-
1
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan, N., Moore, I.K., Fondufe-Mittendorf, Y., Gossett, A.J., Tillo, D., Field, Y., LeProust, E.M., Hughes, T.R., Lieb, J.D., Widom, J. et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362-366
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
LeProust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
-
2
-
-
84862979650
-
A map of nucleosome positions in yeast at base-pair resolution
-
Brogaard, K., Xi, L., Wang, J.P. and Widom, J. (2012) A map of nucleosome positions in yeast at base-pair resolution. Nature, 486, 496-501
-
(2012)
Nature
, vol.486
, pp. 496-501
-
-
Brogaard, K.1
Xi, L.2
Wang, J.P.3
Widom, J.4
-
3
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell, S.C., Drew, H.R. and Travers, A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675
-
(1986)
J. Mol. Biol
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
4
-
-
84866536073
-
Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy
-
van der Heijden, T., van Vugt, J.J., Logie, C. and van Noort, J. (2012) Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy. Proc. Natl Acad. Sci. USA, 109, 2514-2522
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 2514-2522
-
-
Van Der Heijden, T.1
Van Vugt, J.J.2
Logie, C.3
Van Noort, J.4
-
5
-
-
0023777538
-
Statistical distributions of nucleosomes: Nonrandom locations by a stochastic mechanism
-
Kornberg, R.D. and Stryer, L. (1988) Statistical distributions of nucleosomes: Nonrandom locations by a stochastic mechanism. Nucleic Acids Res., 16, 6677-6690
-
(1988)
Nucleic Acids Res
, vol.16
, pp. 6677-6690
-
-
Kornberg, R.D.1
Stryer, L.2
-
6
-
-
76049096122
-
Nucleosome positioning by genomic excluding-energy barriers
-
Milani, P., Chevereau, G., Vaillant, C., Audit, B., Haftek-Terreau, Z., Marilley, M. and Bouvet, P. (2009) Nucleosome positioning by genomic excluding-energy barriers. Proc. Natl Acad. Sci. USA, 106, 22257-22262
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 22257-22262
-
-
Milani, P.1
Chevereau, G.2
Vaillant, C.3
Audit, B.4
Haftek-Terreau, Z.5
Marilley, M.6
Bouvet, P.7
-
7
-
-
79956316470
-
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
-
Zhang, Z., Wippo, C.J., Wal, M., Ward, E., Korber, P. and Pugh, B.F. (2011) A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science, 332, 977-980
-
(2011)
Science
, vol.332
, pp. 977-980
-
-
Zhang, Z.1
Wippo, C.J.2
Wal, M.3
Ward, E.4
Korber, P.5
Pugh, B.F.6
-
8
-
-
80054693934
-
Genome-wide 'Re'-modeling of nucleosome positions
-
Sadeh, R. and Allis, C.D. (2011) Genome-wide 'Re'-modeling of nucleosome positions. Cell, 147, 263-266
-
(2011)
Cell
, vol.147
, pp. 263-266
-
-
Sadeh, R.1
Allis, C.D.2
-
9
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
Mavrich, T.N., Ioshikhes, I.P., Venters, B.J., Jiang, C., Tomsho, L.P., Qi, J., Schuster, S.C., Albert, I. and Pugh, B.F. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res., 18, 1073-1083
-
(2008)
Genome Res
, vol.18
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
Jiang, C.4
Tomsho, L.P.5
Qi, J.6
Schuster, S.C.7
Albert, I.8
Pugh, B.F.9
-
10
-
-
84891754033
-
New insights into two distinct nucleosome distributions: Comparison of cross-platform positioning datasets in the yeast genome
-
Feng, J., Dai, X., Xiang, Q., Dai, Z., Wang, J., Deng, Y. and He, C. (2010) New insights into two distinct nucleosome distributions: Comparison of cross-platform positioning datasets in the yeast genome. BMC Genomics, 33, 1-19
-
(2010)
BMC Genomics
, vol.33
, pp. 1-19
-
-
Feng, J.1
Dai, X.2
Xiang, Q.3
Dai, Z.4
Wang, J.5
Deng, Y.6
He, C.7
-
11
-
-
74949084972
-
A novel strategy of transcription regulation by intragenic nucleosome ordering
-
Vaillant, C., Palmeira, L., Chevereau, G., Audit, B., d'Aubenton Carafa, Y., Thermes, C. and Arneodo, A. (2010) A novel strategy of transcription regulation by intragenic nucleosome ordering. Genome Res., 20, 59-67
-
(2010)
Genome Res
, Issue.20
, pp. 59-67
-
-
Vaillant, C.1
Palmeira, L.2
Chevereau, G.3
Audit, B.4
D'Aubenton Carafa, Y.5
Thermes, C.6
Arneodo, A.7
-
12
-
-
70350751572
-
Thermodynamics of Intragenic Nucleosome Ordering
-
Chevereau, G., Palmeira, L., Thermes, C., Arneodo, A. and Vaillant, C. (2009) Thermodynamics of Intragenic Nucleosome Ordering. Phys. Rev. Lett., 103, 188103
-
(2009)
Phys. Rev. Lett
, vol.103
, pp. 188103
-
-
Chevereau, G.1
Palmeira, L.2
Thermes, C.3
Arneodo, A.4
Vaillant, C.5
-
13
-
-
78049434489
-
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- And downstream of transcription start sites
-
Möbius, W. and Gerland, U. (2010) Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- And Downstream of Transcription Start Sites. PLoS Comput. Biol., 6, 1-11
-
(2010)
PLoS Comput. Biol
, Issue.6
, pp. 1-11
-
-
Möbius, W.1
Gerland, U.2
-
14
-
-
84858062269
-
Nucleosome positioning and nucleosome stacking: Two faces of the same coin
-
Riposo, J. and Mozziconacci, J. (2012) Nucleosome positioning and nucleosome stacking: Two faces of the same coin. Mol. Biosyst., 8, 1172-1178
-
(2012)
Mol. Biosyst
, Issue.8
, pp. 1172-1178
-
-
Riposo, J.1
Mozziconacci, J.2
-
15
-
-
33846804071
-
Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics
-
Yan, J., Maresca, T.J., Skoko, D., Adams, C.D., Xiao, B., Christensen, M.O., Heald, R. and Marko, J.F. (2007) Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics. Mol. Biol. Cell, 18, 464-474
-
(2007)
Mol. Biol. Cell
, vol.18
, pp. 464-474
-
-
Yan, J.1
Maresca, T.J.2
Skoko, D.3
Adams, C.D.4
Xiao, B.5
Christensen, M.O.6
Heald, R.7
Marko, J.F.8
-
16
-
-
84867574713
-
Kinetics and thermodynamics of phenotype: Unwinding and rewinding the nucleosome
-
Mack, A.H., Schlingman, D.J., Ilagan, R.P., Regan, L. and Mochrie, S.G.J. (2012) Kinetics and thermodynamics of phenotype: Unwinding and rewinding the nucleosome. J. Mol. Biol., 423, 687-701
-
(2012)
J. Mol. Biol
, Issue.423
, pp. 687-701
-
-
Mack, A.H.1
Schlingman, D.J.2
Ilagan, R.P.3
Regan, L.4
Mochrie, S.G.J.5
-
17
-
-
79956351217
-
Nucleosome positioning in a model of active chromatin remodeling enzymes
-
Padinhateeri, R. and Marko, J.F. (2011) Nucleosome positioning in a model of active chromatin remodeling enzymes. Proc. Natl Acad. Sci. USA, 108, 7799-7803
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 7799-7803
-
-
Padinhateeri, R.1
Marko, J.F.2
-
18
-
-
84866338436
-
Kinetic control of nucleosome displacement by ISWI/ACF chromatin remodelers
-
Florescu, A.M., Schiessel, H. and Blossey, R. (2012) Kinetic control of nucleosome displacement by ISWI/ACF chromatin remodelers. Phys. Rev. Lett., 109, 118103
-
(2012)
Phys. Rev. Lett
, vol.109
, pp. 118103
-
-
Florescu, A.M.1
Schiessel, H.2
Blossey, R.3
-
19
-
-
73049098277
-
Predicting nucleosome positions on the DNA: Combining intrinsic sequence preferences and remodeler activities
-
Teif, V.B. and Rippe, K. (2009) Predicting nucleosome positions on the DNA: Combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res., 37, 5641-5655
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 5641-5655
-
-
Teif, V.B.1
Rippe, K.2
-
20
-
-
84859371878
-
Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution
-
Korber, P. (2012) Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution. Biochem. Soc. Trans., 40, 377-82
-
(2012)
Biochem. Soc. Trans
, Issue.40
, pp. 377-382
-
-
Korber, P.1
-
21
-
-
84862984796
-
Manipulating nucleosome disfavoring sequences allows fine-Tune regulation of gene expression in yeast
-
Raveh-Sadka, T., Levo, M., Shabi, U., Shany, B., Keren, L., Lotan- Pompan, M., Zeevi, D., Sharon, E., Weinberger, A. and Segal, E. (2012) Manipulating nucleosome disfavoring sequences allows fine-Tune regulation of gene expression in yeast. Nat. Genet., 44, 743-750
-
(2012)
Nat. Genet
, Issue.44
, pp. 743-750
-
-
Raveh-Sadka, T.1
Levo, M.2
Shabi, U.3
Shany, B.4
Keren, L.5
Lotan- Pompan, M.6
Zeevi, D.7
Sharon, E.8
Weinberger, A.9
Segal, E.10
-
22
-
-
79953797454
-
An effect of DNA sequence on nucleosome occupancy and removal
-
Wang, X., Bryant, G.O., Floer, M., Spagna, D. and Ptashne, M. (2011) An effect of DNA sequence on nucleosome occupancy and removal. Nat. Struct. Mol. Biol., 18, 507-509
-
(2011)
Nat. Struct. Mol. Biol
, Issue.18
, pp. 507-509
-
-
Wang, X.1
Bryant, G.O.2
Floer, M.3
Spagna, D.4
Ptashne, M.5
-
23
-
-
84861371523
-
Nucleosome stability dramatically impacts the targeting of somatic hypermutation
-
Kodgire, P., Mukkawar, P., North, J.A., Poirier, M.G. and Storb, U. (2012) Nucleosome stability dramatically impacts the targeting of somatic hypermutation. Mol. Cell. Biol., 32, 2030-2040
-
(2012)
Mol. Cell. Biol
, Issue.32
, pp. 2030-2040
-
-
Kodgire, P.1
Mukkawar, P.2
North, J.A.3
Poirier, M.G.4
Storb, U.5
-
24
-
-
0026079369
-
Stepwise assembly of chromatin during DNA replication in vitro
-
Smith, S. and Stillman, B. (1991) Stepwise assembly of chromatin during DNA replication in vitro. EMBO J., 10, 971-980
-
(1991)
EMBO J.
, vol.10
, pp. 971-980
-
-
Smith, S.1
Stillman, B.2
-
25
-
-
33847076248
-
Chromatin challenges during DNA replication and repair
-
Groth, A., Rocha, W., Verreault, A. and Almouzni, G. (2007) Chromatin challenges during DNA replication and repair. Cell, 128, 721-33
-
(2007)
Cell
, vol.128
, pp. 721-733
-
-
Groth, A.1
Rocha, W.2
Verreault, A.3
Almouzni, G.4
-
26
-
-
33644753839
-
Chromatin remodeling by nucleosome disassembly in vitro
-
Lorch, Y., Maier-Davis, B. and Kornberg, R.D. (2006) Chromatin remodeling by nucleosome disassembly in vitro. Proc. Natl Acad. Sci. USA, 103, 3090-3093
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 3090-3093
-
-
Lorch, Y.1
Maier-Davis, B.2
Kornberg, R.D.3
-
27
-
-
33845356072
-
The chromatin-remodeling enzyme ACF is an ATPdependent DNA length sensor that regulates nucleosome spacing
-
Yang, J.G., Madrid, T.S., Sevastopoulos, E. and Narlikar, G.J. (2006) The chromatin-remodeling enzyme ACF is an ATPdependent DNA length sensor that regulates nucleosome spacing. Nat. Struct. Mol. Biol., 13, 1078-1083
-
(2006)
Nat. Struct. Mol. Biol
, vol.13
, pp. 1078-1083
-
-
Yang, J.G.1
Madrid, T.S.2
Sevastopoulos, E.3
Narlikar, G.J.4
-
28
-
-
33745221438
-
Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes
-
Stockdale, C., Flaus, A., Ferreira, H. and Owen-Hughes, T. (2006) Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J. Biol. Chem., 281, 16279-16288
-
(2006)
J. Biol. Chem
, vol.281
, pp. 16279-16288
-
-
Stockdale, C.1
Flaus, A.2
Ferreira, H.3
Owen-Hughes, T.4
-
29
-
-
79955950854
-
Multiple sequencespecific factors generate the nucleosome-depleted region on CLN2 Promoter
-
Bai, L., Ondracka, A. and Cross, F.R. (2011) Multiple sequencespecific factors generate the nucleosome-depleted region on CLN2 Promoter. Mol. Cell, 42, 465-476
-
(2011)
Mol. Cell
, vol.42
, pp. 465-476
-
-
Bai, L.1
Ondracka, A.2
Cross, F.R.3
-
30
-
-
0029026719
-
Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
-
Iyer, V. and Struhl, K. (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J., 14, 2570-2579
-
(1995)
EMBO J.
, vol.14
, pp. 2570-2579
-
-
Iyer, V.1
Struhl, K.2
-
31
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie, D.T. (1977) Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81, 2340-2361
-
(1977)
J. Phys. Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
32
-
-
35348910082
-
Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts
-
Padinhateeri, R., Yan, J. and Marko, J.F. (2007) Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts. Proc. Natl Acad. Sci. USA, 104, 13649-13654
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 13649-13654
-
-
Padinhateeri, R.1
Yan, J.2
Marko, J.F.3
-
33
-
-
33750449330
-
Effect of force on mononucleosomal dynamics
-
Mihardja, S., Spakowitz, A.J., Zhang, Y. and Bustamante, C. (2006) Effect of force on mononucleosomal dynamics. Proc. Natl Acad. Sci. USA, 103, 15871-15876
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 15871-15876
-
-
Mihardja, S.1
Spakowitz, A.J.2
Zhang, Y.3
Bustamante, C.4
-
34
-
-
72949099482
-
The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes
-
Racki, L.R., Yang, J.G., Naber, N., Partensky, P.D., Acevedo, A., Purcell, T.J., Cooke, R., Cheng, Y. and Narlikar, G.J. (2009) The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature, 462, 1016-1021
-
(2009)
Nature
, vol.462
, pp. 1016-1021
-
-
Racki, L.R.1
Yang, J.G.2
Naber, N.3
Partensky, P.D.4
Acevedo, A.5
Purcell, T.J.6
Cooke, R.7
Cheng, Y.8
Narlikar, G.J.9
-
35
-
-
44949087512
-
Nucleosome switches
-
Schwab, D.J., Bruinsma, R.F., Rudnick, J. and Widom, J. (2008) Nucleosome switches. Phys. Rev. Lett., 100, 228105
-
(2008)
Phys. Rev. Lett
, vol.100
, pp. 228105
-
-
Schwab, D.J.1
Bruinsma, R.F.2
Rudnick, J.3
Widom, J.4
-
36
-
-
77954691462
-
Illuminating eukaryotic transcription start sites
-
Stamatoyannopoulos, J.A. (2010) Illuminating eukaryotic transcription start sites. Nat. Methods, 7, 501-503
-
(2010)
Nat. Methods
, vol.7
, pp. 501-503
-
-
Stamatoyannopoulos, J.A.1
-
37
-
-
33744824906
-
Evolutionary turnover of mammalian transcription start sites
-
Frith, M.C., Ponjavic, J., Fredman, D., Kai, C., Kawai, J., Carninci, P., Hayshizaki, Y. and Sandelin, A. (2006) Evolutionary turnover of mammalian transcription start sites. Genome Res., 16, 713-722
-
(2006)
Genome Res
, vol.16
, pp. 713-722
-
-
Frith, M.C.1
Ponjavic, J.2
Fredman, D.3
Kai, C.4
Kawai, J.5
Carninci, P.6
Hayshizaki, Y.7
Sandelin, A.8
-
38
-
-
80053140931
-
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
-
Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., Workman, J.L., Barton, G.J. and Owen-Hughes, T. (2011) A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science, 333, 1758-1760
-
(2011)
Science
, vol.333
, pp. 1758-1760
-
-
Gkikopoulos, T.1
Schofield, P.2
Singh, V.3
Pinskaya, M.4
Mellor, J.5
Smolle, M.6
Workman, J.L.7
Barton, G.J.8
Owen-Hughes, T.9
-
39
-
-
68249142923
-
Intrinsic histone- DNA interactions are not the major determinant of nucleosome positions in vivo
-
Zhang, Y., Moqtaderi, Z., Rattner, B.P., Euskirchen, G., Snyder, M., Kadonaga, J.T., Liu, X.S. and Struhl, K. (2009) Intrinsic histone- DNA interactions are not the major determinant of nucleosome positions in vivo. Nat. Struct. Mol. Biol., 16, 847-852
-
(2009)
Nat. Struct. Mol. Biol
, vol.16
, pp. 847-852
-
-
Zhang, Y.1
Moqtaderi, Z.2
Rattner, B.P.3
Euskirchen, G.4
Snyder, M.5
Kadonaga, J.T.6
Liu, X.S.7
Struhl, K.8
-
40
-
-
79953775721
-
The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes
-
Wippo, C.J., Israel, L., Watanabe, S., Hochheimer, A., Peterson, C.L. and Korber, P. (2011) The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J., 30, 1277-1288
-
(2011)
EMBO J.
, Issue.30
, pp. 1277-1288
-
-
Wippo, C.J.1
Israel, L.2
Watanabe, S.3
Hochheimer, A.4
Peterson, C.L.5
Korber, P.6
-
41
-
-
70349173215
-
Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome
-
Koerber, R.T., Rhee, H.S., Jiang, C. and Pugh, B.F. (2009) Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol. Cell, 35, 889-902
-
(2009)
Mol. Cell
, vol.35
, pp. 889-902
-
-
Koerber, R.T.1
Rhee, H.S.2
Jiang, C.3
Pugh, B.F.4
-
42
-
-
2942685818
-
Dynamics of molecular motors and polymer translocation with sequence heterogeneity
-
Kafri, Y., Lubensky, D.K. and Nelson, D.R. (2004) Dynamics of molecular motors and polymer translocation with sequence heterogeneity. Biophys. J., 86, 3373-3391
-
(2004)
Biophys. J.
, vol.86
, pp. 3373-3391
-
-
Kafri, Y.1
Lubensky, D.K.2
Nelson, D.R.3
-
43
-
-
0000783134
-
Model for density variation at a fluid surface
-
Percus, J.K. (1976) Model for density variation at a fluid surface. J. Stat. Phys., 15, 423-435
-
(1976)
J. Stat. Phys
, vol.15
, pp. 423-435
-
-
Percus, J.K.1
-
44
-
-
20144384163
-
Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE
-
Zhang, Z and Dietrich, F.S. (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res., 33, 2838-2851
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2838-2851
-
-
Zhang, Z.1
Dietrich, F.S.2
|