1,380
Views
28
CrossRef citations to date
0
Altmetric
Research Paper

Functional redundancy in the nuclear compartmentalization of the late-replicating genome

, , , &
Pages 626-635 | Received 12 Sep 2014, Accepted 24 Oct 2014, Published online: 06 Jan 2015

References

  • Pederson T. The spatial organization of the genome in mammalian cells. Curr Opin Genet Dev 2004; 14:203-9; PMID:15196468
  • Misteli T. Concepts in nuclear architecture. Bioessays 2005; 27:477-87; PMID:15832379
  • Rajapakse I, Groudine M. On emerging nuclear order. J Cell Biol 2011; 192:711-21; PMID:21383074; http://dx.doi.org/10.1083/jcb.201010129
  • Cavalli G, Misteli T. Functional implications of genome topology. Nat Struct Mol Biol 2013; 20:290-9; PMID:23463314; http://dx.doi.org/10.1038/nsmb.2474
  • Heitz E. Das heterochromatin der Moose. Jahrb Wiss Botanik 1928; 69:762-818.
  • Dillon N. Heterochromatin structure and function. Biol Cell 2004; 96:631-7; PMID:15519697
  • Padeken J, Heun P. Nucleolus and nuclear periphery: velcro for heterochromatin. Curr Opin Cell Biol 2014; 28:54-60; PMID:24690547; http://dx.doi.org/10.1016/j.ceb.2014.03.001
  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009; 326:289-93; PMID:19815776; http://dx.doi.org/10.1126/science.1181369
  • Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 2010; 20:761-70; PMID:20430782; http://dx.doi.org/10.1101/gr.099655.109
  • Nakayasu H, Berezney R. Mapping replicational sites in the eucaryotic cell nucleus. J Cell Biol 1989; 108:1-11; PMID:2910875; http://dx.doi.org/10.1083/jcb.108.1.1
  • O'Keefe RT, Henderson SC, Spector DL. Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. J Cell Biol 1992; 116:1095-110; PMID:1740468; http://dx.doi.org/10.1083/jcb.116.5.1095
  • Ferreira J, Paolella G, Ramos C, Lamond AI. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J Cell Biol 1997; 139:1597-610; PMID:9412456; http://dx.doi.org/10.1083/jcb.139.7.1597
  • Sadoni N, Langer S, Fauth C, Bernardi G, Cremer T, Turner BM, Zink D. Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol 1999; 146:1211-26; PMID:10491386; http://dx.doi.org/10.1083/jcb.146.6.1211
  • Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Müller S, Eils R, Cremer C, Speicher MR, et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 2005; 3:e157; PMID:15839726
  • Greil F, Moorman C, Van Steensel B. DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Meth Enzymol 2006; 410:342-59; PMID:16938559; http://dx.doi.org/10.1016/S0076-6879(06)10016-6
  • Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, De Klein A, Wessels L, De Laat W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453:948-51; PMID:18463634; http://dx.doi.org/10.1038/nature06947
  • Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Human Molecular Genetics 2001; 10:211-9; PMID:11159939; http://dx.doi.org/10.1093/hmg/10.3.211
  • Penman S, Vesco C, Penman M. Localization and kinetics of formation of nuclear heterodisperse RNA, cytoplasmic heterodisperse RNA and polyribosome-associated messenger RNA in HeLa cells. J Mol Biol 1968; 34:49-69; PMID:4106524; http://dx.doi.org/10.1016/0022-2836(68)90234-9
  • Perry RP, Kelley DE. Inhibition of RNA synthesis by actinomycin D: characteristic dose-response of different RNA species. J Cell Physiol 1970; 76:127-39; PMID:5500970; http://dx.doi.org/10.1002/jcp.1040760202
  • Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA. Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 1999; 145:1119-31; PMID:10366586; http://dx.doi.org/10.1083/jcb.145.6.1119
  • Cremer M, Hase von J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 2001; 9:541-67; PMID:11721953; http://dx.doi.org/10.1023/A:1012495201697
  • Cremer M. Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 2003; 162:809-20; PMID:12952935
  • Wu R, Terry AV, Singh PB, Gilbert DM. Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol Biol Cell 2005; 16:2872-81; PMID:15788566; http://dx.doi.org/10.1091/mbc.E04-11-0997
  • Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 1997; 91:845-54; PMID:9413993; http://dx.doi.org/10.1016/S0092-8674(00)80472-9
  • Clowney EJ, LeGros MA, Mosley CP, Clowney FG, Markenskoff-Papadimitriou EC, Myllys M, Barnea G, Larabell CA, Lomvardas S. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 2012; 151:724-37; PMID:23141535; http://dx.doi.org/10.1016/j.cell.2012.09.043
  • Tanaka A, Tanizawa H, Sriswasdi S, Iwasaki O, Chatterjee AG, Speicher DW, Levin HL, Noguchi E, Noma K-I. Epigenetic regulation of condensin-mediated genome organization during the cell cycle and upon DNA damage through histone H3 lysine 56 acetylation. Mol Cell 2012; 48:532-46; PMID:23084836; http://dx.doi.org/10.1016/j.molcel.2012.09.011
  • van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, Dunnen den JT, Lamond AI. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell 2010; 21:3735-48; PMID:20826608; http://dx.doi.org/10.1091/mbc.E10-06-0508
  • Németh A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Péterfia B, Solovei I, Cremer T, Dopazo J, Längst G. Initial genomics of the human nucleolus. PLoS Genet 2010; 6:e1000889; PMID:20361057
  • Manuelidis L. Different central nervous system cell types display distinct and nonrandom arrangements of satellite DNA sequences. Proc Natl Acad Sci USA 1984; 81:3123-7; PMID:6587343
  • Carvalho C, Pereira HM, Ferreira J, Pina C, Mendonça D, Rosa AC, Carmo-Fonseca M. Chromosomal G-dark bands determine the spatial organization of centromeric heterochromatin in the nucleus. Mol Biol Cell 2001; 12:3563-72; PMID:11694589; http://dx.doi.org/10.1091/mbc.12.11.3563
  • Solovei I, Schermelleh L, Düring K, Engelhardt A, Stein S, Cremer C, Cremer T. Differences in centromere positioning of cycling and postmitotic human cell types. Chromosoma 2004; 112:410-23; PMID:15197559; http://dx.doi.org/10.1007/s00412-004-0287-3
  • Wiblin AE, Cui W, Clark AJ, Bickmore WA. Distinctive nuclear organisation of centromeres and regions involved in pluripotency in human embryonic stem cells. J Cell Sci 2005; 118:3861-8; PMID:16105879; http://dx.doi.org/10.1242/jcs.02500
  • Chubb JR, Boyle S, Perry P, Bickmore WA. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 2002; 12:439-45; PMID:11909528; http://dx.doi.org/10.1016/S0960-9822(02)00695-4
  • Kind J, Van Steensel B. Stochastic genome-nuclear lamina interactions: modulating roles of Lamin A and BAF. Nucleus 2014; 5:124-30; PMID:24717229; http://dx.doi.org/10.4161/nucl.28825
  • Ragoczy T, Bender MA, Telling A, Byron R, Groudine M. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 2006; 20:1447-57; PMID:16705039; http://dx.doi.org/10.1101/gad.1419506
  • Vogel MJ, Peric-Hupkes D, Van Steensel B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2007; 2:1467-78; PMID:17545983; http://dx.doi.org/10.1038/nprot.2007.148
  • Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002; 12:996-1006; PMID:12045153; http://dx.doi.org/10.1101/gr.229102.
  • Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005; 15:1451-5; PMID:16169926; http://dx.doi.org/10.1101/gr.4086505
  • Blankenberg D, Kuster Von G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010; Chapter 19:Unit19.10.1-21; PMID:20373502
  • Goecks J, Nekrutenko A, Taylor J, Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010; 11:R86; PMID:20738864
  • Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, et al. The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biol 2010; 11:R121; PMID:21182759