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Reports

Temporal separation of replication and transcription during S-phase progression

, , , , , , & show all
Pages 3241-3248 | Received 16 May 2014, Accepted 07 Aug 2014, Published online: 06 Nov 2014

References

  • Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, et al. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol biol Cell 2002; 13:1977-2000; PMID:12058064; http://dx.doi.org/10.1091/mbc.02-02-0030
  • Grant GD, Brooks L, 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Mol biol Cell 2013; 24:3634-50; PMID:24109597; http://dx.doi.org/10.1091/mbc.E13-05-0264
  • Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ. Transcriptional regulation and function during the human cell cycle. Nat Genet 2001; 27:48-54; PMID:11137997
  • Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H, Skiena S, Futcher B, Leatherwood J. The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol 2005; 3:e225; PMID:15966770
  • van der Meijden CM, Lapointe DS, Luong MX, Peric-Hupkes D, Cho B, Stein JL, van Wijnen AJ, Stein GS. Gene profiling of cell cycle progression through S-phase reveals sequential expression of genes required for DNA replication and nucleosome assembly. Cancer Res 2002; 62:3233-43; PMID:12036939
  • Sadasivam S, Duan S, DeCaprio JA. The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression. Genes Dev 2012; 26:474-89; PMID:22391450; http://dx.doi.org/10.1101/gad.181933.111
  • Helmrich A, Ballarino M, Tora L. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol Cell 2011; 44:966-77; PMID:22195969; http://dx.doi.org/10.1016/j.molcel.2011.10.013
  • Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD. Co-orientation of replication and transcription preserves genome integrity. PLoS genetics 2010; 6:e1000810; PMID:20090829; http://dx.doi.org/10.1371/journal.pgen.1000810
  • Wansink DG, Manders EE, van der Kraan I, Aten JA, van Driel R, de Jong L. RNA polymerase II transcription is concentrated outside replication domains throughout S-phase. J Cell Sci 1994; 107(Pt 6):1449-56; PMID:7962188
  • Dimitrova DS. DNA replication initiation patterns and spatial dynamics of the human ribosomal RNA gene loci. J Cell Sci 2011; 124:2743-52; PMID:21807939; http://dx.doi.org/10.1242/jcs.082230
  • Helmrich A, Ballarino M, Nudler E, Tora L. Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 2013; 20:412-8; PMID:23552296; http://dx.doi.org/10.1038/nsmb.2543
  • Davis PK, Ho A, Dowdy SF. Biological methods for cell-cycle synchronization of mammalian cells. BioTechniques 2001; 30:1322-6, 8, 30-1.
  • Fox MH, Read RA, Bedford JS. Comparison of synchronized Chinese hamster ovary cells obtained by mitotic shake-off, hydroxyurea, aphidicolin, or methotrexate. Cytometry 1987; 8:315-20; PMID:3109858; http://dx.doi.org/10.1002/cyto.990080312
  • Petermann E, Orta ML, Issaeva N, Schultz N, Helleday T. Hydroxyurea-stalled replication forks become progressively inactivated and require two different RAD51-mediated pathways for restart and repair. Molecular Cell 2010; 37:492-502; PMID:20188668; http://dx.doi.org/10.1016/j.molcel.2010.01.021
  • Iwamoto F, Stadler M, Chalupnikova K, Oakeley E, Nagamine Y. Transcription-dependent nucleolar cap localization and possible nuclear function of DExH RNA helicase RHAU. Exp Cell Res 2008; 314:1378-91; PMID:18279852; http://dx.doi.org/10.1016/j.yexcr.2008.01.006
  • Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d’Aubenton-Carafa Y, Arneodo A, Hyrien O, et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res 2010; 20:447-57; PMID:20103589; http://dx.doi.org/10.1101/gr.098947.109
  • Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013; 499:214-8; PMID:23770567; http://dx.doi.org/10.1038/nature12213
  • Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP. Replication timing of the human genome. Hum Mol Genet 2004; 13:191-202; PMID:14645202; http://dx.doi.org/10.1093/hmg/ddh016
  • Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A 2005; 102:6419-24; PMID:15845769; http://dx.doi.org/10.1073/pnas.0405088102
  • French S. Consequences of replication fork movement through transcription units in vivo. Science 1992; 258:1362-5; PMID:1455232; http://dx.doi.org/10.1126/science.1455232
  • Deshpande AM, Newlon CS. DNA replication fork pause sites dependent on transcription. Science 1996; 272:1030-3; PMID:8638128; http://dx.doi.org/10.1126/science.272.5264.1030
  • Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Molecular Cell 2009; 34:722-34; PMID:19560424; http://dx.doi.org/10.1016/j.molcel.2009.05.022
  • Coffman FD, He M, Diaz ML, Cohen S. DNA replication initiates at different sites in early and late S phase within human ribosomal RNA genes. Cell Cycle 2005; 4:1223-6; PMID:16082215; http://dx.doi.org/10.4161/cc.4.9.1961
  • Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Mol Syst Biol 2010; 6:433; PMID:21081925
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Nat Acad Sci U S A 2005; 102:15545-50; PMID:16199517; http://dx.doi.org/10.1073/pnas.0506580102
  • Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature genetics 2003; 34:267-73; PMID:12808457; http://dx.doi.org/10.1038/ng1180
  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 2000; 25:25-9; PMID:10802651; http://dx.doi.org/10.1038/75556

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