Cell fate transitions and the replication timing decision point

Journal of Cell Biology

Volumn 191, Issue 5, 2010, Pages 899-903

  Gilbert, David M ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL COMPARTMENTALIZATION; CELL CYCLE G1 PHASE; CELL CYCLE G2 PHASE; CELL CYCLE S PHASE; CELL DIVISION; CELL FATE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; CYTOARCHITECTURE; DNA REPLICATION TIMING; HUMAN; HYPOTHESIS; NONHUMAN; NOTE; PRIORITY JOURNAL; STEM CELL; THREE DIMENSIONAL IMAGING;

CELL CYCLE PROTEINS; CELL DIFFERENTIATION; CHROMATIN; CHROMOSOMES; DNA REPLICATION; G1 PHASE; STEM CELLS;

EID: 78649660785     PISSN: 00219525     EISSN: 00219525     Source Type: Journal    
DOI: 10.1083/jcb.201007125     Document Type: Note

References (46)

1. Aoto, T., N. Saitoh, Y. Sakamoto, S. Watanabe, and M. Nakao. 2008. Polycomb group protein-associated chromatin is reproduced in post-mitotic G1 phase and is required for S phase progression. J. Biol. Chem. 283:18905-18915. doi:10.1074/jbc.M709322200
2. Borghese, L., D. Dolezalova, T. Opitz, S. Haupt, A. Leinhaas, B. Steinfarz, P. Koch, F. Edenhofer, A. Hampl, and O. Brüstle. 2010. Inhibition of notch signaling in human embryonic stem cell-derived neural stem cells delays G1/S phase transition and accelerates neuronal differentiation in vitro and in vivo. Stem Cells. 28:955-964. doi:10.1002/stem.408
3. Chubb, J.R., S. Boyle, P. Perry, and W.A. Bickmore. 2002. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr. Biol. 12:439-445. doi:10.1016/S0960-9822(02)00695-4
4. Deng, W., and G.A. Blobel. 2010. Do chromatin loops provide epigenetic gene expression states? Curr. Opin. Genet. Dev. 20:548-554. doi:10.1016/j.gde. 2010.06.007
5. Dimitrova, D.S., and D.M. Gilbert. 1999. The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol. Cell. 4:983-993. doi:10.1016/S1097-2765(00)80227-0
6. Egli, D., G. Birkhoff, and K. Eggan. 2008. Mediators of reprogramming: transcription factors and transitions through mitosis. Nat. Rev. Mol. Cell Biol. 9:505-516. doi:10.1038/nrm2439 (Pubitemid 351890351)
7. Finlan, L.E., D. Sproul, I. Thomson, S. Boyle, E. Kerr, P. Perry, B. Ylstra, J.R. Chubb, and W.A. Bickmore. 2008. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet. 4:e1000039. doi:10.1371/journal.pgen.1000039
8. Fraser, P., and W. Bickmore. 2007. Nuclear organization of the genome and the potential for gene regulation. Nature. 447:413-417. doi:10.1038/nature05916
9. Gilbert, D.M. 2001. Nuclear position leaves its mark on replication timing. J. Cell Biol. 152:F11-F15. doi:10.1083/jcb.152.2.F11
10. Gilbert, D.M., and S.M. Gasser. 2006. Nuclear structure and DNA replication. In DNA Replication and Human Disease. M.L. DePamphilis, editor. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 175-196.
11. Grimm, O.H., and J.B. Gurdon. 2002. Nuclear exclusion of Smad2 is a mechanism leading to loss of competence. Nat. Cell Biol. 4:519-522. doi:10.1038/ncb812
12. Hakim, O., M.H. Sung, and G.L. Hager. 2010. 3D shortcuts to gene regulation. Curr. Opin. Cell Biol. 22:305-313. doi:10.1016/j.ceb.2010.04.005
13. Hanna, J., A.W. Cheng, K. Saha, J. Kim, C.J. Lengner, F. Soldner, J.P. Cassady, J. Muffat, B.W. Carey, and R. Jaenisch. 2010. Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proc. Natl. Acad. Sci. USA. 107:9222-9227. doi:10.1073/pnas.1004584107
14. Hiratani, I., and D.M. Gilbert. 2010. Autosomal lyonization of replication domains during early mammalian development. In The Cell Biology of Stem Cells. E. Meshorer and K. Plath, editors. Landes and Springer, Austin, TX. 41-58.
15. Hiratani, I., T. Ryba, M. Itoh, T. Yokochi, M. Schwaiger, C.W. Chang, Y. Lyou, T.M. Townes, D. Schübeler, and D.M. Gilbert. 2008. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 6:e245. doi:10.1371/journal.pbio.0060245
16. Hiratani, I., S. Takebayashi, J. Lu, and D.M. Gilbert. 2009. Replication timing and transcriptional control: beyond cause and effect - part II. Curr. Opin. Genet. Dev. 19:142-149. doi:10.1016/j.gde.2009.02.002
17. Hiratani, I., T. Ryba, M. Itoh, J. Rathjen, M. Kulik, B. Papp, E. Fussner, D.P. Bazett-Jones, K. Plath, S. Dalton, et al. 2010. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 20:155-169. doi:10.1101/gr.099796.109
18. Jansen, L.E., B.E. Black, D.R. Foltz, and D.W. Cleveland. 2007. Propagation of centromeric chromatin requires exit from mitosis. J. Cell Biol. 176:795-805. doi:10.1083/jcb.200701066
19. John, S., and J.L. Workman. 1998. Bookmarking genes for activation in condensed mitotic chromosomes. Bioessays. 20:275-279. doi:10.1002/(SICI)1521- 1878(199804)20:4<275::AID-BIES1>3.0.CO;2-P
20. Kasinathan, P., J.G. Knott, Z. Wang, D.J. Jerry, and J.M. Robl. 2001. Production of calves from G1 fibroblasts. Nat. Biotechnol. 19:1176-1178. doi:10.1038/nbt1201-1176
21. Kaufman, P.D., and O.J. Rando. 2010. Chromatin as a potential carrier of heritable information. Curr. Opin. Cell Biol. 22:284-290. doi:10.1016/j.ceb. 2010.02.002
22. Kumaran, R.I., and D.L. Spector. 2008. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J. Cell Biol. 180:51-65. doi:10.1083/jcb.200706060
23. Kundu, S., and C.L. Peterson. 2009. Role of chromatin states in transcriptional memory. Biochim. Biophys. Acta. 1790:445-455.
24. Lanctôt, C., T. Cheutin, M. Cremer, G. Cavalli, and T. Cremer. 2007. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8:104-115. doi:10.1038/nrg2041 (Pubitemid 46122840)
25. Lande-Diner, L., J. Zhang, and H. Cedar. 2009. Shifts in replication timing actively affect histone acetylation during nucleosome reassembly. Mol. Cell. 34:767-774. doi:10.1016/j.molcel.2009.05.027
26. Laster, K., and S.T. Kosak. 2010. Genomic Pangea: coordinate gene regulation and cell-specific chromosomal topologies. Curr. Opin. Cell Biol. 22:314-319. doi:10.1016/j.ceb.2010.04.009
27. Lieberman-Aiden, E., N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, M.O. Dorschner, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 326:289-293. doi:10.1126/science. 1181369
28. Lu, J., F. Li, C.S. Murphy, M.W. Davidson, and D.M. Gilbert. 2010. G2 phase chromatin lacks determinants of replication timing. J. Cell Biol. 189:967-980. doi:10.1083/jcb.201002002
29. Luo, L., K.L. Gassman, L.M. Petell, C.L. Wilson, J. Bewersdorf, and L.S. Shopland. 2009. The nuclear periphery of embryonic stem cells is a transcriptionally permissive and repressive compartment. J. Cell Sci. 122:3729-3737. doi:10.1242/jcs.052555
30. Meshorer, E., and T. Misteli. 2006. Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol. 7:540-546. doi:10.1038/nrm1938 (Pubitemid 44036459)
31. Neganova, I., and M. Lako. 2008. G1 to S phase cell cycle transition in somatic and embryonic stem cells. J. Anat. 213:30-44. doi:10.1111/j.1469-7580. 2008.00931.x
32. Németh, A., A. Conesa, J. Santoyo-Lopez, I. Medina, D. Montaner, B. Péterfia, I. Solovei, T. Cremer, J. Dopazo, and G. Längst. 2010. Initial genomics of the human nucleolus. PLoS Genet. 6:e1000889. doi:10.1371/journal.pgen.1000889
33. Panning, M.M., and D.M. Gilbert. 2005. Spatio-temporal organization of DNA replication in murine embryonic stem, primary, and immortalized cells. J. Cell. Biochem. 95:74-82. doi:10.1002/jcb.20395
34. Peric-Hupkes, D., W. Meuleman, L. Pagie, S.W. Bruggeman, I. Solovei, W. Brugman, S. Gräf, P. Flicek, R.M. Kerkhoven, M. van Lohuizen, et al. 2010. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol. Cell. 38:603-613. doi:10.1016/j.molcel.2010.03.016
35. Pope, B.D., I. Hiratani, and D.M. Gilbert. 2010. Domain-wide regulation of DNA replication timing during mammalian development. Chromosome Res. 18:127-136. doi:10.1007/s10577-009-9100-8
36. Reddy, K.L., J.M. Zullo, E. Bertolino, and H. Singh. 2008. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature. 452:243-247. doi:10.1038/nature06727
37. Ryba, T., I. Hiratani, J. Lu, M. Itoh, M. Kulik, J. Zhang, T.C. Schulz, A.J. Robins, S. Dalton, and D.M. Gilbert. 2010. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 20:761-770. doi:10.1101/gr.099655.109
38. Scharf, A.N., T.K. Barth, and A. Imhof. 2009. Establishment of histone modifications after chromatin assembly. Nucleic Acids Res. 37:5032-5040. doi:10.1093/nar/gkp518
39. Spivakov, M., and A.G. Fisher. 2007. Epigenetic signatures of stem-cell identity. Nat. Rev. Genet. 8:263-271. doi:10.1038/nrg2046
40. Steinbach, O.C., A.P. Wolffe, and R.A. Rupp. 1997. Somatic linker histones cause loss of mesodermal competence in Xenopus. Nature. 389:395-399. doi:10.1038/38755
41. Thomson, A.M., P.J. Gillespie, and J.J. Blow. 2010. Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels. J. Cell Biol. 188:209-221. doi:10.1083/jcb.200911037
42. Walter, J., L. Schermelleh, M. Cremer, S. Tashiro, and T. Cremer. 2003. Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J. Cell Biol. 160:685-697. doi:10.1083/jcb.200211103
43. White, J., and S. Dalton. 2005. Cell cycle control of embryonic stem cells. Stem Cell Rev. 1:131-138. doi:10.1385/SCR:1:2:131
44. Yaffe, E., S. Farkash-Amar, A. Polten, Z. Yakhini, A. Tanay, and I. Simon. 2010. Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet. 6:e1001011. doi:10.1371/journal.pgen.1001011
45. Zaidi, S.K., D.W. Young, M.A. Montecino, J.B. Lian, A.J. van Wijnen, J.L. Stein, and G.S. Stein. 2010. Mitotic bookmarking of genes: a novel dimension to epigenetic control. Nat. Rev. Genet. 11:583-589. doi:10.1038/nrg2827
46. Zhang, X., I. Neganova, S. Przyborski, C. Yang, M. Cooke, S.P. Atkinson, G. Anyfantis, S. Fenyk, W.N. Keith, S.F. Hoare, et al. 2009. A role for NANOG in G1 to S transition in human embryonic stem cells through direct binding of CDK6 and CDC25A. J. Cell Biol. 184:67-82. doi:10.1083/jcb.200801009