-
1
-
-
0034999881
-
Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites
-
Anderson, J. D., and J. Widom, 2001 Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol. Cell. Biol. 21: 3830-3839.
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 3830-3839
-
-
Anderson, J.D.1
Widom, J.2
-
2
-
-
34548737128
-
Chd1 and yFACT act in opposition in regulating transcription
-
Biswas, D., R. Dutta-Biswas, and D. J. Stillman, 2007 Chd1 and yFACT act in opposition in regulating transcription. Mol. Cell. Biol. 27: 6279-6287.
-
(2007)
Mol. Cell. Biol.
, vol.27
, pp. 6279-6287
-
-
Biswas, D.1
Dutta-Biswas, R.2
Stillman, D.J.3
-
3
-
-
70449723345
-
Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF
-
Bouazoune, K., T. B. Miranda, P. A. Jones, and R. E. Kingston, 2009 Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF. Nucleic Acids Res. 37: 5279-5294.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5279-5294
-
-
Bouazoune, K.1
Miranda, T.B.2
Jones, P.A.3
Kingston, R.E.4
-
4
-
-
67650725820
-
The biology of chromatin remodeling complexes
-
Clapier, C. R., and B. R. Cairns, 2009 The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78: 273-304.
-
(2009)
Annu. Rev. Biochem.
, vol.78
, pp. 273-304
-
-
Clapier, C.R.1
Cairns, B.R.2
-
5
-
-
0022230224
-
DNA bending and its relation to nucleosome positioning
-
Drew, H. R., and A. A. Travers, 1985 DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186: 773-790.
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 773-790
-
-
Drew, H.R.1
Travers, A.A.2
-
6
-
-
29244449333
-
Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation
-
Fan, Y., T. Nikitina, J. Zhao, T. J. Fleury, R. Bhattacharyya et al., 2005 Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123: 1199-1212.
-
(2005)
Cell
, vol.123
, pp. 1199-1212
-
-
Fan, Y.1
Nikitina, T.2
Zhao, J.3
Fleury, T.J.4
Bhattacharyya, R.5
-
7
-
-
80053140931
-
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization
-
Gkikopoulos, T., P. Schofield, V. Singh, M. Pinskaya, J. Mellor et al., 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
-
8
-
-
74549125386
-
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
-
Gouy, M., S. Guindon, and O. Gascuel, 2010 SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27: 221-224.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 221-224
-
-
Gouy, M.1
Guindon, S.2
Gascuel, O.3
-
9
-
-
77956522905
-
The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor
-
Hauk, G., J. N. McKnight, I. M. Nodelman, and G. D. Bowman, 2010 The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol. Cell 39: 711-723.
-
(2010)
Mol. Cell
, vol.39
, pp. 711-723
-
-
Hauk, G.1
McKnight, J.N.2
Nodelman, I.M.3
Bowman, G.D.4
-
10
-
-
0027180551
-
The nucleosome repeat length of Kluyveromyces lactis is 16 bp longer than that of Saccharomyces cerevisiae
-
Heus, J. J., B. J. Zonneveld, K. S. Bloom,H.Y. de Steensma, and J. A. van den Berg, 1993 The nucleosome repeat length of Kluyveromyces lactis is 16 bp longer than that of Saccharomyces cerevisiae. Nucleic Acids Res. 21: 2247-2248.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 2247-2248
-
-
Heus, J.J.1
Zonneveld, B.J.2
Bloom, K.S.3
de Steensma, H.Y.4
van den Berg, J.A.5
-
11
-
-
84867371116
-
A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern
-
Hughes, A. L., Y. Jin, O. J. Rando, and K. Struhl, 2012 A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern. Mol. Cell. 48: 5-15
-
(2012)
Mol. Cell
, vol.48
, pp. 5-15
-
-
Hughes, A.L.1
Jin, Y.2
Rando, O.J.3
Struhl, K.4
-
12
-
-
84901980324
-
Mechanisms underlying nucleosome positioning in vivo
-
Hughes, A. L., and O. J. Rando, 2014 Mechanisms underlying nucleosome positioning in vivo. Annu. Rev. Biophys. 43: 41-63
-
(2014)
Annu. Rev. Biophys
, vol.43
, pp. 41-63
-
-
Hughes, A.L.1
Rando, O.J.2
-
13
-
-
0031444148
-
ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor
-
Ito, T., M. Bulger, M. J. Pazin, R. Kobayashi, and J. T. Kadonaga, 1997 ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90: 145-155.
-
(1997)
Cell
, vol.90
, pp. 145-155
-
-
Ito, T.1
Bulger, M.2
Pazin, M.J.3
Kobayashi, R.4
Kadonaga, J.T.5
-
14
-
-
0029026719
-
Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
-
Iyer, V., and K. Struhl, 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
-
15
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan, N., I. K. Moore, Y. Fondufe-Mittendorf, A. J. Gossett, D. Tillo 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
-
16
-
-
84155179192
-
RNA polymerase mapping during stress responses reveals widespread non-productive transcription in yeast
-
Kim, T. S., C. L. Liu, M. Yassour, J. Holik, N. Friedman et al., 2010 RNA polymerase mapping during stress responses reveals widespread non-productive transcription in yeast. Genome Biol. 11: R75.
-
(2010)
Genome Biol.
, vol.11
-
-
Kim, T.S.1
Liu, C.L.2
Yassour, M.3
Holik, J.4
Friedman, N.5
-
17
-
-
84920924163
-
Maintenance of nucleosomal balance in cis by conserved AAA-ATPase Yta7
-
Lombardi, L. M., M. D. Davis, and J. Rine, 2015 Maintenance of nucleosomal balance in cis by conserved AAA-ATPase Yta7. Genetics 199: 105-116.
-
(2015)
Genetics
, vol.199
, pp. 105-116
-
-
Lombardi, L.M.1
Davis, M.D.2
Rine, J.3
-
18
-
-
84875873326
-
Toward a unified physical model of nucleosome patterns flanking transcription start sites
-
Mobius, W., B. Osberg, A. M. Tsankov, O. J. Rando, and U. Gerland, 2013 Toward a unified physical model of nucleosome patterns flanking transcription start sites. Proc. Natl. Acad. Sci. USA 110: 5719-5724.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 5719-5724
-
-
Mobius, W.1
Osberg, B.2
Tsankov, A.M.3
Rando, O.J.4
Gerland, U.5
-
19
-
-
84870510245
-
CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe
-
Pointner, J., J. Persson, P. Prasad, U. Norman-Axelsson, A. Stralfors et al., 2012 CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J. 31: 4388-4403.
-
(2012)
EMBO J.
, vol.31
, pp. 4388-4403
-
-
Pointner, J.1
Persson, J.2
Prasad, P.3
Norman-Axelsson, U.4
Stralfors, A.5
-
20
-
-
84864626931
-
A key role for Chd1 in histone H3 dynamics at the 39 ends of long genes in yeast
-
Radman-Livaja, M., T. K. Quan, L. Valenzuela, J. A. Armstrong, T. van Welsem et al., 2012 A key role for Chd1 in histone H3 dynamics at the 39 ends of long genes in yeast. PLoS Genet. 8: e1002811.
-
(2012)
PLoS Genet.
, vol.8
-
-
Radman-Livaja, M.1
Quan, T.K.2
Valenzuela, L.3
Armstrong, J.A.4
van Welsem, T.5
-
21
-
-
20444403749
-
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
-
Sekinger, E. A., Z. Moqtaderi, and K. Struhl, 2005 Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18: 735-748.
-
(2005)
Mol. Cell
, vol.18
, pp. 735-748
-
-
Sekinger, E.A.1
Moqtaderi, Z.2
Struhl, K.3
-
22
-
-
0345698603
-
Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes
-
Simic, R., D. L. Lindstrom, H. G. Tran, K. L. Roinick, P. J. Costa et al., 2003 Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22: 1846-1856.
-
(2003)
EMBO J.
, vol.22
, pp. 1846-1856
-
-
Simic, R.1
Lindstrom, D.L.2
Tran, H.G.3
Roinick, K.L.4
Costa, P.J.5
-
23
-
-
84866114872
-
Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange
-
Smolle, M., S. Venkatesh, M. M. Gogol, H. Li, Y. Zhang et al., 2012 Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat. Struct. Mol. Biol. 19: 884-892.
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 884-892
-
-
Smolle, M.1
Venkatesh, S.2
Gogol, M.M.3
Li, H.4
Zhang, Y.5
-
24
-
-
33745221438
-
Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes
-
Stockdale, C., A. Flaus, H. Ferreira, and T. Owen-Hughes, 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
-
25
-
-
33746644150
-
HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae
-
Tagwerker, C., H. Zhang, X. Wang, L. S. Larsen, R. H. Lathrop et al., 2006 HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae. Yeast 23: 623-632.
-
(2006)
Yeast
, vol.23
, pp. 623-632
-
-
Tagwerker, C.1
Zhang, H.2
Wang, X.3
Larsen, L.S.4
Lathrop, R.H.5
-
26
-
-
80555156654
-
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
-
Tsankov, A., Y. Yanagisawa, N. Rhind, A. Regev, and O. J. Rando, 2011 Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res. 21: 1851-1862.
-
(2011)
Genome Res.
, vol.21
, pp. 1851-1862
-
-
Tsankov, A.1
Yanagisawa, Y.2
Rhind, N.3
Regev, A.4
Rando, O.J.5
-
27
-
-
77955045449
-
The role of nucleosome positioning in the evolution of gene regulation
-
Tsankov, A. M., D. A. Thompson, A. Socha, A. Regev, and O. J. Rando, 2010 The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 8: e1000414.
-
(2010)
PLoS Biol.
, vol.8
-
-
Tsankov, A.M.1
Thompson, D.A.2
Socha, A.3
Regev, A.4
Rando, O.J.5
-
28
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev, A., S. M. Johnson, S. D. Boyd, C. L. Smith, A. Z. Fire et al., 2011 Determinants of nucleosome organization in primary human cells. Nature 474: 516-520.
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.M.2
Boyd, S.D.3
Smith, C.L.4
Fire, A.Z.5
-
29
-
-
0003903126
-
Chromatin
-
Springer-Verlag, New York
-
Van Holde, K. E., 1989 Chromatin. Springer-Verlag, New York.
-
(1989)
-
-
Van Holde, K.E.1
-
30
-
-
0037214318
-
Yeast Isw1p forms two separable complexes in vivo
-
Vary, J. C., Jr, V. K. Gangaraju, J. Qin, C. C. Landel, C. Kooperberg et al., 2003 Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23: 80-91.
-
(2003)
Mol. Cell. Biol.
, vol.23
, pp. 80-91
-
-
Vary, J.C.1
Gangaraju, V.K.2
Qin, J.3
Landel, C.C.4
Kooperberg, C.5
-
31
-
-
74949110964
-
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
-
Weiner, A., A. Hughes, M. Yassour, O. J. Rando, and N. Friedman, 2010 High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 20: 90-100.
-
(2010)
Genome Res.
, vol.20
, pp. 90-100
-
-
Weiner, A.1
Hughes, A.2
Yassour, M.3
Rando, O.J.4
Friedman, N.5
-
32
-
-
84859927986
-
Genome-wide identification and characterization of replication origins by deep sequencing
-
Xu, J., Y. Yanagisawa, A. M. Tsankov, C. Hart, K. Aoki et al., 2012 Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 13: R27.
-
(2012)
Genome Biol.
, vol.13
-
-
Xu, J.1
Yanagisawa, Y.2
Tsankov, A.M.3
Hart, C.4
Aoki, K.5
-
33
-
-
79955547248
-
Structure and mechanism of the chromatin remodelling factor ISW1a
-
Yamada, K., T. D. Frouws, B. Angst, D. J. Fitzgerald, C. DeLuca et al., 2011 Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 472: 448-453.
-
(2011)
Nature
, vol.472
, pp. 448-453
-
-
Yamada, K.1
Frouws, T.D.2
Angst, B.3
Fitzgerald, D.J.4
DeLuca, C.5
-
34
-
-
33845356072
-
The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing
-
Yang, J. G., T. S. Madrid, E. Sevastopoulos, and G. J. Narlikar, 2006 The chromatin-remodeling enzyme ACF is an ATP-dependent 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
-
35
-
-
38949204996
-
Genomic sequence is highly predictive of local nucleosome depletion
-
Yuan, G. C., and J. S. Liu, 2008 Genomic sequence is highly predictive of local nucleosome depletion. PLOS Comput. Biol. 4: e13.
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Yuan, G.C.1
Liu, J.S.2
-
36
-
-
22744432660
-
Genomescale identification of nucleosome positions in S. cerevisiae
-
Yuan, G. C., Y. J. Liu,M. F. Dion, M. D. Slack, L. F. Wu et al., 2005 Genomescale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.
-
(2005)
Science
, vol.309
, pp. 626-630
-
-
Yuan, G.C.1
Liu, Y.J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
-
37
-
-
84874764239
-
ISWI and CHD chromatin remodelers bind promoters but act in gene bodies
-
Zentner, G. E., T. Tsukiyama, and S. Henikoff, 2013 ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. PLoS Genet. 9: e1003317.
-
(2013)
PLoS Genet.
, vol.9
-
-
Zentner, G.E.1
Tsukiyama, T.2
Henikoff, S.3
-
38
-
-
68249142923
-
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
-
Zhang, Y., Z. Moqtaderi, B. P. Rattner, G. Euskirchen, M. Snyder et al., 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
-
39
-
-
78651477233
-
High-resolution genome-wide mapping of the primary structure of chromatin
-
Zhang, Z., and B. F. Pugh, 2011 High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144: 175-186.
-
(2011)
Cell
, vol.144
, pp. 175-186
-
-
Zhang, Z.1
Pugh, B.F.2
-
40
-
-
79956316470
-
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
-
Zhang, Z., C. J. Wippo, M. Wal, E. Ward, P. Korber et al., 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
|