-
1
-
-
70249121045
-
The logic of chromatin architecture and remodelling at promoters
-
Cairns, B.R. The logic of chromatin architecture and remodelling at promoters. Nature 461, 193-198 (2009).
-
(2009)
Nature
, vol.461
, pp. 193-198
-
-
Cairns, B.R.1
-
2
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
Mavrich, T.N. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358-362 (2008).
-
(2008)
Nature
, vol.453
, pp. 358-362
-
-
Mavrich, T.N.1
-
3
-
-
78651477233
-
High-resolution genome-wide mapping of the primary structure of chromatin
-
Zhang, Z. & Pugh, B.F. High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144, 175-186 (2011).
-
(2011)
Cell
, vol.144
, pp. 175-186
-
-
Zhang, Z.1
Pugh, B.F.2
-
4
-
-
0026629273
-
Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates
-
Izban, M.G. & Luse, D.S. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267, 13647-13655 (1992).
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 13647-13655
-
-
Izban, M.G.1
Luse, D.S.2
-
5
-
-
0023663417
-
Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones
-
Lorch, Y., LaPointe, J.W. & Kornberg, R.D. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49, 203-210 (1987).
-
(1987)
Cell
, vol.49
, pp. 203-210
-
-
Lorch, Y.1
Lapointe, J.W.2
Kornberg, R.D.3
-
6
-
-
0018115860
-
Transcription of nucleosomes from human chromatin
-
Shaw, P.A., Sahasrabuddhe, C.G., Hodo, H.G. & Saunders, G.F. Transcription of nucleosomes from human chromatin. Nucleic Acids Res. 5, 2999-3012 (1978).
-
(1978)
Nucleic Acids Res.
, vol.5
, pp. 2999-3012
-
-
Shaw, P.A.1
Sahasrabuddhe, C.G.2
Hodo, H.G.3
Saunders, G.F.4
-
7
-
-
0023790970
-
Supercoiling of intracellular DNA can occur in eukaryotic cells
-
Giaever, G.N. & Wang, J.C. Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell 55, 849-856 (1988).
-
(1988)
Cell
, vol.55
, pp. 849-856
-
-
Giaever, G.N.1
Wang, J.C.2
-
8
-
-
0023433855
-
Supercoiling of the DNA template during transcription
-
Liu, L.F. & Wang, J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024-7027 (1987).
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 7024-7027
-
-
Liu, L.F.1
Wang, J.C.2
-
9
-
-
0030901608
-
Measurement of unrestrained negative supercoiling and topological domain size in living human cells
-
Kramer, P.R. & Sinden, R.R. Measurement of unrestrained negative supercoiling and topological domain size in living human cells. Biochemistry 36, 3151-3158 (1997).
-
(1997)
Biochemistry
, vol.36
, pp. 3151-3158
-
-
Kramer, P.R.1
Sinden, R.R.2
-
10
-
-
4444234129
-
Visualization of unconstrained negative supercoils of DNA on polytene chromosomes of Drosophila
-
Matsumoto, K. & Hirose, S. Visualization of unconstrained negative supercoils of DNA on polytene chromosomes of Drosophila. J. Cell Sci. 117, 3797-3805 (2004).
-
(2004)
J. Cell Sci.
, vol.117
, pp. 3797-3805
-
-
Matsumoto, K.1
Hirose, S.2
-
11
-
-
78049363149
-
A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
-
Bermúdez, I., García-Martínez, J., Pérez-Ortín, J.E. & Roca, J. A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding. Nucleic Acids Res. 38, e182 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Bermúdez, I.1
García-Martínez, J.2
Pérez- Ortín, J.E.3
Roca, J.4
-
12
-
-
84875185055
-
Transcription-dependent dynamic supercoiling is a short-range genomic force
-
Kouzine, F. et al. Transcription-dependent dynamic supercoiling is a short-range genomic force. Nat. Struct. Mol. Biol. 20, 396-403 (2013).
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 396-403
-
-
Kouzine, F.1
-
13
-
-
84875134984
-
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
-
Naughton, C. et al. Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures. Nat. Struct. Mol. Biol. 20, 387-395 (2013).
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 387-395
-
-
Naughton, C.1
-
14
-
-
73449148377
-
Nucleosome assembly depends on the torsion in the dna molecule: A magnetic tweezers study
-
Gupta, P., Zlatanova, J. & Tomschik, M. Nucleosome assembly depends on the torsion in the dna molecule: a magnetic tweezers study. Biophys. J. 97, 3150-3157 (2009).
-
(2009)
Biophys. J.
, vol.97
, pp. 3150-3157
-
-
Gupta, P.1
Zlatanova, J.2
Tomschik, M.3
-
15
-
-
84878732407
-
Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin
-
Pang, B. et al. Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin. Nat. Commun. 4, 1908 (2013).
-
(1908)
Nat. Commun.
, vol.4
, pp. 2013
-
-
Pang, B.1
-
16
-
-
84877585708
-
Doxorubicin enhances nucleosome turnover around promoters
-
Yang, F., Kemp, C.J. & Henikoff, S. Doxorubicin enhances nucleosome turnover around promoters. Curr. Biol. 23, 782-787 (2013).
-
(2013)
Curr. Biol.
, vol.23
, pp. 782-787
-
-
Yang, F.1
Kemp, C.J.2
Henikoff, S.3
-
17
-
-
81055141350
-
Epigenome characterization at single base-pair resolution
-
Henikoff, J.G., Belsky, J.A., Krassovsky, K., MacAlpine, D.M. & Henikoff, S. Epigenome characterization at single base-pair resolution. Proc. Natl. Acad. Sci. USA 108, 18318-18323 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 18318-18323
-
-
Henikoff, J.G.1
Belsky, J.A.2
Krassovsky, K.3
Macalpine, D.M.4
Henikoff, S.5
-
18
-
-
67149086996
-
Extensive demethylation of repetitive elements during seed development underlies gene imprinting
-
Gehring, M., Bubb, K.L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447-1451 (2009).
-
(2009)
Science
, vol.324
, pp. 1447-1451
-
-
Gehring, M.1
Bubb, K.L.2
Henikoff, S.3
-
19
-
-
0028966004
-
Specialized chromatin structure domain boundary elements fanking a Drosophila heat shock gene locus are under torsional strain in vivo
-
Jupe, E.R., Sinden, R.R. & Cartwright, I.L. Specialized chromatin structure domain boundary elements fanking a Drosophila heat shock gene locus are under torsional strain in vivo. Biochemistry 34, 2628-2633 (1995).
-
(1995)
Biochemistry
, vol.34
, pp. 2628-2633
-
-
Jupe, E.R.1
Sinden, R.R.2
Cartwright, I.L.3
-
20
-
-
0027409470
-
Stably maintained microdomain of localized unrestrained supercoiling at a Drosophila heat shock gene locus
-
Jupe, E.R., Sinden, R.R. & Cartwright, I.L. Stably maintained microdomain of localized unrestrained supercoiling at a Drosophila heat shock gene locus. EMBO J. 12, 1067-1075 (1993).
-
(1993)
EMBO J.
, vol.12
, pp. 1067-1075
-
-
Jupe, E.R.1
Sinden, R.R.2
Cartwright, I.L.3
-
21
-
-
81055135515
-
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide
-
Teves, S.S. & Henikoff, S. Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 25, 2387-2397 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 2387-2397
-
-
Teves, S.S.1
Henikoff, S.2
-
22
-
-
77954957199
-
Topoisomerase i regulates open chromatin and controls gene expression in vivo
-
Durand-Dubief, M.l., Persson, J., Norman, U., Hartsuiker, E. & Ekwall, K. Topoisomerase I regulates open chromatin and controls gene expression in vivo. EMBO J. 29, 2126-2134 (2010).
-
(2010)
EMBO J.
, vol.29
, pp. 2126-2134
-
-
Durand-Dubief, M.L.1
Persson, J.2
Norman, U.3
Hartsuiker, E.4
Ekwall, K.5
-
23
-
-
79961225321
-
Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase i to enhance recruitment of RNA Pol II in budding yeast
-
Sperling, A.S., Jeong, K.S., Kitada, T. & Grunstein, M. Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast. Proc. Natl. Acad. Sci. USA 108, 12693-12698 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 12693-12698
-
-
Sperling, A.S.1
Jeong, K.S.2
Kitada, T.3
Grunstein, M.4
-
24
-
-
0018936893
-
DNA-protein interactions in the Drosophila melanogaster mitochondrial genome as deduced from trimethylpsoralen crosslinking patterns
-
Potter, D.A., Fostel, J.M., Berninger, M., Pardue, M.L. & Cech, T.R. DNA-protein interactions in the Drosophila melanogaster mitochondrial genome as deduced from trimethylpsoralen crosslinking patterns. Proc. Natl. Acad. Sci. USA 77, 4118-4122 (1980).
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 4118-4122
-
-
Potter, D.A.1
Fostel, J.M.2
Berninger, M.3
Pardue, M.L.4
Cech, T.R.5
-
25
-
-
79952470122
-
Transcriptional inhibition by DNA torsional stress
-
Roca, J. Transcriptional inhibition by DNA torsional stress. Transcription 2, 82-85 (2011).
-
(2011)
Transcription
, vol.2
, pp. 82-85
-
-
Roca, J.1
-
26
-
-
78649884849
-
H2A.Z nucleosomes enriched over active genes are homotypic
-
Weber, C.M., Henikoff, J.G. & Henikoff, S. H2A.Z nucleosomes enriched over active genes are homotypic. Nat. Struct. Mol. Biol. 17, 1500-1507 (2010).
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 1500-1507
-
-
Weber, C.M.1
Henikoff, J.G.2
Henikoff, S.3
-
27
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core, L.J., Waterfall, J.J. & Lis, J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
28
-
-
78149477660
-
Pausing of RNA polymerase II disrupts DNA-specifed nucleosome organization to enable precise gene regulation
-
Gilchrist, D.A. et al. Pausing of RNA polymerase II disrupts DNA-specifed nucleosome organization to enable precise gene regulation. Cell 143, 540-551 (2010).
-
(2010)
Cell
, vol.143
, pp. 540-551
-
-
Gilchrist, D.A.1
-
29
-
-
0026049391
-
RNA polymerase II pauses at the 5′ end of the transcriptionally induced Drosophila hsp70 gene
-
O'Brien, T. & Lis, J.T. RNA polymerase II pauses at the 5′ end of the transcriptionally induced Drosophila hsp70 gene. Mol. Cell. Biol. 11, 5285-5290 (1991).
-
(1991)
Mol. Cell. Biol.
, vol.11
, pp. 5285-5290
-
-
O'Brien, T.1
Lis, J.T.2
-
30
-
-
0035019156
-
Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells
-
Wysocka, J., Reilly, P.T. & Herr, W. Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells. Mol. Cell. Biol. 21, 3820-3829 (2001).
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 3820-3829
-
-
Wysocka, J.1
Reilly, P.T.2
Herr, W.3
-
31
-
-
74549132843
-
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
-
Nechaev, S. et al. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327, 335-338 (2010).
-
(2010)
Science
, vol.327
, pp. 335-338
-
-
Nechaev, S.1
-
32
-
-
0346414510
-
Localization of RNA polymerase in polytene chromosomes of Drosophila melanogaster
-
Jamrich, M., Greenleaf, A.L. & Bautz, E.K. Localization of RNA polymerase in polytene chromosomes of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 74, 2079-2083 (1977).
-
(1977)
Proc. Natl. Acad. Sci. USA
, vol.74
, pp. 2079-2083
-
-
Jamrich, M.1
Greenleaf, A.L.2
Bautz, E.K.3
-
33
-
-
33747072028
-
Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling
-
Tenney, K. et al. Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling. Proc. Natl. Acad. Sci. USA 103, 11970-11974 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 11970-11974
-
-
Tenney, K.1
-
34
-
-
0030013733
-
Effect of differential gene expression on the chromatin structure of the DHFR gene domain in vivo
-
Ljungman, M. Effect of differential gene expression on the chromatin structure of the DHFR gene domain in vivo. Biochim. Biophys. Acta 1307, 171-177 (1996).
-
(1996)
Biochim. Biophys. Acta
, vol.1307
, pp. 171-177
-
-
Ljungman, M.1
-
35
-
-
74949123158
-
DNA topoisomerase i inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1 gene locus
-
Baranello, L., Bertozzi, D., Fogli, M.V., Pommier, Y. & Capranico, G. DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1 gene locus. Nucleic Acids Res. 38, 159-171 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 159-171
-
-
Baranello, L.1
Bertozzi, D.2
Fogli, M.V.3
Pommier, Y.4
Capranico, G.5
-
36
-
-
61849170193
-
Genome-wide profling of salt fractions maps physical properties of chromatin
-
Henikoff, S., Henikoff, J.G., Sakai, A., Loeb, G.B. & Ahmad, K. Genome-wide profling of salt fractions maps physical properties of chromatin. Genome Res. 19, 460-469 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 460-469
-
-
Henikoff, S.1
Henikoff, J.G.2
Sakai, A.3
Loeb, G.B.4
Ahmad, K.5
-
37
-
-
0018161110
-
Fractionation of nucleosomes by salt elution from micrococcal nuclease-digested nuclei
-
Sanders, M.M. Fractionation of nucleosomes by salt elution from micrococcal nuclease-digested nuclei. J. Cell Biol. 79, 97-109 (1978).
-
(1978)
J. Cell Biol.
, vol.79
, pp. 97-109
-
-
Sanders, M.M.1
-
38
-
-
0025939524
-
Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes
-
Lee, M.S. & Garrard, W.T. Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes. Proc. Natl. Acad. Sci. USA 88, 9675-9679 (1991).
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 9675-9679
-
-
Lee, M.S.1
Garrard, W.T.2
-
39
-
-
77952996319
-
Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones
-
Deal, R.B., Henikoff, J.G. & Henikoff, S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328, 1161-1164 (2010).
-
(2010)
Science
, vol.328
, pp. 1161-1164
-
-
Deal, R.B.1
Henikoff, J.G.2
Henikoff, S.3
-
40
-
-
57849140661
-
Divergent transcription from active promoters
-
Seila, A.C. et al. Divergent transcription from active promoters. Science 322, 1849-1851 (2008).
-
(2008)
Science
, vol.322
, pp. 1849-1851
-
-
Seila, A.C.1
-
41
-
-
79952481593
-
Topoisomerases chromatin and transcription termination
-
Durand-Dubief, M., Svensson, J.P., Persson, J. & Ekwall, K. Topoisomerases, chromatin and transcription termination. Transcription 2, 66-70 (2011).
-
(2011)
Transcription
, vol.2
, pp. 66-70
-
-
Durand-Dubief, M.1
Svensson, J.P.2
Persson, J.3
Ekwall, K.4
-
42
-
-
0022651277
-
In vivo localization of DNA topoisomerase II cleavage sites on Drosophila heat shock chromatin
-
Rowe, T.C., Wang, J.C. & Liu, L.F. In vivo localization of DNA topoisomerase II cleavage sites on Drosophila heat shock chromatin. Mol. Cell. Biol. 6, 985-992 (1986).
-
(1986)
Mol. Cell. Biol.
, vol.6
, pp. 985-992
-
-
Rowe, T.C.1
Wang, J.C.2
Liu, L.F.3
-
43
-
-
0023639882
-
DNA topoisomerase activity is required as a swivel for DNA replication and for ribosomal RNA transcription
-
Brill, S.J., DiNardo, S., Voelkel-Meiman, K. & Sternglanz, R. DNA topoisomerase activity is required as a swivel for DNA replication and for ribosomal RNA transcription. NCI Monogr. 11-15 (1987).
-
(1987)
NCI Monogr
, pp. 11-15
-
-
Brill, S.J.1
Dinardo, S.2
Voelkel-Meiman, K.3
Sternglanz, R.4
-
44
-
-
0022067647
-
Eukaryotic type i topoisomerase is enriched in the nucleolus and catalytically active on ribosomal DNA
-
Muller, M.T., Pfund, W.P., Mehta, V.B. & Trask, D.K. Eukaryotic type I topoisomerase is enriched in the nucleolus and catalytically active on ribosomal DNA. EMBO J. 4, 1237-1243 (1985).
-
(1985)
EMBO J.
, vol.4
, pp. 1237-1243
-
-
Muller, M.T.1
Pfund, W.P.2
Mehta, V.B.3
Trask, D.K.4
-
45
-
-
0025335205
-
Camptothecin-stabilized topoisomerase I-DNA adducts cause premature termination of transcription
-
Bendixen, C., Thomsen, B., Alsner, J. & Westergaard, O. Camptothecin-stabilized topoisomerase I-DNA adducts cause premature termination of transcription. Biochemistry 29, 5613-5619 (1990).
-
(1990)
Biochemistry
, vol.29
, pp. 5613-5619
-
-
Bendixen, C.1
Thomsen, B.2
Alsner, J.3
Westergaard, O.4
-
46
-
-
0035200324
-
Transcriptional consequences of topoisomerase inhibition
-
Collins, I., Weber, A. & Levens, D. Transcriptional consequences of topoisomerase inhibition. Mol. Cell. Biol. 21, 8437-8451 (2001).
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 8437-8451
-
-
Collins, I.1
Weber, A.2
Levens, D.3
-
47
-
-
0027138674
-
Identifcation of human DNA topoisomerase i as a cofactor for activator-dependent transcription by RNA polymerase II
-
Kretzschmar, M., Meisterernst, M. & Roeder, R.G. Identifcation of human DNA topoisomerase I as a cofactor for activator-dependent transcription by RNA polymerase II. Proc. Natl. Acad. Sci. USA 90, 11508-11512 (1993).
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 11508-11512
-
-
Kretzschmar, M.1
Meisterernst, M.2
Roeder, R.G.3
-
48
-
-
0027186443
-
DNA topoisomerase i is involved in both repression and activation of transcription
-
Merino, A., Madden, K.R., Lane, W.S., Champoux, J.J. & Reinberg, D. DNA topoisomerase I is involved in both repression and activation of transcription. Nature 365, 227-232 (1993).
-
(1993)
Nature
, vol.365
, pp. 227-232
-
-
Merino, A.1
Madden, K.R.2
Lane, W.S.3
Champoux, J.J.4
Reinberg, D.5
-
49
-
-
36549061004
-
RNA polymerase is poised for activation across the genome
-
Muse, G.W. et al. RNA polymerase is poised for activation across the genome. Nat. Genet. 39, 1507-1511 (2007).
-
(2007)
Nat. Genet.
, vol.39
, pp. 1507-1511
-
-
Muse, G.W.1
-
50
-
-
77749306483
-
Transcription within condensed chromatin: Steric hindrance facilitates elongation
-
Bécavin, C., Barbi, M., Victor, J.-M. & Lesne, A. Transcription within condensed chromatin: steric hindrance facilitates elongation. Biophys. J. 98, 824-833 (2010).
-
(2010)
Biophys. J.
, vol.98
, pp. 824-833
-
-
Bécavin, C.1
Barbi, M.2
Victor, J.-M.3
Lesne, A.4
-
51
-
-
84867229716
-
Dynamics of DNA supercoils
-
van Loenhout, M.T.J., de Grunt, M.V. & Dekker, C. Dynamics of DNA supercoils. Science 338, 94-97 (2012).
-
(2012)
Science
, vol.338
, pp. 94-97
-
-
Van Loenhout, M.T.J.1
De Grunt, M.V.2
Dekker, C.3
-
52
-
-
46149108345
-
Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci
-
Petesch, S.J. & Lis, J.T. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 134, 74-84 (2008).
-
(2008)
Cell
, vol.134
, pp. 74-84
-
-
Petesch, S.J.1
Lis, J.T.2
|