Reviews (Peter R Cook's group)

Transcription factories

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]

Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]

Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [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]

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., Faro-Trindade, I., and Cook, P.R. (2007). What are the molecular ties that maintain genomic loops? Trends Genet. 23, 126-133. [PubMed]

Carter, D.R.F., Eskiw, C., and Cook, P.R. (2008). Transcription factories. Biochem. Soc. Trans. 36, 585-589. [PubMed]

Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1–10. [PubMed] [pdf]

Transcription

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] [Text]

Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]

Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [PubMed]

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., and Cook, P.R. (2011). Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2, 41-44. [PubMed] [pdf]

Finan, K., and Cook, P.R. (2011). 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.

Gene regulation

Cook, P.R. (2003). Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483-4491. [ PubMed] [PDF file, with permission of J. Cell Sci (http://jcs.biologists.org).]

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]

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]

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] [pdf]

Chromosome structure during interphase and metaphase

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] [Text]

Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [PubMed]

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]

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]

Transcriptional basis of chromosome pairing

Cook, P.R. (1997). The transcriptional basis of chromosome pairing. J. Cell Sci. 110, 1033-1040. [PubMed] [Text]

Xu, M., and Cook, P.R. (2008). The role of specialized transcription factories in chromosome pairing. Biochem. Biophys. Acta, 1783, 2155-2160. [PubMed]

Replication factories

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]

Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]

Replication

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]

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.

Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]

Translation in the nucleus

Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). The case for nuclear translation. J. Cell Sci. 117, 5713-5720. [ PubMed] [PDF file, with permission of J. Cell Sci (http://jcs.biologists.org).]

Non-specific entropic forces and nuclear structure

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]

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] [pdf]

Nucleoids and superhelical DNA

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]

Artefacts and chromatin structure

Cook, P.R. (1988). The nucleoskeleton: artefact, passive framework or active site? J. Cell Sci. 90, 1-6. [PubMed]

	Nuclear Structure and Function Research Group
	Peter R Cook's group at The Sir William Dunn School of Pathology University of Oxford
	Home Our science Publications Images Students Book
Quick links Contacts, visiting Oxford Model for all genomes EpiGenSys Students: Lecture notes Reading lists Resources Movies: 1. Transcription cycle 2. Mobile/fixed polymerases? Catalogs: 1. Proteomes of factories 2. Engaged polymerases	Publications / Reviews
	Transcription factories 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] Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed] Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [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] 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., Faro-Trindade, I., and Cook, P.R. (2007). What are the molecular ties that maintain genomic loops? Trends Genet. 23, 126-133. [PubMed] Carter, D.R.F., Eskiw, C., and Cook, P.R. (2008). Transcription factories. Biochem. Soc. Trans. 36, 585-589. [PubMed] Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1–10. [PubMed] [pdf] Transcription 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] [Text] Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed] Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [PubMed] 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., and Cook, P.R. (2011). Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2, 41-44. [PubMed] [pdf] Finan, K., and Cook, P.R. (2011). 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. Gene regulation Cook, P.R. (2003). Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483-4491. [ PubMed] [PDF file, with permission of J. Cell Sci (http://jcs.biologists.org).] 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] 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] 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] [pdf] Chromosome structure during interphase and metaphase 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] [Text] Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [PubMed] 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] 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] Transcriptional basis of chromosome pairing Cook, P.R. (1997). The transcriptional basis of chromosome pairing. J. Cell Sci. 110, 1033-1040. [PubMed] [Text] Xu, M., and Cook, P.R. (2008). The role of specialized transcription factories in chromosome pairing. Biochem. Biophys. Acta, 1783, 2155-2160. [PubMed] Replication factories 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] Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed] Replication 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] 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. Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed] Translation in the nucleus Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). The case for nuclear translation. J. Cell Sci. 117, 5713-5720. [ PubMed] [PDF file, with permission of J. Cell Sci (http://jcs.biologists.org).] Non-specific entropic forces and nuclear structure 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] 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] [pdf] Nucleoids and superhelical DNA 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] Artefacts and chromatin structure Cook, P.R. (1988). The nucleoskeleton: artefact, passive framework or active site? J. Cell Sci. 90, 1-6. [PubMed] Top \| Home \| Maintained by Peter Cook \|

Nuclear Structure and Function Research Group

Quick links