![Transcription factories in a Hela cell [from Cook PR (1999) Science 284, 1790]](../images/pombo.png)
Transcription factories, regulation of transcription
Chromosome #microfluidicsstructure during interphase and metaphase
Entropic forces and nuclear structure
Chromosome pairing
Replication factories, replication
Translation
Nucleoids and superhelical DNA
Artefacts and chromatin structure
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]
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] [pdf]
Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed] [pdf]
Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [PubMed] [pdf]
Cook, P.R. (2003). Nongenic transcription, gene regulation and action at a distance. J. Cell Sci. 116, 4483-4491. [ 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]
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., Faro-Trindade, I., and Cook, P.R. (2007). What are the molecular ties that maintain genomic loops? Trends Genet. 23, 126-133. [PubMed] [pdf]
Carter, D.R.F., Eskiw, C., and Cook, P.R. (2008). Transcription factories. Biochem. Soc. Trans. 36, 585-589. [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]
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. [pdf]
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]
Papantonis, A., and Cook, P.R. (2013). Transcription factories; genome organization and gene regulation. Chem. Rev. 113, 8683-8705. [PubMed] [pdf]
Feuerborn, A., and Cook, P.R. (2015). Why the activity of a gene depends on its neighbors. Trends Genet. 91, 483-490. [PubMed] [pdf]
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] [link to journal] [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] [pdf]
Cook, P.R. (2002). Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352. [PubMed] [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]
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]
Feuerborn, A., and Cook, P.R. (2015). Why the activity of a gene depends on its neighbors. Trends Genet. 91, 483-490. [PubMed] [pdf]
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] [pdf]
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] [pdf]
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]
Chromosome pairing
Cook, P.R. (1997). The transcriptional basis of chromosome pairing. J. Cell Sci. 110, 1033-1040. [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]
Replication factories, 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]
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]
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] [pdf]
Translation
Iborra, F.J., Jackson, D.A., and Cook, P.R. (2004). The case for nuclear
translation. J. Cell Sci. 117, 5713-5720. [ PubMed] [pdf]
Baboo, S., and Cook, P.R. (2014). ‘Dark matter' worlds of unstable RNA and protein. Nucleus 5, 281-286. [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]
Deroy, C., Nebuloni, F., Cook, P.R., and Walsh, E.J. (2021). Microfluidics on standard Petri dishes for bioscientists. Small Methods 2021, 2100724. [PubMed] [journal] [pdf]