R., and Marenduzzo, D. (2011). Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes. Chromosome Res. 19, 53-61. [PubMed]
Melnik, S., Deng, B., Papantonis, A., Baboo, S., Carr, I.M., and Cook, P.R. (2011). The proteomes of transcription factories containing RNA polymerases I, II, or III. Nat. Methods 8, 962-968. [PubMed] [A method for partially purifying factories]
Finan, K., and Cook, P.R. (2012). Transcriptional initiation: frequency, bursting, and transcription factories. In: Rippe, K., editor. Genome organization and function in the cell nucleus, Wiley-VCH Verlag GmbH & Co, KGaA, pp 235-254.
Kolovos, P., Knoch, T.A., Grosveld, F.G., Cook, P.R., and Papantonis, A. (2012). Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 5, 1. [PubMed] [Enhancers and silencers are just active transcription units]
Finan, K., Torella, J.P., Kapanidis, A.N., and Cook, P.R. (2012). T7 RNA polymerase functions in vitro without clustering. PLoS One 7, e40207. [PubMed]
Larkin, J.D., Cook, P.R., and Papantonis, A. (2012). Dynamic reconfiguration of long human genes during one transcription cycle. Mol. Cell. Biol. 32, 2738-2747. [PubMed]
Larkin, J.D., and Cook, P.R. (2012). A maximum precision closed-form solution for localizing diffraction-limited spots in noisy images. Optics Express 20, 18478-18493. [PubMed]
Papantonis, A., Kohro, T., Baboo, S., Larkin, J., Deng, B., Short, P., Tsutsumi, T., Taylor, S., Kanki, Y., Kobayashi, M., Li, G., Poh, H.-M., Ruan, X., Aburatani, H., Ruan, Y., Kodama, T., Wada, Y., and Cook, P.R. (2012). TNFα signals through specialized factories where responsive coding and micro-RNA genes are transcribed. EMBO J. 31, 4404-4414. [PubMed]
Larkin, J.D., Papantonis, A., Cook, P.R., and Marenduzzo, D. (2013). Space exploration by the promoter of a long human gene during one transcription cycle. Nucl. Acids Res. 41, 2216-2227. [PubMed]
Deng, B., Melnik, S., and Cook, P.R. (2013). Transcription factories, chromatin loops, and the dysregulation of gene expression in malignancy. Semin. Cancer Biol. 23, 65-71. [PubMed]
Larkin, J.D., Papantonis, A., and Cook, P.R. (2013). Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J. Cell Sci. 126, 2052-2059. [PubMed]
Papantonis, A., and Cook, P.R. (2013). Transcription factories; genome organization and gene regulation. Chem. Rev. 113, 8683-8705. [PubMed] [Comprehensive review]
Endesfelder, U., Finan, K., Holden, S.J., Cook, P.R., Kapanidis, A.N., and Heilemann, M. (2013). Multiscale spatial organization of RNA polymerase in Escherichia coli. Biophys. J. 105, 172-181. [PubMed]
Brackley, C.A., Taylor, S., Papantonis, A., Cook, P.R., and Marenduzzo, D. (2013). Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization. Proc. Natl. Acad. Sci. USA 110, E3605-3611. [PubMed] [A new and powerful entropic force]
Baboo, S., Bhushan, B., Jiang, H., Grovenor, C.R.M., Pierre, P., Davis, B.G., and Cook, P.R. (2014). Most human proteins made in both nucleus and cytoplasm turn over within minutes. PLoS One 9, e99346. [PubMed] [Adding one heresy (most proteins are degraded as soon as they are made) to another (some translation occurs in nuclear factories)]
Baboo, S., and Cook, P.R. (2014). ‘Dark matter' worlds of unstable RNA and protein. Nucleus 5, 281-286. [PubMed]
Diermeier, S., Kolovos, P., Heizinger, L., Schwartz, U., Georgomanolis, T., Zirkel, A., Wedemann, G., Grosveld, G., Knoch, T.A., Merkl, R., Cook, P.R., Längst, G., and Papantonis, A. (2014). TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol. 15, 536. [PubMed]
Johnson, J., Brackley, C.A., Cook, P.R., and Marenduzzo, D. (2015). A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction. J. Phys. Condens. Matter 27, 064119. [PubMed]
Kelly, S., Greenman, C., Cook, P.R., and Papantonis, A. (2015). Exon skipping is correlated with exon circularization. J. Mol. Biol. 427, 2414-2417. [PubMed]
Caudron-Herger, M., Cook, P.R., Rippe, K., and Papantonis, A. (2015). Dissecting the nascent human transcriptome by analyzing the RNA content of transcription factories. Nucleic Acids Res.43, e95. [PubMed] [The nascent transcriptome in factories]
Kelly, S., Georgomanolis, T., Zirkel, A., Diermeier, S., O'Reilly, D., Murphy, S., Längst, G., Cook, P.R., Papantonis, A. (2015). Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res. 43, 4721-4732. [PubMed] [‘Recursive’ splicing occurring co-transcriptionally]
Feuerborn, A., Prastowo, A., Cook, P.R., and Walsh, E. (2015). Merging drops in a Teflon tube, and transferring fluid between them, illustrated by protein crystallization and drug screening. Lab Chip 15, 3766-3775. [PubMed]
Feuerborn, A., and Cook, P.R. (2015). Why the activity of a gene depends on its neighbors. Trends Genet. 91, 483-490. [PubMed] [Introducing the heresy that eQTLs act co-transcriptionally in factories.]
Melnik, S., Caudron-Herger, M., Brant, L., Carr, I.M., Rippe, K., Cook, P.R., and Papantonis, A. (2016). Isolation of the protein and RNA content of active sites of transcription from mammalian cells. Nat. Protoc. 11, 553-565. [PubMed]
Larkin, J.D., and Cook, P.R. (2016). Super-resolution measurement of distance between transcription sites using RNA FISH with intronic probes. Methods 98, 150-157. [PubMed]
Brackley, C.A, Johnson, J., Kelly, S., Cook, P.R., and Marenduzzo, D. (2016). Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains. Nucleic Acids Res. 44, 3503-3512. [PubMed] [Different ‘transcription factors’ spontaneously assemble into different 'factories']
Walsh, E., Feuerborn, A., Cook, P.R. (2016). Formation of droplet interface bilayers in a Teflon tube. Sci. Rep. 6, 34355. [PubMed]
Kolovos, P., Georgomanolis, T., Koeferle, A., Larkin, J.D., Brant, L., Nikolicæ, M., Gusmao, E.G., Zirkel, A., Knoch, T.A., van Ijcken, W.F., Cook, P.R., Costa, I.G., Grosveld, F.G., and Papantonis, A. (2016). Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res. 26, 1478-1489. [PubMed]
Brackley, C.A., Michieletto, D., Mouvet, F., Johnson, J., Kelly, S., Cook, P.R., and Marenduzzo, D. (2016). Simulating topological domains in human chromosomes with a fitting-free model. Nucleus 7, 453-461. [PubMed]
Prastowo, A., Feuerborn, A., Cook, P.R., and Walsh, E.J. (2016). Biocompatibility of fluids for multiphase drops-in-drops microfluidics. Biomed. Microdevices 18, 114. [PubMed]
Brackley, C.A., Liebchen, B., Michieletto, D., Mouvet, F., Cook, P.R., and Marenduzzo, D. (2017). Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains. Biophys. J. 112, 1085-1093. [PubMed]
Brackley, C.A., Johnson, J., Michieletto, D., Morozov, A.N., Nicodemi, M., Cook, P.R., and Marenduzzo, D. (2017). Non-equilibrium chromosome looping via molecular slip-links. Phys. Rev. Lett. 119, 138101. [PubMed]
Walsh, E.J., Feuerborn, A., Wheeler, J.H.R., Tan, A.N., Durham, W.M., Foster, K.R., and Cook, P.R. (2017). Microfluidics with fluid walls. Nat. Commun. 8, 816. [PubMed]
Brackley, C.A., Johnson, J., Michieletto, D., Morozov, A.N., Nicodemi, M., Cook, P.R., and Marenduzzo, D. (2018). Extrusion without a motor: a new take on the loop extrusion model of genome organization. Nucleus 9, 95-103. [PubMed]
Michieletto, D., Chiang, M., Colì, D., Papantonis, A., Orlandini, E., Cook, P.R., and Marenduzzo, D. (2018). Shaping epigenetic memory via genomic bookmarking. Nucl. Acids Res. 46, 83-93. [PubMed]
Soitu, C., Feuerborn, A., Tan, A.N., Walker, H., Walsh, P.A., Castrejon-Pita, A.A., Cook, P.R., and Walsh, E.J. (2018). Microfluidic chambers using fluid walls for cell biology. Proc. Natl. Acad. Sci. USA 115, E5926-E5933. [PubMed]
Cook, P.R., and Marenduzzo, D. (2018). Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations. Nucl. Acids Res. 46, 9895-9906. [PubMed].
Soitu, C., Feuerborn, A., Deroy, C., Castrejón-Pita, A.A., Cook, P.R., and Walsh. E.J. (2019). Raising fluid walls around living cells. Sci. Adv. 5, eaav8002. [PubMed]
Soitu, C., Deroy, C., Castrejón-Pita, A.A., Cook, P.R., and Walsh, E.J. (2020). Using fluid walls for single-cell cloning provides assurance in monoclonality. SLAS Technol. 25, 267-275. [PubMed]
Soitu, C., Stovall-Kurtz, N., Deroy, C., Castrejón-Pita, A.A., Cook, P.R., and Walsh, E.J. (2020). Jet-printing microfluidic devices on demand. Advanced Science 7, 2001854. [PubMed]