-
1
-
-
33846283384
-
Dynamic genome architecture in the nuclear space: Regulation of gene expression in three dimensions
-
Lanctôt, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8, 104-115 (2007).
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 104-115
-
-
Lanctôt, C.1
Cheutin, T.2
Cremer, M.3
Cavalli, G.4
Cremer, T.5
-
2
-
-
21844444077
-
Three-dimensional maps of all chromosomes in human male fbroblast nuclei and prometaphase rosettes
-
Bolzer, A. et al. Three-dimensional maps of all chromosomes in human male fbroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157 (2005).
-
(2005)
PLoS Biol.
, vol.3
-
-
Bolzer, A.1
-
3
-
-
2442695407
-
Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription
-
Chambeyron, S. & Bickmore, W.A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 18, 1119-1130 (2004).
-
(2004)
Genes Dev.
, vol.18
, pp. 1119-1130
-
-
Chambeyron, S.1
Bickmore, W.A.2
-
4
-
-
0034065032
-
Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei
-
Volpi, E.V. et al. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J. Cell Sci. 113, 1565-1576 (2000).
-
(2000)
J. Cell Sci.
, vol.113
, pp. 1565-1576
-
-
Volpi, E.V.1
-
5
-
-
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. 4, e138 (2006).
-
(2006)
PLoS Biol.
, vol.4
-
-
Branco, M.R.1
Pombo, A.2
-
6
-
-
46149115158
-
Virus infection induces NF-κB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression
-
Apostolou, E. & Thanos, D. Virus infection induces NF-κB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell 134, 85-96 (2008).
-
(2008)
Cell
, vol.134
, pp. 85-96
-
-
Apostolou, E.1
Thanos, D.2
-
7
-
-
20444494936
-
Interchromosomal associations between alternatively expressed loci
-
Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R. & Flavell, R.A. Interchromosomal associations between alternatively expressed loci. Nature 435, 637-645 (2005).
-
(2005)
Nature
, vol.435
, pp. 637-645
-
-
Spilianakis, C.G.1
Lalioti, M.D.2
Town, T.3
Lee, G.R.4
Flavell, R.A.5
-
8
-
-
33750203582
-
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions
-
Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat. Genet. 38, 1341-1347 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 1341-1347
-
-
Zhao, Z.1
-
9
-
-
0033083793
-
Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division
-
Brown, K.E., Baxter, J., Graf, D., Merkenschlager, M. & Fisher, A.G. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell 3, 207-217 (1999).
-
(1999)
Mol. Cell
, vol.3
, pp. 207-217
-
-
Brown, K.E.1
Baxter, J.2
Graf, D.3
Merkenschlager, M.4
Fisher, A.G.5
-
10
-
-
34548210885
-
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh
-
Osborne, C.S. et al. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 5, e192 (2007).
-
(2007)
PLoS Biol.
, vol.5
-
-
Osborne, C.S.1
-
11
-
-
35848952522
-
Gene regulation through nuclear organization
-
Sexton, T., Schober, H., Fraser, P. & Gasser, S.M. Gene regulation through nuclear organization. Nat. Struct. Mol. Biol. 14, 1049-1055 (2007).
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 1049-1055
-
-
Sexton, T.1
Schober, H.2
Fraser, P.3
Gasser, S.M.4
-
12
-
-
0027499230
-
Visualization of focal sites of transcription within human nuclei
-
Jackson, D.A., Hassan, A.B., Errington, R.J. & Cook, P.R. Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065 (1993).
-
(1993)
EMBO J.
, vol.12
, pp. 1059-1065
-
-
Jackson, D.A.1
Hassan, A.B.2
Errington, R.J.3
Cook, P.R.4
-
13
-
-
38149133051
-
Transcription factories are nuclear subcompartments that remain in the absence of transcription
-
Mitchell, J.A. & Fraser, P. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev. 22, 20-25 (2008).
-
(2008)
Genes Dev.
, vol.22
, pp. 20-25
-
-
Mitchell, J.A.1
Fraser, P.2
-
14
-
-
5444243359
-
Active genes dynamically colocalize to shared sites of ongoing transcription
-
Osborne, C.S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36, 1065-1071 (2004).
-
(2004)
Nat. Genet.
, vol.36
, pp. 1065-1071
-
-
Osborne, C.S.1
-
15
-
-
33744779614
-
The locus control region is required for association of the murine β-globin locus with engaged transcription factories during erythroid maturation
-
Ragoczy, T., Bender, M.A., Telling, A., Byron, R. & Groudine, M. The locus control region is required for association of the murine β-globin locus with engaged transcription factories during erythroid maturation. Genes Dev. 20, 1447-1457 (2006).
-
(2006)
Genes Dev.
, vol.20
, pp. 1447-1457
-
-
Ragoczy, T.1
Bender, M.A.2
Telling, A.3
Byron, R.4
Groudine, M.5
-
16
-
-
0027305616
-
Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus
-
Wansink, D.G. et al. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122, 283-293 (1993).
-
(1993)
J. Cell Biol.
, vol.122
, pp. 283-293
-
-
Wansink, D.G.1
-
17
-
-
0029973080
-
Active RNA polymerases are localized within discrete transcription "factories"
-
Iborra, F.J., Pombo, A., Jackson, D.A. & Cook, P.R. Active RNA polymerases are localized within discrete transcription "factories" in human nuclei. J. Cell Sci. 109, 1427-1436 (1996).
-
(1996)
In Human Nuclei. J. Cell Sci.
, vol.109
, pp. 1427-1436
-
-
Iborra, F.J.1
Pombo, A.2
Jackson, D.A.3
Cook, P.R.4
-
18
-
-
33646591544
-
Transcriptional pulsing of a developmental gene
-
Chubb, J.R., Trcek, T., Shenoy, S.M. & Singer, R.H. Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 1018-1025 (2006).
-
(2006)
Curr. Biol.
, vol.16
, pp. 1018-1025
-
-
Chubb, J.R.1
Trcek, T.2
Shenoy, S.M.3
Singer, R.H.4
-
19
-
-
0037008488
-
Single-cell gene expression profling
-
Levsky, J.M., Shenoy, S.M., Pezo, R.C. & Singer, R.H. Single-cell gene expression profling. Science 297, 836-840 (2002).
-
(2002)
Science
, vol.297
, pp. 836-840
-
-
Levsky, J.M.1
Shenoy, S.M.2
Pezo, R.C.3
Singer, R.H.4
-
20
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
-
(2006)
PLoS Biol.
, vol.4
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
21
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306-1311 (2002).
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
22
-
-
52249111620
-
Association between active genes occurs at nuclear speckles and is modulated by chromatin environment
-
Brown, J.M. et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell Biol. 182, 1083-1097 (2008).
-
(2008)
J. Cell Biol.
, vol.182
, pp. 1083-1097
-
-
Brown, J.M.1
-
23
-
-
30944469000
-
Coregulated human globin genes are frequently in spatial proximity when active
-
Brown, J.M. et al. Coregulated human globin genes are frequently in spatial proximity when active. J. Cell Biol. 172, 177-187 (2006).
-
(2006)
J. Cell Biol.
, vol.172
, pp. 177-187
-
-
Brown, J.M.1
-
24
-
-
58049208232
-
Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules
-
Hu, Q. et al. Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc. Natl. Acad. Sci. USA 105, 19199-19204 (2008).
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 19199-19204
-
-
Hu, Q.1
-
25
-
-
0033593806
-
Processing of endogenous pre-mRNAs in association with SC35 domains is gene specifc
-
Smith, K.P., Moen, P.T., Wydner, K.L., Coleman, J.R. & Lawrence, J.B. Processing of endogenous pre-mRNAs in association with SC35 domains is gene specifc. J. Cell Biol. 144, 617-629 (1999).
-
(1999)
J. Cell Biol.
, vol.144
, pp. 617-629
-
-
Smith, K.P.1
Moen, P.T.2
Wydner, K.L.3
Coleman, J.R.4
Lawrence, J.B.5
-
26
-
-
0029615378
-
Nonrandom gene organization: Structural arrangements of specifc pre-mRNA transcription and splicing with SC35 domains
-
Xing, Y., Johnson, C.V., Moen, P.T. Jr., McNeil, J.A. & Lawrence, J. Nonrandom gene organization: structural arrangements of specifc pre-mRNA transcription and splicing with SC35 domains. J. Cell Biol. 131, 1635-1647 (1995).
-
(1995)
J. Cell Biol.
, vol.131
, pp. 1635-1647
-
-
Xing, Y.1
Johnson, C.V.2
Moen Jr., P.T.3
McNeil, J.A.4
Lawrence, J.5
-
27
-
-
33751090746
-
Phosphorylation and functions of the RNA polymerase II CTD
-
Phatnani, H.P. & Greenleaf, A.L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922-2936 (2006).
-
(2006)
Genes Dev.
, vol.20
, pp. 2922-2936
-
-
Phatnani, H.P.1
Greenleaf, A.L.2
-
28
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
-
Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348-1354 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 1348-1354
-
-
Simonis, M.1
-
29
-
-
30344478870
-
A global map of p53 transcription-factor binding sites in the human genome
-
Wei, C.L. et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 124, 207-219 (2006).
-
(2006)
Cell
, vol.124
, pp. 207-219
-
-
Wei, C.L.1
-
30
-
-
0033561153
-
Regional specialization in human nuclei: Visualization of discrete sites of transcription by RNA polymerase III
-
Pombo, A. et al. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241-2253 (1999).
-
(1999)
EMBO J.
, vol.18
, pp. 2241-2253
-
-
Pombo, A.1
-
31
-
-
0027211845
-
A novel, erythroid cell-specifc murine transcription factor that binds to the CACCC element and is related to the Kruppel family of nuclear proteins
-
Miller, I.J. & Bieker, J.J. A novel, erythroid cell-specifc murine transcription factor that binds to the CACCC element and is related to the Kruppel family of nuclear proteins. Mol. Cell. Biol. 13, 2776-2786 (1993).
-
(1993)
Mol. Cell. Biol.
, vol.13
, pp. 2776-2786
-
-
Miller, I.J.1
Bieker, J.J.2
-
32
-
-
33646140805
-
Chromatin-binding in vivo of the erythroid Kruppel-like factor, EKLF, in the murine globin loci
-
Shyu, Y.C. et al. Chromatin-binding in vivo of the erythroid Kruppel-like factor, EKLF, in the murine globin loci. Cell Res. 16, 347-355 (2006).
-
(2006)
Cell Res.
, vol.16
, pp. 347-355
-
-
Shyu, Y.C.1
-
33
-
-
34247272882
-
Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression
-
Vernimmen, D., De Gobbi, M., Sloane-Stanley, J.A., Wood, W.G. & Higgs, D.R. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J. 26, 2041-2051 (2007).
-
(2007)
EMBO J.
, vol.26
, pp. 2041-2051
-
-
Vernimmen, D.1
De Gobbi, M.2
Sloane-Stanley, J.A.3
Wood, W.G.4
Higgs, D.R.5
-
34
-
-
0029010790
-
Defective haematopoiesis in fetal liver resulting from inactivation of the EKLF gene
-
Nuez, B., Michaolovich, D., Bygrave, A., Ploemacher, R. & Grosveld, F. Defective haematopoiesis in fetal liver resulting from inactivation of the EKLF gene. Nature 375, 316-318 (1995).
-
(1995)
Nature
, vol.375
, pp. 316-318
-
-
Nuez, B.1
Michaolovich, D.2
Bygrave, A.3
Ploemacher, R.4
Grosveld, F.5
-
35
-
-
0028990264
-
Lethal β-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF
-
Perkins, A.C., Sharpe, A.H. & Orkin, S.H. Lethal β-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF. Nature 375, 318-322 (1995).
-
(1995)
Nature
, vol.375
, pp. 318-322
-
-
Perkins, A.C.1
Sharpe, A.H.2
Orkin, S.H.3
-
36
-
-
20344364878
-
The erythroid phenotype of EKLF-null mice: Defects in hemoglobin metabolism and membrane stability
-
Drissen, R. et al. The erythroid phenotype of EKLF-null mice: defects in hemoglobin metabolism and membrane stability. Mol. Cell. Biol. 25, 5205-5214 (2005).
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 5205-5214
-
-
Drissen, R.1
-
37
-
-
33645743530
-
A global role for EKLF in defnitive and primitive erythropoiesis
-
Hodge, D. et al. A global role for EKLF in defnitive and primitive erythropoiesis. Blood 107, 3359-3370 (2006).
-
(2006)
Blood
, vol.107
, pp. 3359-3370
-
-
Hodge, D.1
-
38
-
-
33646675621
-
Major erythrocyte membrane protein genes in EKLF-defcient mice
-
Nilson, D.G., Sabatino, D.E., Bodine, D.M. & Gallagher, P.G. Major erythrocyte membrane protein genes in EKLF-defcient mice. Exp. Hematol. 34, 705-712 (2006).
-
(2006)
Exp. Hematol.
, vol.34
, pp. 705-712
-
-
Nilson, D.G.1
Sabatino, D.E.2
Bodine, D.M.3
Gallagher, P.G.4
-
39
-
-
0029861514
-
Silencing of human fetal globin expression is impaired in the absence of the adult β-globin gene activator protein EKLF
-
Perkins, A.C., Gaensler, K.M. & Orkin, S.H. Silencing of human fetal globin expression is impaired in the absence of the adult β-globin gene activator protein EKLF. Proc. Natl. Acad. Sci. USA 93, 12267-12271 (1996).
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 12267-12271
-
-
Perkins, A.C.1
Gaensler, K.M.2
Orkin, S.H.3
-
40
-
-
0029829779
-
The role of EKLF in human β-globin gene competition
-
Wijgerde, M. et al. The role of EKLF in human β-globin gene competition. Genes Dev. 10, 2894-2902 (1996).
-
(1996)
Genes Dev.
, vol.10
, pp. 2894-2902
-
-
Wijgerde, M.1
-
41
-
-
0024506821
-
A dominant control region from the human β-globin gene locus conferring integration site-independent gene expression
-
Talbot, D. et al. A dominant control region from the human β-globin gene locus conferring integration site-independent gene expression. Nature 338, 352-355 (1989).
-
(1989)
Nature
, vol.338
, pp. 352-355
-
-
Talbot, D.1
-
42
-
-
40949086353
-
Non-random subcellular distribution of variant EKLF in erythroid cells
-
Quadrini, K.J., Gruzglin, E. & Bieker, J.J. Non-random subcellular distribution of variant EKLF in erythroid cells. Exp. Cell Res. 314, 1595-1604 (2008).
-
(2008)
Exp. Cell Res.
, vol.314
, pp. 1595-1604
-
-
Quadrini, K.J.1
Gruzglin, E.2
Bieker, J.J.3
-
43
-
-
5444255213
-
The active spatial organization of the β-globin locus requires the transcription factor EKLF
-
Drissen, R. et al. The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485-2490 (2004).
-
(2004)
Genes Dev.
, vol.18
, pp. 2485-2490
-
-
Drissen, R.1
-
44
-
-
34249307315
-
Nuclear organization of the genome and the potential for gene regulation
-
Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413-417 (2007).
-
(2007)
Nature
, vol.447
, pp. 413-417
-
-
Fraser, P.1
Bickmore, W.2
-
46
-
-
45749154811
-
Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription
-
Palstra, R.J. et al. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One 3, e1661 (2008).
-
(2008)
PLoS One
, vol.3
-
-
Palstra, R.J.1
-
47
-
-
0033153298
-
Structure and function of the nucleolus
-
Scheer, U. & Hock, R. Structure and function of the nucleolus. Curr. Opin. Cell Biol. 11, 385-390 (1999).
-
(1999)
Curr. Opin. Cell Biol.
, vol.11
, pp. 385-390
-
-
Scheer, U.1
Hock, R.2
-
48
-
-
0344012605
-
Nucleolar clustering of dispersed tRNA genes
-
Thompson, M., Haeusler, R.A., Good, P.D. & Engelke, D.R. Nucleolar clustering of dispersed tRNA genes. Science 302, 1399-1401 (2003).
-
(2003)
Science
, vol.302
, pp. 1399-1401
-
-
Thompson, M.1
Haeusler, R.A.2
Good, P.D.3
Engelke, D.R.4
-
49
-
-
33644770293
-
RNAi components are required for nuclear clustering of Polycomb group response elements
-
Grimaud, C. et al. RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124, 957-971 (2006).
-
(2006)
Cell
, vol.124
, pp. 957-971
-
-
Grimaud, C.1
-
50
-
-
46449119367
-
A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
-
Tiwari, V.K., Cope, L., McGarvey, K.M., Ohm, J.E. & Baylin, S.B. A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res. 18, 1171-1179 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 1171-1179
-
-
Tiwari, V.K.1
Cope, L.2
McGarvey, K.M.3
Ohm, J.E.4
Baylin, S.B.5
-
51
-
-
44149106396
-
Similar active genes cluster in specialized transcription factories
-
Xu, M. & Cook, P.R. Similar active genes cluster in specialized transcription factories. J. Cell Biol. 181, 615-623 (2008).
-
(2008)
J. Cell Biol.
, vol.181
, pp. 615-623
-
-
Xu, M.1
Cook, P.R.2
-
52
-
-
85052429852
-
Multicolor 3D fuorescence in situ hybridization for imaging interphase chromosomes
-
ed. R. Hancock Humana Press, New York
-
Cremer, M. et al. Multicolor 3D fuorescence in situ hybridization for imaging interphase chromosomes. in Methods in Molecular Biology (ed. R. Hancock) 205-239 (Humana Press, New York, 2008).
-
(2008)
Methods in Molecular Biology
, pp. 205-239
-
-
Cremer, M.1
-
54
-
-
0033602445
-
Effects of altered gene order or orientation of the locus control region on human beta-globin gene expression in mice
-
Tanimoto, K., Liu, Q., Bungert, J. & Engel, J.D. Effects of altered gene order or orientation of the locus control region on human beta-globin gene expression in mice. Nature 398, 344-348 (1999).
-
(1999)
Nature
, vol.398
, pp. 344-348
-
-
Tanimoto, K.1
Liu, Q.2
Bungert, J.3
Engel, J.D.4
-
55
-
-
0347125328
-
JASPAR: An open-access database for eukaryotic transcription factor binding profles
-
Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. & Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profles. Nucleic Acids Res. 32, D91-D94 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
56
-
-
0036677662
-
TFBS: Computational framework for transcription factor binding site analysis
-
Lenhard, B. & Wasserman, W.W. TFBS: computational framework for transcription factor binding site analysis. Bioinformatics 18, 1135-1136 (2002).
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(2002)
Bioinformatics
, vol.18
, pp. 1135-1136
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Lenhard, B.1
Wasserman, W.W.2
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