-
1
-
-
33846283384
-
Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions
-
Lanctot C., Cheutin T., Cremer M., Cavalli G., Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nature Rev Genet 2007, 8:104-115.
-
(2007)
Nature Rev Genet
, vol.8
, pp. 104-115
-
-
Lanctot, C.1
Cheutin, T.2
Cremer, M.3
Cavalli, G.4
Cremer, T.5
-
2
-
-
33847077659
-
Beyond the sequence: cellular organization of genome function
-
Misteli T. Beyond the sequence: cellular organization of genome function. Cell 2007, 128:787-800.
-
(2007)
Cell
, vol.128
, pp. 787-800
-
-
Misteli, T.1
-
3
-
-
84875190221
-
Genome architecture: domain organization of interphase chromosomes
-
Bickmore W.A., van Steensel B. Genome architecture: domain organization of interphase chromosomes. Cell 2013, 152:1270-1284.
-
(2013)
Cell
, vol.152
, pp. 1270-1284
-
-
Bickmore, W.A.1
van Steensel, B.2
-
4
-
-
33646729244
-
Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations
-
Branco M.R., Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 2006, 4:e138.
-
(2006)
PLoS Biol
, vol.4
-
-
Branco, M.R.1
Pombo, A.2
-
5
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon J.R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y., Hu M., Liu J.S., Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012, 485:376-380.
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
Hu, M.7
Liu, J.S.8
Ren, B.9
-
6
-
-
84861100147
-
Spatial partitioning of the regulatory landscape of the X-inactivation centre
-
Nora E.P., Lajoie B.R., Schulz E.G., Giorgetti L., Okamoto I., Servant N., Piolot T., van Berkum N.L., Meisig J., Sedat J., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012, 485:381-385.
-
(2012)
Nature
, vol.485
, pp. 381-385
-
-
Nora, E.P.1
Lajoie, B.R.2
Schulz, E.G.3
Giorgetti, L.4
Okamoto, I.5
Servant, N.6
Piolot, T.7
van Berkum, N.L.8
Meisig, J.9
Sedat, J.10
-
7
-
-
0033561153
-
Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III
-
Pombo A., Jackson D.A., Hollinshead M., Wang Z., Roeder R.G., Cook P.R. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J 1999, 18:2241-2253.
-
(1999)
EMBO J
, vol.18
, pp. 2241-2253
-
-
Pombo, A.1
Jackson, D.A.2
Hollinshead, M.3
Wang, Z.4
Roeder, R.G.5
Cook, P.R.6
-
8
-
-
34548210885
-
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh
-
Osborne C.S., Chakalova L., Mitchell J.A., Horton A., Wood A.L., Bolland D.J., Corcoran A.E., Fraser P. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 2007, 5:e192.
-
(2007)
PLoS Biol
, vol.5
-
-
Osborne, C.S.1
Chakalova, L.2
Mitchell, J.A.3
Horton, A.4
Wood, A.L.5
Bolland, D.J.6
Corcoran, A.E.7
Fraser, P.8
-
9
-
-
75749100247
-
Poised transcription factories prime silent uPA gene prior to activation
-
Ferrai C., Xie S.Q., Luraghi P., Munari D., Ramirez F., Branco M.R., Pombo A., Crippa M.P. Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol 2010, 8:e1000270.
-
(2010)
PLoS Biol
, vol.8
-
-
Ferrai, C.1
Xie, S.Q.2
Luraghi, P.3
Munari, D.4
Ramirez, F.5
Branco, M.R.6
Pombo, A.7
Crippa, M.P.8
-
10
-
-
73349090560
-
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
-
Schoenfelder S., Sexton T., Chakalova L., Cope N.F., Horton A., Andrews S., Kurukuti S., Mitchell J.A., Umlauf D., Dimitrova D.S., et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 2010, 42:53-61.
-
(2010)
Nat Genet
, vol.42
, pp. 53-61
-
-
Schoenfelder, S.1
Sexton, T.2
Chakalova, L.3
Cope, N.F.4
Horton, A.5
Andrews, S.6
Kurukuti, S.7
Mitchell, J.A.8
Umlauf, D.9
Dimitrova, D.S.10
-
11
-
-
0032559794
-
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
-
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 1998, 140:1285-1295.
-
(1998)
J Cell Biol
, vol.140
, pp. 1285-1295
-
-
Jackson, D.A.1
Pombo, A.2
-
12
-
-
33645286183
-
Polymer chain models of DNA and chromatin
-
Langowski J. Polymer chain models of DNA and chromatin. Eur Phys J E Soft Matter 2006, 19:241-249.
-
(2006)
Eur Phys J E Soft Matter
, vol.19
, pp. 241-249
-
-
Langowski, J.1
-
13
-
-
68349128355
-
The physics behind the larger scale organization of DNA in eukaryotes
-
Emanuel M., Radja N.H., Henriksson A., Schiessel H. The physics behind the larger scale organization of DNA in eukaryotes. Phys Biol 2009, 6:025008.
-
(2009)
Phys Biol
, vol.6
, pp. 025008
-
-
Emanuel, M.1
Radja, N.H.2
Henriksson, A.3
Schiessel, H.4
-
14
-
-
79952807125
-
Chromatin folding-from biology to polymer models and back
-
Tark-Dame M., van Driel R., Heermann D.W. Chromatin folding-from biology to polymer models and back. J Cell Sci 2011, 124:839-845.
-
(2011)
J Cell Sci
, vol.124
, pp. 839-845
-
-
Tark-Dame, M.1
van Driel, R.2
Heermann, D.W.3
-
15
-
-
84882957073
-
Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus
-
Barbieri M., Scialdone A., Gamba A., Pombo A., Nicodemi M. Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus. Soft Mat 2013, 9:8631-8635.
-
(2013)
Soft Mat
, vol.9
, pp. 8631-8635
-
-
Barbieri, M.1
Scialdone, A.2
Gamba, A.3
Pombo, A.4
Nicodemi, M.5
-
16
-
-
2142772663
-
Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code
-
Kreth G., Finsterle J., von Hase J., Cremer M., Cremer C. Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code. Biophys J 2004, 86:2803-2812.
-
(2004)
Biophys J
, vol.86
, pp. 2803-2812
-
-
Kreth, G.1
Finsterle, J.2
von Hase, J.3
Cremer, M.4
Cremer, C.5
-
19
-
-
50949125193
-
Structure and dynamics of interphase chromosomes
-
Rosa A., Everaers R. Structure and dynamics of interphase chromosomes. PLoS Comput Biol 2008, 4:e1000153.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Rosa, A.1
Everaers, R.2
-
20
-
-
0033758019
-
Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture
-
Cremer T., Kreth G., Koester H., Fink R.H., Heintzmann R., Cremer M., Solovei I., Zink D., Cremer C. Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Crit Rev Eukaryot Gene Expr 2000, 10:179-212.
-
(2000)
Crit Rev Eukaryot Gene Expr
, vol.10
, pp. 179-212
-
-
Cremer, T.1
Kreth, G.2
Koester, H.3
Fink, R.H.4
Heintzmann, R.5
Cremer, M.6
Solovei, I.7
Zink, D.8
Cremer, C.9
-
21
-
-
33847386173
-
Chromosome organization: new facts, new models
-
Branco M.R., Pombo A. Chromosome organization: new facts, new models. Trends Cell Biol 2007, 17:127-134.
-
(2007)
Trends Cell Biol
, vol.17
, pp. 127-134
-
-
Branco, M.R.1
Pombo, A.2
-
22
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
-
23
-
-
84867070913
-
Complexity of chromatin folding is captured by the strings and binders switch model
-
Barbieri M., Chotalia M., Fraser J., Lavitas L.M., Dostie J., Pombo A., Nicodemi M. Complexity of chromatin folding is captured by the strings and binders switch model. PNAS 2012, 109:16173-16178.
-
(2012)
PNAS
, vol.109
, pp. 16173-16178
-
-
Barbieri, M.1
Chotalia, M.2
Fraser, J.3
Lavitas, L.M.4
Dostie, J.5
Pombo, A.6
Nicodemi, M.7
-
24
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker J., Rippe K., Dekker M., Kleckner N. Capturing chromosome conformation. Science 2002, 295:1306-1311.
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
25
-
-
0036923833
-
Looping and interaction between hypersensitive sites in the active beta-globin locus
-
Tolhuis B., Palstra R.J., Splinter E., Grosveld F., de Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 2002, 10:1453-1465.
-
(2002)
Mol Cell
, vol.10
, pp. 1453-1465
-
-
Tolhuis, B.1
Palstra, R.J.2
Splinter, E.3
Grosveld, F.4
de Laat, W.5
-
26
-
-
70149094741
-
Global identification of yeast chromosome interactions using genome conformation capture
-
Rodley C.D., Bertels F., Jones B., O'Sullivan J.M. Global identification of yeast chromosome interactions using genome conformation capture. Fungal Genet Biol 2009, 46:879-886.
-
(2009)
Fungal Genet Biol
, vol.46
, pp. 879-886
-
-
Rodley, C.D.1
Bertels, F.2
Jones, B.3
O'Sullivan, J.M.4
-
27
-
-
84888018217
-
Organization of the mitotic chromosome
-
Naumova N., Imakaev M., Fudenberg G., Zhan Y., Lajoie B.R., Mirny L.A., Dekker J. Organization of the mitotic chromosome. Science 2013, 342:948-953.
-
(2013)
Science
, vol.342
, pp. 948-953
-
-
Naumova, N.1
Imakaev, M.2
Fudenberg, G.3
Zhan, Y.4
Lajoie, B.R.5
Mirny, L.A.6
Dekker, J.7
-
28
-
-
84856747483
-
Three-dimensional folding and functional organization principles of the Drosophila genome
-
Sexton T., Yaffe E., Kenigsberg E., Bantignies F., Leblanc B., Hoichman M., Parrinello H., Tanay A., Cavalli G. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 2012, 148:458-472.
-
(2012)
Cell
, vol.148
, pp. 458-472
-
-
Sexton, T.1
Yaffe, E.2
Kenigsberg, E.3
Bantignies, F.4
Leblanc, B.5
Hoichman, M.6
Parrinello, H.7
Tanay, A.8
Cavalli, G.9
-
29
-
-
77952744854
-
A three-dimensional model of the yeast genome
-
Duan Z., Andronescu M., Schutz K., McIlwain S., Kim Y.J., Lee C., Shendure J., Fields S., Blau C.A., Noble W.S. A three-dimensional model of the yeast genome. Nature 2010, 465:363-367.
-
(2010)
Nature
, vol.465
, pp. 363-367
-
-
Duan, Z.1
Andronescu, M.2
Schutz, K.3
McIlwain, S.4
Kim, Y.J.5
Lee, C.6
Shendure, J.7
Fields, S.8
Blau, C.A.9
Noble, W.S.10
-
30
-
-
84898015781
-
Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes
-
Benedetti F., Dorier J., Burnier Y., Stasiak A. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes. Nucleic Acids Res 2013, 42:2848-2855.
-
(2013)
Nucleic Acids Res
, vol.42
, pp. 2848-2855
-
-
Benedetti, F.1
Dorier, J.2
Burnier, Y.3
Stasiak, A.4
-
31
-
-
84862917808
-
Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
-
Kalhor R., Tjong H., Jayathilaka N., Alber F., Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 2011, 30:90-98.
-
(2011)
Nat Biotechnol
, vol.30
, pp. 90-98
-
-
Kalhor, R.1
Tjong, H.2
Jayathilaka, N.3
Alber, F.4
Chen, L.5
-
33
-
-
45849119056
-
A thermodynamic switch for chromosome colocalization
-
Nicodemi M., Panning B., Prisco A. A thermodynamic switch for chromosome colocalization. Genetics 2008, 179:717-721.
-
(2008)
Genetics
, vol.179
, pp. 717-721
-
-
Nicodemi, M.1
Panning, B.2
Prisco, A.3
-
34
-
-
66149104488
-
Thermodynamic pathways to genome spatial organization in the cell nucleus
-
Nicodemi M., Prisco A. Thermodynamic pathways to genome spatial organization in the cell nucleus. Biophys J 2009, 96:2168-2177.
-
(2009)
Biophys J
, vol.96
, pp. 2168-2177
-
-
Nicodemi, M.1
Prisco, A.2
-
35
-
-
78149259827
-
Diffusion-based DNA target colocalization by thermodynamic mechanisms
-
Scialdone A., Nicodemi M. Diffusion-based DNA target colocalization by thermodynamic mechanisms. Development 2010, 137:3877-3885.
-
(2010)
Development
, vol.137
, pp. 3877-3885
-
-
Scialdone, A.1
Nicodemi, M.2
-
36
-
-
80055067857
-
Conformation regulation of the X chromosome inactivation center: a model
-
Scialdone A., Cataudella I., Barbieri M., Prisco A., Nicodemi M. Conformation regulation of the X chromosome inactivation center: a model. PLoS Comput Biol 2011, 7:e1002229.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Scialdone, A.1
Cataudella, I.2
Barbieri, M.3
Prisco, A.4
Nicodemi, M.5
-
37
-
-
77957867310
-
Diffusion-driven looping provides a consistent framework for chromatin organization
-
Bohn M., Heermann D.W. Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 2010, 5:e12218.
-
(2010)
PLoS ONE
, vol.5
-
-
Bohn, M.1
Heermann, D.W.2
-
38
-
-
84887322004
-
High-resolution mapping of the spatial organization of a bacterial chromosome
-
Le T.B., Imakaev M.V., Mirny L.A., Laub M.T. High-resolution mapping of the spatial organization of a bacterial chromosome. Science 2013, 342:731-734.
-
(2013)
Science
, vol.342
, pp. 731-734
-
-
Le, T.B.1
Imakaev, M.V.2
Mirny, L.A.3
Laub, M.T.4
-
39
-
-
84881255212
-
Spatial dynamics of chromosome translocations in living cells
-
Roukos V., Voss T.C., Schmidt C.K., Lee S., Wangsa D., Misteli T. Spatial dynamics of chromosome translocations in living cells. Science 2013, 341:660-664.
-
(2013)
Science
, vol.341
, pp. 660-664
-
-
Roukos, V.1
Voss, T.C.2
Schmidt, C.K.3
Lee, S.4
Wangsa, D.5
Misteli, T.6
-
40
-
-
84887461569
-
The statistical-mechanics of chromosome conformation capture
-
O'Sullivan J.M., Hendy M.D., Pichugina T., Wake G.C., Langowski J. The statistical-mechanics of chromosome conformation capture. Nucleus 2013, 4:390-398.
-
(2013)
Nucleus
, vol.4
, pp. 390-398
-
-
O'Sullivan, J.M.1
Hendy, M.D.2
Pichugina, T.3
Wake, G.C.4
Langowski, J.5
-
41
-
-
84887942741
-
Large-scale chromatin organization: the good, the surprising, and the still perplexing
-
Belmont A.S. Large-scale chromatin organization: the good, the surprising, and the still perplexing. Curr Opin Cell Biol 2014, 26C:69-78.
-
(2014)
Curr Opin Cell Biol
, vol.26 C
, pp. 69-78
-
-
Belmont, A.S.1
-
43
-
-
81255146230
-
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation
-
Umbarger M.A., Toro E., Wright M.A., Porreca G.J., Bau D., Hong S.H., Fero M.J., Zhu L.J., Marti-Renom M.A., McAdams H.H., et al. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 2011, 44:252-264.
-
(2011)
Mol Cell
, vol.44
, pp. 252-264
-
-
Umbarger, M.A.1
Toro, E.2
Wright, M.A.3
Porreca, G.J.4
Bau, D.5
Hong, S.H.6
Fero, M.J.7
Zhu, L.J.8
Marti-Renom, M.A.9
McAdams, H.H.10
-
44
-
-
84885617426
-
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
-
Nagano T., Lubling Y., Stevens T.J., Schoenfelder S., Yaffe E., Dean W., Laue E.D., Tanay A., Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 2013, 502:59-64.
-
(2013)
Nature
, vol.502
, pp. 59-64
-
-
Nagano, T.1
Lubling, Y.2
Stevens, T.J.3
Schoenfelder, S.4
Yaffe, E.5
Dean, W.6
Laue, E.D.7
Tanay, A.8
Fraser, P.9
-
46
-
-
36348974524
-
Chromosome territories have a highly nonspherical morphology and nonrandom positioning
-
Khalil A., Grant J.L., Caddle L.B., Atzema E., Mills K.D., Arneodo A. Chromosome territories have a highly nonspherical morphology and nonrandom positioning. Chromosome Res 2007, 15:899-916.
-
(2007)
Chromosome Res
, vol.15
, pp. 899-916
-
-
Khalil, A.1
Grant, J.L.2
Caddle, L.B.3
Atzema, E.4
Mills, K.D.5
Arneodo, A.6
|