-
1
-
-
77955410104
-
Nucleosome sequence preferences influence in vivo nucleosome organization
-
N. Kaplan, I. Moore, Y. Fondufe-Mittendorf, A.J. Gossett, D. Tillo, Y. Field, T.R. Hughes, J.D. Lieb, J. Widom, and E. Segal Nucleosome sequence preferences influence in vivo nucleosome organization Nature 17 2010 918 920
-
(2010)
Nature
, vol.17
, pp. 918-920
-
-
Kaplan, N.1
Moore, I.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
Hughes, T.R.7
Lieb, J.D.8
Widom, J.9
Segal, E.10
-
2
-
-
77955365269
-
Evidence against a genomic code for nucleosome positioning
-
Y. Zhang, Z. Moqtaderi, B.P. Rattner, G. Euskirchen, M. Snyder, J.T. Kadonaga, X.S. Liu, and K. Struhl Evidence against a genomic code for nucleosome positioning Nature 17 2010 920 923
-
(2010)
Nature
, vol.17
, pp. 920-923
-
-
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
-
3
-
-
77955388311
-
A preoccupied position on nucleosomes
-
B.F. Pugh A preoccupied position on nucleosomes Nature 17 2010 923
-
(2010)
Nature
, vol.17
, pp. 923
-
-
Pugh, B.F.1
-
4
-
-
33747500567
-
A genomic code for nucleosome positioning
-
DOI 10.1038/nature04979, PII NATURE04979
-
E. Segal, Y. Fondufe-Mittendorf, L. Chen, A. Thåström, Y. Field, I.K. Moore, J.Z. Wang, and J. Widom A genomic code for nucleosome positioning Nature 442 2006 772 778 (Pubitemid 44258903)
-
(2006)
Nature
, vol.442
, Issue.7104
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thastrom, A.4
Field, Y.5
Moore, I.K.6
Wang, J.-P.Z.7
Widom, J.8
-
5
-
-
33749153628
-
Nucleosome positions predicted through comparative genomics
-
DOI 10.1038/ng1878, PII NG1878
-
P. Ioshikhes, I. Albert, S.J. Zanton, and B.F. Pugh Nucleosome positions predicted through comparative genomics Nat. Genet. 38 2006 1210 1215 (Pubitemid 44470369)
-
(2006)
Nature Genetics
, vol.38
, Issue.10
, pp. 1210-1215
-
-
Ioshikhes, I.P.1
Albert, I.2
Zanton, S.J.3
Pugh, B.F.4
-
6
-
-
34547643563
-
Nucleosome positioning signals in genomic DNA
-
DOI 10.1101/gr.6101007
-
H.E. Peckham, R.E. Thurman, Y. Fu, J.A. Stamatoyannopoulos, W.S. Noble, K. Struhl, and Z.P. Weng Nucleosome positioning signals in genomic DNA Genome Res. 17 2007 1170 1177 (Pubitemid 47204860)
-
(2007)
Genome Research
, vol.17
, Issue.8
, pp. 1170-1177
-
-
Peckham, H.E.1
Thurman, R.E.2
Fu, Y.3
Stamatoyannopoulos, J.A.4
Noble, W.S.5
Struhl, K.6
Weng, Z.7
-
7
-
-
34447644439
-
A Novel Roll-and-Slide Mechanism of DNA Folding in Chromatin: Implications for Nucleosome Positioning
-
DOI 10.1016/j.jmb.2007.05.048, PII S002228360700695X
-
M.Y. Tolstorukov, A.V. Colasanti, D.M. McCandlish, W.K. Olson, and V.B. Zhurkin A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning J. Mol. Biol. 371 2007 725 738 (Pubitemid 47087819)
-
(2007)
Journal of Molecular Biology
, vol.371
, Issue.3
, pp. 725-738
-
-
Tolstorukov, M.Y.1
Colasanti, A.V.2
McCandlish, D.M.3
Olson, W.K.4
Zhurkin, V.B.5
-
8
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
DOI 10.1038/ng2117, PII NG2117
-
W. Lee, D. Tillo, N. Bray, R.H. Morse, R.W. Davis, T.R. Hughes, and C. Nislow A high-resolution atlas of nucleosome occupancy in yeast Nat. Genet. 39 2007 1235 1244 (Pubitemid 47482684)
-
(2007)
Nature Genetics
, vol.39
, Issue.10
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
Hughes, T.R.6
Nislow, C.7
-
9
-
-
50949096918
-
Predicting human nucleosome occupancy from primary sequence
-
S. Gupta, S. Dennis, R.E. Thurman, Y. Fu, J.A. Stamatoyannopoulos, and W.S. Noble Predicting human nucleosome occupancy from primary sequence PLoS Comput. Biol. 4 2008 e1000134
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000134
-
-
Gupta, S.1
Dennis, S.2
Thurman, R.E.3
Fu, Y.4
Stamatoyannopoulos, J.A.5
Noble, W.S.6
-
10
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
DOI 10.1101/gr.078261.108
-
T.N. Mavrich, I.P. Ioshikhes, B.J. Venters, C. Jiang, L.P. Tomsho, J. Qi, S.C. Schuster, I. Albert, and B.F. Pugh A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome Genome Res. 18 2008 1073 1083 (Pubitemid 351931158)
-
(2008)
Genome Research
, vol.18
, Issue.7
, 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
-
11
-
-
53549103033
-
Nucleosome positioning in human HOX gene clusters
-
P.V. Kharchenko, C.J. Woo, M.Y. Tolstorukov, R.E. Kingston, and P.J. Park Nucleosome positioning in human HOX gene clusters Genome Res. 18 2008 1554 1561
-
(2008)
Genome Res.
, vol.18
, pp. 1554-1561
-
-
Kharchenko, P.V.1
Woo, C.J.2
Tolstorukov, M.Y.3
Kingston, R.E.4
Park, P.J.5
-
12
-
-
38949204996
-
Genomic sequence is highly predictive of local nucleosome depletion
-
G.C. Yuan, and J.S. Liu Genomic sequence is highly predictive of local nucleosome depletion PLoS Comput. Biol. 4 2008 e13
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 13
-
-
Yuan, G.C.1
Liu, J.S.2
-
13
-
-
57149119464
-
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
-
Y. Field, N. Kaplan, Y. Fondufe-Mittendorf, I.K. Moore, E. Sharon, Y. Lubling, J. Widom, and E. Segal Distinct modes of regulation by chromatin encoded through nucleosome positioning signals PLoS Comput. Biol. 4 2008 e1000216
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000216
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
Lubling, Y.6
Widom, J.7
Segal, E.8
-
14
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
N. Kaplan, I.K. Moore, Y. Fondufe-Mittendorf, A.J. Gossett, D. Tillo, Y. Field, E.M. Leproust, T.R. Hughes, J.D. Lieb, J. Widom, and E. Segal The DNA-encoded nucleosome organization of a eukaryotic genome Nature 458 2009 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
Segal, E.11
-
15
-
-
77949393272
-
High nucleosome occupancy is encoded at human regulatory sequences
-
D. Tillo, N. Kaplan, I.K. Moore, Y. Fondufe-Mittendorf, A.J. Gossett, Y. Field, J.D. Lieb, J. Widom, E. Segal, and T.R. Hughes High nucleosome occupancy is encoded at human regulatory sequences PLoS ONE 5 2010 e9129
-
(2010)
PLoS ONE
, vol.5
, pp. 9129
-
-
Tillo, D.1
Kaplan, N.2
Moore, I.K.3
Fondufe-Mittendorf, Y.4
Gossett, A.J.5
Field, Y.6
Lieb, J.D.7
Widom, J.8
Segal, E.9
Hughes, T.R.10
-
16
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
DOI 10.1016/0022-2836(86)90452-3
-
S. Satchwell, H.R. Drew, and A.A. Travers Sequence periodicities in chicken nucleosome core DNA J. Mol. Biol. 191 1986 659 675 (Pubitemid 17185964)
-
(1986)
Journal of Molecular Biology
, vol.191
, Issue.4
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
17
-
-
0022230224
-
DNA bending and its relation to nucleosome positioning
-
H.R. Drew, and A.A. Travers DNA bending and its relation to nucleosome positioning J. Mol. Biol. 186 1985 773 790 (Pubitemid 16087267)
-
(1985)
Journal of Molecular Biology
, vol.186
, Issue.4
, pp. 773-790
-
-
Drew, H.R.1
Travers, A.A.2
-
18
-
-
0026074664
-
The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning
-
D. Boffelli, P. De Santis, A. Palleschi, and M. Savino The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning Biophys. Chem. 39 1991 127 136
-
(1991)
Biophys. Chem.
, vol.39
, pp. 127-136
-
-
Boffelli, D.1
De Santis, P.2
Palleschi, A.3
Savino, M.4
-
19
-
-
0027512862
-
Theoretical prediction of the gel electrophoretic retardation changes due to point mutations in a tract of SV40 DNA
-
P. De Santis, M. Fuà, A. Palleschi, and M. Savino Theoretical prediction of the gel electrophoretic retardation changes due to point mutations in a tract of SV40 DNA Biophys. Chem. 46 1993 193 204
-
(1993)
Biophys. Chem.
, vol.46
, pp. 193-204
-
-
De Santis, P.1
Fuà, M.2
Palleschi, A.3
Savino, M.4
-
20
-
-
22744432660
-
Molecular biology: Genome-scale identification of nucleosome positions in S. cerevisiae
-
DOI 10.1126/science.1112178
-
G.C. Yuan, Y.J. Liu, M.F. Dion, M.D. Slack, L.F. Wu, S.J. Altschuler, and O.J. Rando Genome-scale identification of nucleosome positions in S. cerevisiae Science 309 2005 626 630 (Pubitemid 41033649)
-
(2005)
Science
, vol.309
, Issue.5734
, pp. 626-630
-
-
Yuan, G.-C.1
Liu, Y.-J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
Altschuler, S.J.6
Rando, O.J.7
-
21
-
-
68249142923
-
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
-
Y. Zhang, Z. Moqtaderi, B.P. Rattner, G. Euskirchen, M. Snyder, J.T. Kadonaga, X.S. Liu, and K. Struhl Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo Nat. Struct. Mol. Biol. 16 2009 847 853
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 847-853
-
-
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
-
23
-
-
0021100990
-
Nucleotide sequence-directed mapping of the nucleosomes
-
G. Mengeritsky, and E.N. Trifonov Nucleotide sequence-directed mapping of the nucleosomes Nucleic Acids Res. 11 1983 3833 3851
-
(1983)
Nucleic Acids Res.
, vol.11
, pp. 3833-3851
-
-
Mengeritsky, G.1
Trifonov, E.N.2
-
24
-
-
0030595138
-
Nucleosome RNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
-
DOI 10.1006/jmbi.1996.0503
-
Ioshikhes, A. Bolshoy, K. Derenshteyn, M. Borodovsky, and E.N. Trifonov Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences J. Mol. Biol. 262 1996 129 139 (Pubitemid 26326967)
-
(1996)
Journal of Molecular Biology
, vol.262
, Issue.2
, pp. 129-139
-
-
Ioshikhes, I.1
Bolshoy, A.2
Derenshteyn, K.3
Borodovsky, M.4
Trifonov, E.N.5
-
25
-
-
57749182426
-
Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans
-
F. Salih, B. Salih, and E.N. Trifonov Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans J. Biomol. Struct. Dyn. 26 2008 273 282
-
(2008)
J. Biomol. Struct. Dyn.
, vol.26
, pp. 273-282
-
-
Salih, F.1
Salih, B.2
Trifonov, E.N.3
-
27
-
-
78049298053
-
G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae
-
J.A. Capra, K. Paeschke, M. Singh, and V.A. Zakian G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae PLoS Comput. Biol. 6 2010 e1000861
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000861
-
-
Capra, J.A.1
Paeschke, K.2
Singh, M.3
Zakian, V.A.4
-
28
-
-
33745221438
-
Analysis of nucleosome repositioning by yeast |SW| and Chd1 chromatin remodeling complexes
-
C. Stockdale, A. Flaus, H. Ferreira, and T. Owen-Hughes Analysis of nucleosome repositioning by yeast |SW| and Chd1 chromatin remodeling complexes J. Biol. Chem. 281 2006 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
-
-
34248633105
-
Telomeric Nucleosomes Are Intrinsically Mobile
-
DOI 10.1016/j.jmb.2007.04.027, PII S0022283607004986
-
S. Pisano, E. Marchione, A. Galati, S. Mechelli, M. Savino, and S. Cacchione Telomeric nucleosomes are intrinsically mobile J. Mol. Biol. 369 2007 1153 1162 (Pubitemid 46770779)
-
(2007)
Journal of Molecular Biology
, vol.369
, Issue.5
, pp. 1153-1162
-
-
Pisano, S.1
Marchioni, E.2
Galati, A.3
Mechelli, R.4
Savino, M.5
Cacchione, S.6
-
30
-
-
57149115121
-
Structure of a RSC-nucleosome complex and insights into chromatin remodeling
-
Y. Chaban, C. Ezeokonkwo, W.H. Chung, F. Zhang, R.D. Kornberg, B. Maier-Davis, Y. Lorch, and F.J. Asturias Structure of a RSC-nucleosome complex and insights into chromatin remodeling Nat. Struct. Mol. Biol. 15 2008 1272 1277
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 1272-1277
-
-
Chaban, Y.1
Ezeokonkwo, C.2
Chung, W.H.3
Zhang, F.4
Kornberg, R.D.5
Maier-Davis, B.6
Lorch, Y.7
Asturias, F.J.8
-
31
-
-
68149108057
-
Using DNA mechanics to predict in vitro nucleosome positions and formation energies
-
A.V. Morozov, K. Fortney, D.A. Gaykalova, V.M. Studitsky, J. Widom, and E.D. Siggia Using DNA mechanics to predict in vitro nucleosome positions and formation energies Nucleic Acids Res. 37 2009 4707 4722
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4707-4722
-
-
Morozov, A.V.1
Fortney, K.2
Gaykalova, D.A.3
Studitsky, V.M.4
Widom, J.5
Siggia, E.D.6
-
33
-
-
0025144957
-
Effects of DNA sequence and histone-histone interactions on nucleosome placement
-
T.E. Shrader, and D.M. Crothers Effects of DNA sequence and histone-histone interactions on nucleosome placement J. Mol. Biol. 216 1990 69 84 (Pubitemid 20376175)
-
(1990)
Journal of Molecular Biology
, vol.216
, Issue.1
, pp. 69-84
-
-
Shrader, T.E.1
Crothers, D.M.2
-
34
-
-
17544367055
-
Nucleosome assembly on CTG triplet repeats
-
DOI 10.1074/jbc.271.25.15222
-
S. Godde, and A.P. Wolffe Nucleosome assembly on CTG triplet repeats J. Biol. Chem. 271 1996 15222 15229 (Pubitemid 26195003)
-
(1996)
Journal of Biological Chemistry
, vol.271
, Issue.25
, pp. 15222-15229
-
-
Godde, J.S.1
Wolffe, A.P.2
-
35
-
-
0029744342
-
Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter
-
DOI 10.1074/jbc.271.40.24325
-
S. Godde, S.U. Kass, M.C. Hirst, and A.P. Wolffe Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter J. Biol. Chem. 271 1996 24325 24328 (Pubitemid 26333159)
-
(1996)
Journal of Biological Chemistry
, vol.271
, Issue.40
, pp. 24325-24328
-
-
Godde, J.S.1
Kass, S.U.2
Hirst, M.C.3
Wolffe, A.P.4
-
36
-
-
0030575839
-
Long CCG triplet repeat blocks exclude nucleosomes: A possible mechanism for the nature of fragile sites in chromosomes
-
DOI 10.1006/jmbi.1996.0593
-
Y. Wang, R. Gellibolian, M. Shimizu, R.D. Wells, and J. Griffith Long CCG triplet repeat blocks exclude nucleosomes: a possible mechanism for the nature of fragile sites in chromosomes J. Mol. Biol. 263 1996 511 516 (Pubitemid 26382070)
-
(1996)
Journal of Molecular Biology
, vol.263
, Issue.4
, pp. 511-516
-
-
Wang, Y.-H.1
Gellibolian, R.2
Shimizu, M.3
Wells, R.D.4
Griffith, J.5
-
37
-
-
0031564633
-
Identification and characterization of genomic nucleosome-positioning sequences
-
DOI 10.1006/jmbi.1997.0916
-
H.R. Widlund, H. Cao, S. Simonsson, E. Magnusson, T. Simonsson, P.E. Nielsen, J.D. Kahn, D.M. Crothers, and M. Kubista Identification and characterization of genomic nucleosome-positioning sequences J. Mol. Biol. 267 1997 807 817 (Pubitemid 27192655)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.4
, pp. 807-817
-
-
Widlund, H.R.1
Cao, H.2
Simonsson, S.3
Magnusson, E.4
Simonsson, T.5
Nielsen, P.E.6
Kahn, J.D.7
Crothers, D.M.8
Kubista, M.9
-
38
-
-
0031031106
-
In vitro low propensity to form nucleosomes of four telomeric sequences
-
DOI 10.1016/S0014-5793(96)01318-X, PII S001457939601318X
-
S. Cacchione, A.M. Cerone, and M. Savino In vitro low propensity to form nucleosomes of four telomeric sequences FEBS Lett. 400 1997 37 41 (Pubitemid 27046817)
-
(1997)
FEBS Letters
, vol.400
, Issue.1
, pp. 37-41
-
-
Cacchione, S.1
Cerone, M.A.2
Savino, M.3
-
39
-
-
0032512794
-
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
-
DOI 10.1006/jmbi.1997.1494
-
P.T. Lowary, and J. Widom New DNA sequence rules for high affinity binding to histone octamer and sequence directed nucleosome positioning J. Mol. Biol. 276 1998 19 42 (Pubitemid 28085408)
-
(1998)
Journal of Molecular Biology
, vol.276
, Issue.1
, pp. 19-42
-
-
Lowary, P.T.1
Widom, J.2
-
40
-
-
0032510809
-
Nucleosome assembly on telomeric sequences
-
DOI 10.1021/bi9726180
-
L. Rossetti, S. Cacchione, M. Fuà, and M. Savino Nucleosome assembly on telomeric sequences Biochemistry 37 1998 6727 6737 (Pubitemid 28228106)
-
(1998)
Biochemistry
, vol.37
, Issue.19
, pp. 6727-6737
-
-
Rossetti, L.1
Cacchione, S.2
Fua, M.3
Savino, M.4
-
41
-
-
0032503961
-
DNA superstructural features and nucleosomal organization of the two centromeres of Kluyveromyces lactis chromosome 1 and Saccharomyces cerevisiae chromosome 6
-
DOI 10.1016/S0014-5793(98)00702-9, PII S0014579398007029
-
M. Del Cornò, P. De Santis, B. Sampaolese, M. Savino, M. Del Cornò, P. De Santis, B. Sampaolese, and M. Savino DNA superstructural features and nucleosomal organization on the two centromers of Kluyveromyces lactis chromosome 1 and Saccharomyces cerevisiae chromosome 6 FEBS Lett. 431 1998 66 70 (Pubitemid 28330854)
-
(1998)
FEBS Letters
, vol.431
, Issue.1
, pp. 66-70
-
-
Del Corno, M.1
De Santis, P.2
Sampaolese, B.3
Savino, M.4
-
42
-
-
0032516764
-
TGGA repeats impair nucleosome formation
-
DOI 10.1006/jmbi.1998.1925
-
H. Cao, H.R. Widlund, T. Simonsson, and M. Kubista TGGA repeats impair nucleosome formation J. Mol. Biol. 281 1998 253 260 (Pubitemid 28360592)
-
(1998)
Journal of Molecular Biology
, vol.281
, Issue.2
, pp. 253-260
-
-
Cao, H.1
Widlund, H.R.2
Simonsson, T.3
Kubista, M.4
-
43
-
-
0032103910
-
Unique translational positioning of nucleosomes on synthetic DNAs
-
DOI 10.1093/nar/26.11.2526
-
D.J. Fitzgerald, and J.N. Anderson Unique translational positioning of nucleosomes on synthetic DNAs Nucleic Acids Res. 26 1998 2526 2535 (Pubitemid 28297361)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.11
, pp. 2526-2535
-
-
Fitzgerald, D.J.1
Anderson, J.N.2
-
44
-
-
0032760667
-
DNA distortion as a factor in nucleosome positioning
-
DOI 10.1006/jmbi.1999.3171
-
D.J. Fitzgerald, and J.N. Anderson DNA distortion as a factor in nucleosome positioning J. Mol. Biol. 293 1999 477 491 (Pubitemid 29512050)
-
(1999)
Journal of Molecular Biology
, vol.293
, Issue.3
, pp. 477-491
-
-
Fitzgerald, D.J.1
Anderson, J.N.2
-
45
-
-
0033988692
-
The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs
-
DOI 10.1016/S0301-4622(99)00143-X, PII S030146229900143X
-
Filesi, S. Cacchione, P. De Santis, L. Rossetti, and M. Savino The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs Biophys. Chem. 83 1999 223 237 (Pubitemid 30012086)
-
(2000)
Biophysical Chemistry
, vol.83
, Issue.3
, pp. 223-237
-
-
Filesi, I.1
Cacchione, S.2
De Santis, P.3
Rossetti, L.4
Savino, M.5
-
46
-
-
0037134772
-
Nucleosome organization on Kluyveromyces lactis centromeric DNAs
-
DOI 10.1016/S0301-4622(02)00066-2, PII S0301462202000662
-
S. Mattei, B. Sampaolese, P. De Santis, and M. Savino Nucleosome organization on Kluyveromyces lactis centromeric DNAs Biophys. Chem. 97 2002 173 187 (Pubitemid 34603751)
-
(2002)
Biophysical Chemistry
, vol.97
, Issue.2-3
, pp. 173-187
-
-
Mattei, S.1
Sampaolese, B.2
De Santis, P.3
Savino, M.4
-
47
-
-
0037811016
-
Acetylated nucleosome assembly on telomeric DNAs
-
DOI 10.1016/S0301-4622(03)00028-0
-
S. Cacchione, J.L. Rodriguez, R. Mechelli, L. Franco, and M. Savino Acetylated nucleosome assembly on telomeric DNAs Biophys. Chem. 104 2003 381 392 (Pubitemid 36871025)
-
(2003)
Biophysical Chemistry
, vol.104
, Issue.2
, pp. 381-392
-
-
Cacchione, S.1
Rodriguez, J.L.2
Mechelli, R.3
Franco, L.4
Savino, M.5
-
48
-
-
1042267433
-
Dual role of sequence-dependent DNA curvature in nucleosome stability: The critical test of highly bent Crithidia fasciculata DNA tract
-
DOI 10.1016/S0301-4622(03)00214-X
-
A. Scipioni, S. Pisano, C. Anselmi, M. Savino, and P. De Santis Dual role of sequence-dependent DNA curvature in nucleosome stability: the critical test of highly bent Crithidia fasciculata DNA tract Biophys. Chem. 107 2004 7 17 (Pubitemid 38197977)
-
(2004)
Biophysical Chemistry
, vol.107
, Issue.1
, pp. 7-17
-
-
Scipioni, A.1
Pisano, S.2
Anselmi, C.3
Savino, M.4
De Santis, P.5
-
49
-
-
4444221204
-
The influence of DNA stiffness upon nucleosome formation
-
J. Virstedt, T. Berge, R.M. Henderson, M.J. Waring, and A.A. Travers The influence of DNA stiffness upon nucleosome formation J. Struct. Biol. 148 2004 2408 2418
-
(2004)
J. Struct. Biol.
, vol.148
, pp. 2408-2418
-
-
Virstedt, J.1
Berge, T.2
Henderson, R.M.3
Waring, M.J.4
Travers, A.A.5
-
51
-
-
0028931709
-
B-DNA twisting correlates with base-pair morphology
-
A.A. Gorin, V.B. Zhurkin, and W.K. Olson B-DNA twisting correlates with base-pair morphology J. Mol. Biol. 247 1995 34 48
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
52
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
DOI 10.1073/pnas.95.19.11163
-
W.K. Olson, A.A. Gorin, X.-J. Lu, L.M. Hock, and V.B. Zhurkin DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl Acad. Sci. U.S.A. 95 1998 11163 11168 (Pubitemid 28450099)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.19
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.-J.3
Hock, L.M.4
Zhurkin, V.B.5
-
53
-
-
0034614487
-
Sequence-dependent DNA structure: Tetranucleotide conformational maps
-
DOI 10.1006/jmbi.1999.3237
-
M.J. Packer, M.P. Dauncey, and C.A. Hunter Sequence-dependent DNA structure: tetranucleotide conformational maps J. Mol. Biol. 295 2000 85 103 (Pubitemid 30025903)
-
(2000)
Journal of Molecular Biology
, vol.295
, Issue.1
, pp. 85-103
-
-
Packer, M.J.1
Dauncey, M.P.2
Hunter, C.A.3
-
54
-
-
51049119256
-
Geometry of the nucleosomal DNA superhelix
-
T.J. Bishop Geometry of the nucleosomal DNA superhelix Biophys. J. 95 2008 1007 1017
-
(2008)
Biophys. J.
, vol.95
, pp. 1007-1017
-
-
Bishop, T.J.1
-
55
-
-
46449103738
-
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
DOI 10.1101/gr.076463.108
-
A. Valouev, J. Ichikawa, T. Tonthat, J. Stuart, S. Ranade, H. Peckham, K. Zeng, J.A. Malek, G. Costa, K. McKernan, A. Sidow, A. Fire, and S.M. Johnson A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning Genome Res. 18 2008 1051 1063 (Pubitemid 351931156)
-
(2008)
Genome Research
, vol.18
, Issue.7
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
Stuart, J.4
Ranade, S.5
Peckham, H.6
Zeng, K.7
Malek, J.A.8
Costa, G.9
McKernan, K.10
Sidow, A.11
Fire, A.12
Johnson, S.M.13
-
56
-
-
70449702038
-
A translational signature for nucleosome positioning in vivo
-
M. Caserta, E. Agricola, M. Churcher, E. Hiriart, L. Verdone, E. Di Mauro, and A. Travers A translational signature for nucleosome positioning in vivo Nucleic Acids Res. 37 2009 5309 5321
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5309-5321
-
-
Caserta, M.1
Agricola, E.2
Churcher, M.3
Hiriart, E.4
Verdone, L.5
Di Mauro, E.6
Travers, A.7
-
57
-
-
33845298285
-
Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
-
DOI 10.1101/gr.5560806
-
S.M. Johnson, F.J. Tan, H.L. McCullough, D.P. Riordan, and A.Z. Fire Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin Genome Res. 16 2006 1505 1516 (Pubitemid 44878489)
-
(2006)
Genome Research
, vol.16
, Issue.12
, pp. 1505-1516
-
-
Johnson, S.M.1
Tan, F.J.2
McCullough, H.L.3
Riordan, D.P.4
Fire, A.Z.5
-
58
-
-
0017331464
-
Structure of chromatin
-
R.D. Kornberg Structure of chromatin Annu. Rev. Biochem. 46 1977 931 954
-
(1977)
Annu. Rev. Biochem.
, vol.46
, pp. 931-954
-
-
Kornberg, R.D.1
-
59
-
-
0017619403
-
Small angle neutron scattering studies of chromatin subunits in solution
-
H.P. Hjelm, G.G. Kneale, P. Sabau, J.P. Baldwin, E.M. Bradbury, and K. Ibel Small angle neutron scattering studies of chromatin subunits in solution Cell 10 1977 139 151 (Pubitemid 8046484)
-
(1977)
Cell
, vol.10
, Issue.1
, pp. 139-151
-
-
Hjelm, R.P.1
Kneale, G.G.2
Suau, P.3
-
60
-
-
0019200870
-
A low resolution structure for the histone core of the nucleosome
-
DOI 10.1038/287509a0
-
A. Klug, D. Rhodes, J. Smith, T.J. Finch, and J.O. Thomas A low resolution structure for the histone core of the nucleosome Nature 287 1980 509 516 (Pubitemid 11232848)
-
(1980)
Nature
, vol.287
, Issue.5782
, pp. 509-516
-
-
Klug, A.1
Rhodes, D.2
Smith, J.3
-
61
-
-
0021760689
-
Structure of the nucleosome core particle at 7 Å resolution
-
T.J. Richmond, J.T. Finch, B. Rushton, D. Rhodes, and A. Klug Structure of the nucleosome core particle at 7 Å resolution Nature 311 1984 532 537
-
(1984)
Nature
, vol.311
, pp. 532-537
-
-
Richmond, T.J.1
Finch, J.T.2
Rushton, B.3
Rhodes, D.4
Klug, A.5
-
62
-
-
1842411320
-
Crystal structure of the nucleosome core particle at 2.8 A resolution
-
DOI 10.1038/38444
-
K. Lüger, A.W. Mader, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 1997 251 260 (Pubitemid 27406632)
-
(1997)
Nature
, vol.389
, Issue.6648
, pp. 251-260
-
-
Luger, K.1
Mader, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
64
-
-
77953320684
-
DNA architecture, deformability, and nucleosome positioning
-
F. Xu, and W.K. Olson DNA architecture, deformability, and nucleosome positioning J. Biomol. Struct. Dyn. 27 2010 725 739
-
(2010)
J. Biomol. Struct. Dyn.
, vol.27
, pp. 725-739
-
-
Xu, F.1
Olson, W.K.2
-
65
-
-
0037160543
-
From the sequence to the superstructural properties of DNAs
-
DOI 10.1016/S0301-4622(01)00246-0, PII S0301462201002460
-
C. Anselmi, P. De Santis, R. Paparcone, M. Savino, and A. Scipioni From the sequence to the superstructural properties of DNAs Biophys. Chem. 95 2002 23 47 (Pubitemid 34203674)
-
(2002)
Biophysical Chemistry
, vol.95
, Issue.1
, pp. 23-47
-
-
Anselmi, C.1
De Santis, P.2
Paparcone, R.3
Savino, M.4
Scipioni, A.5
-
66
-
-
0030572367
-
Sequence dependent circularization of DNAs: A physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending
-
P. De Santis, M. Fuà, M. Savino, C. Anselmi, and G. Bocchinfuso Sequence dependent circularization of DNAs: a physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending J. Phys. Chem. 100 1996 9968 9976 (Pubitemid 126788735)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.23
, pp. 9968-9976
-
-
De Santis, P.1
Fua, M.2
Savino, M.3
Anselmi, C.4
Bocchinfuso, G.5
-
67
-
-
0035853038
-
Mapping the intrinsic curvature and flexibility along the DNA chain
-
DOI 10.1073/pnas.051631198
-
G. Zuccheri, A. Scipioni, V. Cavaliere, G. Gargiulo, M. Savino, P. De Santis, and B. Samorì Mapping the intrinsic curvature and the flexibility along the DNA chain Proc. Natl Acad. Sci. U.S.A. 98 2001 3074 3079 (Pubitemid 32220801)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.6
, pp. 3074-3079
-
-
Zuccheri, G.1
Scipioni, A.2
Cavaliere, V.3
Gargiulo, G.4
De Santis, P.5
Samori, B.6
-
68
-
-
0036840332
-
Sequence-dependent DNA curvature and flexibility from scanning force microscopy images
-
A. Scipioni, C. Anselmi, G. Zuccheri, B. Samorì, and P. De Santis Sequence-dependent DNA curvature and flexibility from scanning force microscopy images Biophys. J. 83 2002 2408 2418 (Pubitemid 35265737)
-
(2002)
Biophysical Journal
, vol.83
, Issue.5
, pp. 2408-2418
-
-
Scipioni, A.1
Anselmi, C.2
Zuccheri, G.3
Samori, B.4
De Santis, P.5
-
69
-
-
0033548524
-
Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability
-
DOI 10.1006/jmbi.1998.2575
-
C. Anselmi, G. Bocchinfuso, P. De Santis, M. Savino, and A. Scipioni Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability J. Mol. Biol. 286 1999 1293 1301 (Pubitemid 29121716)
-
(1999)
Journal of Molecular Biology
, vol.286
, Issue.5
, pp. 1293-1301
-
-
Anselmi, C.1
Bocchinfuso, G.2
De Santis, P.3
Savino, M.4
Scipioni, A.5
-
70
-
-
0033869101
-
A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability
-
C. Anselmi, G. Bocchinfuso, P. De Santis, M. Savino, and A. Scipioni A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability Biophys. J. 79 2000 601 613 (Pubitemid 30626158)
-
(2000)
Biophysical Journal
, vol.79
, Issue.2
, pp. 601-613
-
-
Anselmi, C.1
Bocchinfuso, G.2
De Santis, P.3
Savino, M.4
Scipioni, A.5
-
71
-
-
0004032961
-
-
McGraw-Hill Book Company New York
-
M.R. Spiegel Fourier Analysis 1974 McGraw-Hill Book Company New York
-
(1974)
Fourier Analysis
-
-
Spiegel, M.R.1
-
72
-
-
0001448835
-
Statistical thermodynamic approach for evaluating the writhe transformations in circular DNAs
-
C. Anselmi, G. Bocchinfuso, P. De Santis, M. Fuà, A. Scipioni, and M. Savino Statistical thermodynamic approach for evaluating the writhe transformations in circular DNAs J. Phys. Chem. B 102 1998 5704 5714 (Pubitemid 128581131)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.29
, pp. 5704-5714
-
-
Anselmi, C.1
Bocchinfuso, G.2
De Santis, P.3
Fua, M.4
Scipioni, A.5
Savino, M.6
-
73
-
-
84985667623
-
Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles
-
O. Gotoh, and Y. Tagashira Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles Biopolymers 20 1981 1033 1042
-
(1981)
Biopolymers
, vol.20
, pp. 1033-1042
-
-
Gotoh, O.1
Tagashira, Y.2
-
75
-
-
0019843568
-
Structure of a B-DNA dodecamer. III. Geometry of hydration
-
H.R. Drew, and R.E. Dickerson Structure of a B-DNA dodecamer. III. Geometry of hydration J. Mol. Biol. 151 1981 535 556 (Pubitemid 12252694)
-
(1981)
Journal of Molecular Biology
, vol.151
, Issue.3
, pp. 535-556
-
-
Drew, H.R.1
Dickerson, R.E.2
-
76
-
-
0027058824
-
NMR observation of individual molecules of hydration water bound to DNA duplexes: Direct evidence for a spine of hydration water present in aqueous solution
-
E. Liepinsh, G. Otting, and K. Wuthrich NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution Nucleic Acids Res. 20 1992 6549 6553 (Pubitemid 23052674)
-
(1992)
Nucleic Acids Research
, vol.20
, Issue.24
, pp. 6549-6553
-
-
Liepinsh, E.1
Otting, G.2
Wuthrich, K.3
-
77
-
-
71749089641
-
A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes
-
A. Scipioni, S. Morosetti, and P. De Santis A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes Biopolymers 91 2009 1143 1153
-
(2009)
Biopolymers
, vol.91
, pp. 1143-1153
-
-
Scipioni, A.1
Morosetti, S.2
De Santis, P.3
-
78
-
-
77953314889
-
Prediction of nucleosome positioning in genomes: Limits and perspectives of physical and bioinformatic approaches
-
A. Scipioni, S. Morosetti, and P. De Santis Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches J. Biomol. Struct. Dyn. 27 2010 747 764
-
(2010)
J. Biomol. Struct. Dyn.
, vol.27
, pp. 747-764
-
-
Scipioni, A.1
Morosetti, S.2
De Santis, P.3
-
79
-
-
46349097649
-
DNA physical properties determine nucleosome occupancy from yeast to fly
-
DOI 10.1093/nar/gkn262
-
V. Miele, C. Vaillant, Y. d'Aubenton-Carafa, C. Thermes, and T. Grange DNA physical properties determine nucleosome occupancy from yeast to fly Nucleic Acid Res. 36 2008 3746 3756 (Pubitemid 351917536)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.11
, pp. 3746-3756
-
-
Miele, V.1
Vaillant, C.2
D'Aubenton-carafa, Y.3
Thermes, C.4
Grange, T.5
-
80
-
-
0026517738
-
A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells
-
J. Widom A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells Proc. Natl Acad. Sci. U.S.A. 89 1992 1095 1099
-
(1992)
Proc. Natl Acad. Sci. U.S.A.
, vol.89
, pp. 1095-1099
-
-
Widom, J.1
-
81
-
-
77951978209
-
Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin
-
A. Scipioni, G. Turchetti, S. Morosetti, and P. De Santis Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin Biophys. Chem. 148 2010 56 67
-
(2010)
Biophys. Chem.
, vol.148
, pp. 56-67
-
-
Scipioni, A.1
Turchetti, G.2
Morosetti, S.3
De Santis, P.4
-
82
-
-
52949092297
-
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae
-
J.P. Wang, Y. Fondufe-Mittendorf, L. Xi, G.F. Tsai, E. Segal, and J. Widom Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae PLoS Comput. Biol. 4 2008 e1000175
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000175
-
-
Wang, J.P.1
Fondufe-Mittendorf, Y.2
Xi, L.3
Tsai, G.F.4
Segal, E.5
Widom, J.6
|