Replication and transcription: Shaping the landscape of the genome (original) (raw)
McNairn, A. J. & Gilbert, D. M. Epigenomic replication: linking epigenetics to DNA replication. Bioessays25, 647–656 (2003). CASPubMed Google Scholar
Goren, A. & Cedar, H. Replicating by the clock. Nature Rev. Mol. Cell Biol.4, 25–32 (2003). CAS Google Scholar
Gilbert, D. M. Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol.14, 377–383 (2002). CASPubMed Google Scholar
Schubeler, D. et al. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nature Genet.32, 438–442 (2002). PubMed Google Scholar
Woodfine, K. et al. Replication timing of the human genome. Hum. Mol. Genet.13, 191–202 (2004). CASPubMed Google Scholar
Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science308, 1149–1154 (2005). An extensive and unbiased study showing that the human transcriptome is composed of a complex network of overlapping poly(A)+, poly(A)−and bimorphic RNA species, most of which are non-coding. CASPubMed Google Scholar
Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science296, 916–919 (2002). CASPubMed Google Scholar
Peterson, C. L. & Laniel, M. A. Histones and histone modifications. Curr. Biol.14, R546–R551 (2004). CASPubMed Google Scholar
Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell116, 259–272 (2004). CASPubMed Google Scholar
Elgin, S. C. & Grewal, S. I. Heterochromatin: silence is golden. Curr. Biol.13, R895–R898 (2003). CASPubMed Google Scholar
Hatton, K. S. et al. Replication program of active and inactive multigene families in mammalian cells. Mol. Cell. Biol.8, 2149–2158 (1988). CASPubMedPubMed Central Google Scholar
Diffley, J. F. Regulation of early events in chromosome replication. Curr. Biol.14, R778–R786 (2004). CASPubMed Google Scholar
Ma, H. et al. Spatial and temporal dynamics of DNA replication sites in mammalian cells. J. Cell Biol.143, 1415–1425 (1998). CASPubMedPubMed Central Google Scholar
Jackson, D. A. & Pombo, A. Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J. Cell Biol.140, 1285–1295 (1998). CASPubMedPubMed Central Google Scholar
Philimonenko, A. A. et al. Dynamics of DNA replication: an ultrastructural study. J. Struct. Biol.148, 279–289 (2004). CASPubMed Google Scholar
Quivy, J. P. et al. A CAF-1 dependent pool of HP1 during heterochromatin duplication. EMBO J.23, 3516–3526 (2004). CASPubMedPubMed Central Google Scholar
Sadoni, N., Cardoso, M. C., Stelzer, E. H., Leonhardt, H. & Zink, D. Stable chromosomal units determine the spatial and temporal organization of DNA replication. J. Cell Sci.117, 5353–5365 (2004). The authors describe elegant experiments in live cells showing that during S-phase progression, replication sequentially proceeds through spatially adjacent sets of chromosomal domains. CASPubMed Google Scholar
Sporbert, A., Gahl, A., Ankerhold, R., Leonhardt, H. & Cardoso, M. C. DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. Mol. Cell10, 1355–1365 (2002). CASPubMed Google Scholar
Abney, J. R., Cutler, B., Fillbach, M. L., Axelrod, D. & Scalettar, B. A. Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J. Cell Biol.137, 1459–1468 (1997). CASPubMedPubMed Central Google Scholar
Chubb, J. R., Boyle, S., Perry, P. & Bickmore, W. A. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr. Biol.12, 439–445 (2002). This report shows that nuclear substructures, including the nucleolus and nuclear periphery, constrain the movements of chromatin and have a role in the three-dimensional organization of chromatin in the nucleus. CASPubMed Google Scholar
Molenaar, C. et al. Visualizing telomere dynamics in living mammalian cells using PNA probes. EMBO J.22, 6631–6641 (2003). CASPubMedPubMed Central Google Scholar
MacAlpine, D. M., Rodriguez, H. K. & Bell, S. P. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev.18, 3094–3105 (2004). CASPubMedPubMed Central Google Scholar
Azuara, V. et al. Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication. Nature Cell Biol.5, 668–674 (2003). CASPubMed Google Scholar
Belyakin, S. N. et al. Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proc. Natl Acad. Sci. USA102, 8269–8274 (2005). CASPubMedPubMed Central Google Scholar
Hiratani, I., Leskovar, A. & Gilbert, D. M. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores. Proc. Natl Acad. Sci. USA101, 16861–16866 (2004). CASPubMedPubMed Central Google Scholar
Bozhenok, L., Wade, P. A. & Varga-Weisz, P. WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J.21, 2231–2241 (2002). CASPubMedPubMed Central Google Scholar
Taddei, A., Roche, D., Sibarita, J. B., Turner, B. M. & Almouzni, G. Duplication and maintenance of heterochromatin domains. J. Cell Biol.147, 1153–1166 (1999). CASPubMedPubMed Central Google Scholar
Rountree, M. R., Bachman, K. E. & Baylin, S. B. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nature Genet.25, 269–277 (2000). CASPubMed Google Scholar
Collins, N. et al. An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nature Genet.32, 627–632 (2002). CASPubMed Google Scholar
Fisher, D. & Mechali, M. Vertebrate HoxB gene expression requires DNA replication. EMBO J.22, 3737–3748 (2003). This paper demonstrates that induction ofHoxBgenes requires only one cell cycle and occurs in a DNA replication-dependent manner, without a change in replication timing. CASPubMedPubMed Central Google Scholar
Cimbora, D. M. et al. Long-distance control of origin choice and replication timing in the human β-globin locus are independent of the locus control region. Mol. Cell. Biol.20, 5581–5591 (2000). CASPubMedPubMed Central Google Scholar
White, E. J. et al. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc. Natl Acad. Sci. USA101, 17771–17776 (2004). CASPubMedPubMed Central Google Scholar
Dimitrova, D. S. & Gilbert, D. M. The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol. Cell4, 983–993 (1999). The authors demonstrate that the replication timing programme is established independently of origin specification. CASPubMed Google Scholar
Li, F. et al. The replication timing program of the Chinese hamster β-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase. J. Cell Biol.154, 283–292 (2001). CASPubMedPubMed Central Google Scholar
Li, F., Chen, J., Solessio, E. & Gilbert, D. M. Spatial distribution and specification of mammalian replication origins during G1 phase. J. Cell Biol.161, 257–266 (2003). CASPubMedPubMed Central Google Scholar
Lin, C. M., Fu, H., Martinovsky, M., Bouhassira, E. & Aladjem, M. I. Dynamic alterations of replication timing in mammalian cells. Curr. Biol.13, 1019–1028 (2003). CASPubMed Google Scholar
Smith, Z. E. & Higgs, D. R. The pattern of replication at a human telomeric region (16p13.3): its relationship to chromosome structure and gene expression. Hum. Mol. Genet.8, 1373–1386 (1999). CASPubMed Google Scholar
Vyas, P. et al. _Cis_-acting sequences regulating expression of the human α-globin cluster lie within constitutively open chromatin. Cell69, 781–793 (1992). CASPubMed Google Scholar
Flint, J. et al. The relationship between chromosome structure and function at a human telomeric region. Nature Genet.15, 252–257 (1997). CASPubMed Google Scholar
Epner, E., Forrester, W. C. & Groudine, M. Asynchronous DNA replication within the human β-globin gene locus. Proc. Natl Acad. Sci. USA85, 8081–8085 (1988). CASPubMedPubMed Central Google Scholar
Simon, I. et al. Developmental regulation of DNA replication timing at the human β globin locus. EMBO J.20, 6150–6157 (2001). CASPubMedPubMed Central Google Scholar
Owen-Hughes, T. & Workman, J. L. Experimental analysis of chromatin function in transcription control. Crit. Rev. Eukaryot. Gene Expr.4, 403–441 (1994). CASPubMed Google Scholar
Sims, R. J. 3rd, Belotserkovskaya, R. & Reinberg, D. Elongation by RNA polymerase II: the short and long of it. Genes Dev.18, 2437–2468 (2004). CASPubMed Google Scholar
Belotserkovskaya, R. et al. FACT facilitates transcription-dependent nucleosome alteration. Science301, 1090–1093 (2003). CASPubMed Google Scholar
Kireeva, M. L. et al. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell9, 541–552 (2002). CASPubMed Google Scholar
Cavalli, G. & Paro, R. The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell93, 505–518 (1998). CASPubMed Google Scholar
Cavalli, G. & Paro, R. Epigenetic inheritance of active chromatin after removal of the main transactivator. Science286, 955–958 (1999). CASPubMed Google Scholar
Bender, W. & Fitzgerald, D. P. Transcription activates repressed domains in the Drosophila bithorax complex. Development129, 4923–4930 (2002). CASPubMed Google Scholar
Hogga, I. & Karch, F. Transcription through the _iab-7 cis_-regulatory domain of the bithorax complex interferes with maintenance of _Polycomb_-mediated silencing. Development129, 4915–4922 (2002). CASPubMed Google Scholar
Schwartz, B. E. & Ahmad, K. Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev.19, 804–814 (2005). CASPubMedPubMed Central Google Scholar
Schmitt, S., Prestel, M. & Paro, R. Intergenic transcription through a Polycomb group response element counteracts silencing. Genes Dev.19, 697–708 (2005). This paper demonstrates that intergenic transcription through a Polycomb group response element is required for the switch from a silenced to an activated state. CASPubMedPubMed Central Google Scholar
Ahmad, K. & Henikoff, S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell9, 1191–1200 (2002). CASPubMed Google Scholar
Henikoff, S., Furuyama, T. & Ahmad, K. Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet.20, 320–326 (2004). CASPubMed Google Scholar
McKittrick, E., Gafken, P. R., Ahmad, K. & Henikoff, S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl Acad. Sci. USA101, 1525–1530 (2004). References 50,52–54 describe a pathway for replication-independent chromatin assembly through histone replacement in transcribed genomic regions. CASPubMedPubMed Central Google Scholar
Cawley, S. E. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell116, 499–509 (2004). CASPubMed Google Scholar
Impey, S. et al. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell119, 1041–1054 (2004). CASPubMed Google Scholar
Yelin, R. et al. Widespread occurrence of antisense transcription in the human genome. Nature Biotechnol.21, 379–386 (2003). CAS Google Scholar
Mattick, J. S. RNA regulation: a new genetics? Nature Rev. Genet.5, 316–323 (2004). CASPubMed Google Scholar
Navarro, P., Pichard, S., Ciaudo, C., Avner, P. & Rougeulle, C. Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation. Genes Dev.19, 1474–1482 (2005). CASPubMedPubMed Central Google Scholar
Martens, J. A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature429, 571–574 (2004). CASPubMed Google Scholar
Shibata, S. & Lee, J. T. Tsix transcription- versus RNA-based mechanisms in Xist repression and epigenetic choice. Curr. Biol.14, 1747–1754 (2004). CASPubMed Google Scholar
Lipshitz, H. D., Peattie, D. A. & Hogness, D. S. Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev.1, 307–322 (1987). CASPubMed Google Scholar
Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R. & Fraser, P. Intergenic transcription and developmental remodeling of chromatin subdomains in the human β-globin locus. Mol. Cell5, 377–386 (2000). CASPubMed Google Scholar
Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. & Proudfoot, N. J. Intergenic transcription and transinduction of the human β-globin locus. Genes Dev.11, 2494–2509 (1997). CASPubMedPubMed Central Google Scholar
Drewell, R. A., Bae, E., Burr, J. & Lewis, E. B. Transcription defines the embryonic domains of _cis_-regulatory activity at the Drosophila bithorax complex. Proc. Natl Acad. Sci. USA99, 16853–16858 (2002). CASPubMedPubMed Central Google Scholar
Bolland, D. J. et al. Antisense intergenic transcription in V(D)J recombination. Nature Immunol.5, 630–637 (2004). CAS Google Scholar
Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell120, 169–181 (2005). CASPubMed Google Scholar
Rogan, D. F., Cousins, D. J. & Staynov, D. Z. Intergenic transcription occurs throughout the human IL-4/IL-13 gene cluster. Biochem. Biophys. Res. Commun.255, 556–561 (1999). CASPubMed Google Scholar
Bae, E., Calhoun, V. C., Levine, M., Lewis, E. B. & Drewell, R. A. Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc. Natl Acad. Sci. USA99, 16847–168452 (2002). CASPubMedPubMed Central Google Scholar
Ogawa, Y. & Lee, J. T. Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol. Cell11, 731–743 (2003). CASPubMed Google Scholar
Rogan, D. F. et al. Analysis of intergenic transcription in the human IL-4/IL-13 gene cluster. Proc. Natl Acad. Sci. USA101, 2446–2451 (2004). CASPubMedPubMed Central Google Scholar
Wilson, C. J. et al. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell84, 235–244 (1996). CASPubMed Google Scholar
Cho, H. et al. A human RNA polymerase II complex containing factors that modify chromatin structure. Mol. Cell. Biol.18, 5355–5363 (1998). CASPubMedPubMed Central Google Scholar
Wittschieben, B. O. et al. A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol. Cell4, 123–128 (1999). CASPubMed Google Scholar
Wittschieben, B. O., Fellows, J., Du, W., Stillman, D. J. & Svejstrup, J. Q. Overlapping roles for the histone acetyltransferase activities of SAGA and elongator in vivo. EMBO J.19, 3060–3068 (2000). CASPubMedPubMed Central Google Scholar
Schaft, D. et al. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res.31, 2475–2482 (2003). CASPubMedPubMed Central Google Scholar
Jackson, D. A., Hassan, A. B., Errington, R. J. & Cook, P. R. Visualization of focal sites of transcription within human nuclei. EMBO J.12, 1059–1065 (1993). CASPubMedPubMed Central Google Scholar
Wansink, D. G. et al. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol.122, 283–93 (1993). References 77 and 78 show that all nascent transcription occurs in distinct nuclear foci or transcription factories. CASPubMed Google Scholar
Wansink, D. G., Sibon, O. C., Cremers, F. F., van Driel, R. & de Jong, L. Ultrastructural localization of active genes in nuclei of A431 cells. J. Cell. Biochem.62, 10–18 (1996). CASPubMed Google Scholar
Jackson, D. A., Iborra, F. J., Manders, E. M. & Cook, P. R. Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell9, 1523–1536 (1998). CASPubMedPubMed Central Google Scholar
Pombo, A. et al. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J.18, 2241–2253 (1999). CASPubMedPubMed Central Google Scholar
Iborra, F. J., Pombo, A., Jackson, D. A. & Cook, P. R. Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. J. Cell Sci.109, 1427–1436 (1996). CASPubMed Google Scholar
Grande, M. A., van der Kraan, I., de Jong, L. & van Driel, R. Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci.110, 1781–1791 (1997). CASPubMed Google Scholar
Hieda, M., Winstanley, H., Maini, P., Iborra, F. J. & Cook, P. R. Different populations of RNA polymerase II in living mammalian cells. Chromosome Res.13, 135–144 (2005). CASPubMed Google Scholar
Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet.36, 1065–1071 (2004). This article provides the first demonstration that during transcriptionin vivo, distant genes co-localize to the same transcription factory. CASPubMed Google Scholar
Ross, I. L., Browne, C. M. & Hume, D. A. Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. Immunol. Cell Biol.72, 177–185 (1994). CASPubMed Google Scholar
Kimura, H., Sugaya, K. & Cook, P. R. The transcription cycle of RNA polymerase II in living cells. J. Cell Biol.159, 777–782 (2002). CASPubMedPubMed Central Google Scholar
Levsky, J. M., Shenoy, S. M., Pezo, R. C. & Singer, R. H. Single-cell gene expression profiling. Science297, 836–840 (2002). This paper reveals that genes are not continuously transcribed and individual cells consequently show unique patterns of gene transcription. CASPubMed Google Scholar
Vazquez, J., Belmont, A. S. & Sedat, J. W. Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr. Biol.11, 1227–1239 (2001). Live cell analysis provides direct evidence for cell-cycle regulated changes in interphase chromatin motion. CASPubMed Google Scholar
Brown, K. E. et al. Expression of α- and β-globin genes occurs within different nuclear domains in haemopoietic cells. Nature Cell Biol.3, 602–606 (2001). CASPubMed Google Scholar
Kosak, S. T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science296, 158–162 (2002). CASPubMed Google Scholar
Gribnau, J., Hochedlinger, K., Hata, K., Li, E. & Jaenisch, R. Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization. Genes Dev.17, 759–773 (2003). CASPubMedPubMed Central Google Scholar
Chambeyron, S. & Bickmore, W. A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev.18, 1119–1130 (2004). CASPubMedPubMed Central Google Scholar
Zink, D. et al. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J. Cell Biol.166, 815–825 (2004). CASPubMedPubMed Central Google Scholar
Carter, D., Chakalova, L., Osborne, C. S., Dai, Y. F. & Fraser, P. Long-range chromatin regulatory interactions in vivo. Nature Genet.32, 623–626 (2002). CASPubMed Google Scholar
Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell10, 1453–1465 (2002). CASPubMed Google Scholar
Murrell, A., Heeson, S. & Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nature Genet.36, 889–893 (2004). CASPubMed Google Scholar
Horike, S., Cai, S., Miyano, M., Cheng, J. F. & Kohwi-Shigematsu, T. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nature Genet.37, 31–40 (2005). CASPubMed Google Scholar
Spilianakis, C. G. & Flavell, R. A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nature Immunol.5, 1017–1027 (2004). CAS Google Scholar
Blanton, J., Gaszner, M. & Schedl, P. Protein: protein interactions and the pairing of boundary elements in vivo. Genes Dev.17, 664–675 (2003). CASPubMedPubMed Central Google Scholar
Farrell, C. M., West, A. G. & Felsenfeld, G. Conserved CTCF insulator elements flank the mouse and human β-globin loci. Mol. Cell. Biol.22, 3820–3831 (2002). CASPubMedPubMed Central Google Scholar
Long, Q., Bengra, C., Li, C., Kutlar, F. & Tuan, D. A long terminal repeat of the human endogenous retrovirus ERV-9 is located in the 5′ boundary area of the human β-globin locus control region. Genomics54, 542–555 (1998). CASPubMed Google Scholar
Leach, K. M. et al. Reconstitution of human β-globin locus control region hypersensitive sites in the absence of chromatin assembly. Mol. Cell. Biol.21, 2629–2940 (2001). CASPubMedPubMed Central Google Scholar
Routledge, S. J. & Proudfoot, N. J. Definition of transcriptional promoters in the human β globin locus control region. J. Mol. Biol.323, 601–611 (2002). CASPubMed Google Scholar
Palstra, R. J. et al. The β-globin nuclear compartment in development and erythroid differentiation. Nature Genet.35, 190–194 (2003). CASPubMed Google Scholar
Patrinos, G. P. et al. Multiple interactions between regulatory regions are required to stabilize an active chromatin hub. Genes Dev.18, 1495–1509 (2004). CASPubMedPubMed Central Google Scholar
Lettice, L. A. et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet.12, 1725–1735 (2003). CASPubMed Google Scholar
Nobrega, M. A., Ovcharenko, I., Afzal, V. & Rubin, E. M. Scanning human gene deserts for long-range enhancers. Science302, 413 (2003). CASPubMed Google Scholar
Kleinjan, D. A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet.76, 8–32 (2005). CASPubMed Google Scholar
Kimura, H., Tao, Y., Roeder, R. G. & Cook, P. R. 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 (1999). CASPubMedPubMed Central Google Scholar
Cook, P. R. Predicting three-dimensional genome structure from transcriptional activity. Nature Genet.32, 347–352 (2002). CASPubMed Google Scholar
Iborra, F. J., Pombo, A., McManus, J., Jackson, D. A. & Cook, P. R. The topology of transcription by immobilized polymerases. Exp. Cell Res.229, 167–173 (1996). CASPubMed Google Scholar
Yin, H. et al. Transcription against an applied force. Science270, 1653–1657 (1995). CASPubMed Google Scholar
Wang, H. Y., Elston, T., Mogilner, A. & Oster, G. Force generation in RNA polymerase. Biophys. J.74, 1186–1202 (1998). CASPubMedPubMed Central Google Scholar
Cook, P. R. Nongenic transcription, gene regulation and action at a distance. J. Cell Sci.116, 4483–4491 (2003). CASPubMed Google Scholar
Velagaleti, G. V. et al. Position effects due to chromosome breakpoints that map ∼900 Kb upstream and ∼1.3 Mb downstream of SOX9 in two patients with campomelic dysplasia. Am. J. Hum. Genet.76, 652–662 (2005). CASPubMedPubMed Central Google Scholar
Sawado, T., Halow, J., Bender, M. A. & Groudine, M. The β-globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev.17, 1009–1018 (2003). CASPubMedPubMed Central Google Scholar
Vieira, K. F. et al. Recruitment of transcription complexes to the β-globin gene locus in vivo and in vitro. J. Biol. Chem.279, 50350–50357 (2004). CASPubMed Google Scholar
Hassan, A. B., Errington, R. J., White, N. S., Jackson, D. A. & Cook, P. R. Replication and transcription sites are colocalized in human cells. J. Cell Sci.107, 425–434 (1994). CASPubMed Google Scholar
Wei, X. et al. Segregation of transcription and replication sites into higher order domains. Science281, 1502–1506 (1998). This paper provides evidence that transcription and replication occur in spatially distinct nuclear zones during S phase. CASPubMed Google Scholar
Perry, P. et al. A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction. Cell Cycle3, 1645–1650 (2004). CASPubMed Google Scholar
Henikoff, S. Histone modifications: combinatorial complexity or cumulative simplicity? Proc. Natl Acad. Sci. USA102, 5308–5309 (2005). CASPubMedPubMed Central Google Scholar
Marshall, W. F. et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol.7, 930–939 (1997). CASPubMed Google Scholar
Gerlich, D. et al. Global chromosome positions are transmitted through mitosis in mammalian cells. Cell112, 751–764 (2003). CASPubMed Google Scholar
Caron, H. et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science291, 1289–1292 (2001). CASPubMed Google Scholar
Lercher, M. J., Urrutia, A. O. & Hurst, L. D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet.31, 180–183 (2002). CASPubMed Google Scholar
Versteeg, R. et al. The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res.13, 1998–2004 (2003). CASPubMedPubMed Central Google Scholar