Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

Cell

Volumn 163, Issue 1, 2015, Pages 134-147

  Kind, Jop ^a,b   Pagie, Ludo ^a   De Vries, Sandra S ^a   Nahidiazar, Leila ^a   Dey, Siddharth S ^b   Bienko, Magda ^f   Zhan, Ye ^c   Lajoie, Bryan ^c   De Graaf, Carolyn A ^a,h   Amendola, Mario ^a   Fudenberg, Geoffrey ^d   Imakaev, Maxim ^e   Mirny, Leonid A ^e,g   Jalink, Kees ^a   Dekker, Job ^c   Van Oudenaarden, Alexander ^b   Van Steensel, Bas ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^d HARVARD UNIVERSITY   (United States)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^f KAROLINSKA INSTITUTE   (Sweden)

^g Massachusetts Institute of Technology Cambridge   (United States)

^h WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL INTERACTION; CELL SELECTION; CHROMOSOME; CLONAL CELL LINE; CONTROLLED STUDY; CYTOARCHITECTURE; G1 PHASE CELL CYCLE CHECKPOINT; GENE MAPPING; GENE SEQUENCE; HUMAN; HUMAN CELL; INTERPHASE; NUCLEAR LAMINA; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; CHEMISTRY; CHROMATIN; FLUORESCENCE IN SITU HYBRIDIZATION; GENOME-WIDE ASSOCIATION STUDY; METABOLISM; PROCEDURES; SINGLE CELL ANALYSIS; TUMOR CELL LINE;

CHROMATIN;

CELL LINE, TUMOR; CHROMATIN; CHROMOSOMES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INTERPHASE; NUCLEAR LAMINA; SINGLE-CELL ANALYSIS;

EID: 84948587544     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.08.040     Document Type: Article

References (43)

1. D. Baù, A. Sanyal, B.R. Lajoie, E. Capriotti, M. Byron, J.B. Lawrence, J. Dekker, and M.A. Marti-Renom The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules Nat. Struct. Mol. Biol. 18 2011 107 114
2. J.M. Belton, R.P. McCord, J.H. Gibcus, N. Naumova, Y. Zhan, and J. Dekker Hi-C: a comprehensive technique to capture the conformation of genomes Methods 58 2012 268 276
3. Q. Bian, N. Khanna, J. Alvikas, and A.S. Belmont β-globin cis-elements determine differential nuclear targeting through epigenetic modifications J. Cell Biol. 203 2013 767 783
4. W.A. Bickmore The spatial organization of the human genome Annu. Rev. Genomics Hum. Genet. 14 2013 67 84
5. W.A. Bickmore, and B. van Steensel Genome architecture: domain organization of interphase chromosomes Cell 152 2013 1270 1284
6. A. Bolzer, G. Kreth, I. Solovei, D. Koehler, K. Saracoglu, C. Fauth, S. Müller, R. Eils, C. Cremer, M.R. Speicher, and T. Cremer Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes PLoS Biol. 3 2005 e157
7. T. Bürckstümmer, C. Banning, P. Hainzl, R. Schobesberger, C. Kerzendorfer, F.M. Pauler, D. Chen, N. Them, F. Schischlik, M. Rebsamen, and et al. A reversible gene trap collection empowers haploid genetics in human cells Nat. Methods 10 2013 965 971
8. G. Cavalli, and T. Misteli Functional implications of genome topology Nat. Struct. Mol. Biol. 20 2013 290 299
9. M. Cremer, J. von Hase, T. Volm, A. Brero, G. Kreth, J. Walter, C. Fischer, I. Solovei, C. Cremer, and T. Cremer Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells Chromosome Res. 9 2001 541 567
10. J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague, and W.A. Bickmore Differences in the localization and morphology of chromosomes in the human nucleus J. Cell Biol. 145 1999 1119 1131
11. E. de Wit, and W. de Laat A decade of 3C technologies: insights into nuclear organization Genes Dev. 26 2012 11 24
12. J. Dekker, M.A. Marti-Renom, and L.A. Mirny Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data Nat. Rev. Genet. 14 2013 390 403
13. J.R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J.S. Liu, and B. Ren Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 2012 376 380
14. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
15. L.E. Finlan, D. Sproul, I. Thomson, S. Boyle, E. Kerr, P. Perry, B. Ylstra, J.R. Chubb, and W.A. Bickmore Recruitment to the nuclear periphery can alter expression of genes in human cells PLoS Genet. 4 2008 e1000039
16. J. Fölling, M. Bossi, H. Bock, R. Medda, C.A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S.W. Hell Fluorescence nanoscopy by ground-state depletion and single-molecule return Nat. Methods 5 2008 943 945
17. J.H. Gibcus, and J. Dekker The hierarchy of the 3D genome Mol. Cell 49 2013 773 782
18. L. Giorgetti, R. Galupa, E.P. Nora, T. Piolot, F. Lam, J. Dekker, G. Tiana, and E. Heard Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription Cell 157 2014 950 963
19. D. Grün, L. Kester, and A. van Oudenaarden Validation of noise models for single-cell transcriptomics Nat. Methods 11 2014 637 640
20. L. Guelen, L. Pagie, E. Brasset, W. Meuleman, M.B. Faza, W. Talhout, B.H. Eussen, A. de Klein, L. Wessels, W. de Laat, and B. van Steensel Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions Nature 453 2008 948 951
21. R. Kalhor, H. Tjong, N. Jayathilaka, F. Alber, and L. Chen Genome architectures revealed by tethered chromosome conformation capture and population-based modeling Nat. Biotechnol. 30 2012 90 98
22. J. Kind, L. Pagie, H. Ortabozkoyun, S. Boyle, S.S. de Vries, H. Janssen, M. Amendola, L.D. Nolen, W.A. Bickmore, and B. van Steensel Single-cell dynamics of genome-nuclear lamina interactions Cell 153 2013 178 192
23. S.T. Kosak, J.A. Skok, K.L. Medina, R. Riblet, M.M. Le Beau, A.G. Fisher, and H. Singh Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development Science 296 2002 158 162
24. M. Kotecki, P.S. Reddy, and B.H. Cochran Isolation and characterization of a near-haploid human cell line Exp. Cell Res. 252 1999 273 280
25. B.R. Lajoie, J. Dekker, and N. Kaplan The hitchhiker's guide to Hi-C analysis: practical guidelines Methods 72 2015 65 75
26. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, M.O. Dorschner, and et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
27. L. Manuelidis, and J. Borden Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed by in situ hybridization and three-dimensional reconstruction Chromosoma 96 1988 397 410
28. W.F. Marshall, A.F. Dernburg, B. Harmon, D.A. Agard, and J.W. Sedat Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster Mol. Biol. Cell 7 1996 825 842
29. J. Mateos-Langerak, M. Bohn, W. de Leeuw, O. Giromus, E.M. Manders, P.J. Verschure, M.H. Indemans, H.J. Gierman, D.W. Heermann, R. van Driel, and S. Goetze Spatially confined folding of chromatin in the interphase nucleus Proc. Natl. Acad. Sci. USA 106 2009 3812 3817
30. W. Meuleman, D. Peric-Hupkes, J. Kind, J.B. Beaudry, L. Pagie, M. Kellis, M. Reinders, L. Wessels, and B. van Steensel Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence Genome Res. 23 2013 270 280
31. T. Nagano, Y. Lubling, T.J. Stevens, S. Schoenfelder, E. Yaffe, W. Dean, E.D. Laue, A. Tanay, and P. Fraser Single-cell Hi-C reveals cell-to-cell variability in chromosome structure Nature 502 2013 59 64
32. E.P. Nora, B.R. Lajoie, E.G. Schulz, L. Giorgetti, I. Okamoto, N. Servant, T. Piolot, N.L. van Berkum, J. Meisig, J. Sedat, and et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre Nature 485 2012 381 385
33. R.L. Ochs, and R.I. Press Centromere autoantigens are associated with the nucleolus Exp. Cell Res. 200 1992 339 350
34. M. Ovesný, P. Křížek, J. Borkovec, Z. Svindrych, and G.M. Hagen ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging Bioinformatics 30 2014 2389 2390
35. D. Peric-Hupkes, W. Meuleman, L. Pagie, S.W. Bruggeman, I. Solovei, W. Brugman, S. Gräf, P. Flicek, R.M. Kerkhoven, M. van Lohuizen, and et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation Mol. Cell 38 2010 603 613
36. S.S. Rao, M.H. Huntley, N.C. Durand, E.K. Stamenova, I.D. Bochkov, J.T. Robinson, A.L. Sanborn, I. Machol, A.D. Omer, E.S. Lander, and E.L. Aiden A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159 2014 1665 1680
37. K.L. Reddy, J.M. Zullo, E. Bertolino, and H. Singh Transcriptional repression mediated by repositioning of genes to the nuclear lamina Nature 452 2008 243 247
38. A. Sakaue-Sawano, H. Kurokawa, T. Morimura, A. Hanyu, H. Hama, H. Osawa, S. Kashiwagi, K. Fukami, T. Miyata, H. Miyoshi, and et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression Cell 132 2008 487 498
39. P. Therizols, R.S. Illingworth, C. Courilleau, S. Boyle, A.J. Wood, and W.A. Bickmore Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells Science 346 2014 1238 1242
40. B.D. Towbin, C. González-Aguilera, R. Sack, D. Gaidatzis, V. Kalck, P. Meister, P. Askjaer, and S.M. Gasser Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery Cell 150 2012 934 947
41. B. van Steensel, and J. Dekker Genomics tools for unraveling chromosome architecture Nat. Biotechnol. 28 2010 1089 1095
42. M.J. Vogel, D. Peric-Hupkes, and B. van Steensel Detection of in vivo protein-DNA interactions using DamID in mammalian cells Nat. Protoc. 2 2007 1467 1478
43. J.M. Zullo, I.A. Demarco, R. Piqué-Regi, D.J. Gaffney, C.B. Epstein, C.J. Spooner, T.R. Luperchio, B.E. Bernstein, J.K. Pritchard, K.L. Reddy, and H. Singh DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina Cell 149 2012 1474 1487