-
1
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. 2007. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
-
(2007)
Nature
, vol.446
, pp. 572-576
-
-
Albert, I.1
Mavrich, T.N.2
Tomsho, L.P.3
Qi, J.4
Zanton, S.J.5
Schuster, S.C.6
Pugh, B.F.7
-
2
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. 2008. High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322.
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
Davis, S.2
Shulha, H.P.3
Meltzer, P.4
Margulies, E.H.5
Weng, Z.6
Furey, T.S.7
Crawford, G.E.8
-
3
-
-
84862979650
-
A map of nucleosome positions in yeast at base-pair resolution
-
Brogaard K, Xi L, Wang P, 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, P.3
Widom, J.4
-
4
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, et al. 2010. Relationship between nucleosome positioning and DNA methylation. Nature 466: 388-392.
-
(2010)
Nature
, vol.466
, pp. 388-392
-
-
Chodavarapu, R.K.1
Feng, S.2
Bernatavichute, Y.V.3
Chen, P.Y.4
Stroud, H.5
Yu, Y.6
Hetzel, J.A.7
Kuo, F.8
Kim, J.9
Cokus, S.J.10
-
5
-
-
0347914548
-
Redefinition of the cleavage sites of DNase i on the nucleosome core particle
-
Cousins DJ, Islam SA, Sanderson MR, Proykova YG, Crane-Robinson C, Staynov DZ. 2004. Redefinition of the cleavage sites of DNase I on the nucleosome core particle. JMB 335: 1199-1211.
-
(2004)
JMB
, vol.335
, pp. 1199-1211
-
-
Cousins, D.J.1
Islam, S.A.2
Sanderson, M.R.3
Proykova, Y.G.4
Crane-Robinson, C.5
Staynov, D.Z.6
-
6
-
-
84857111200
-
DNASE1 sensitivity QTLs are a major determinant of human expression variation
-
Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, Leon SD, Michelini K, Lewellen N, Crawford GE, et al. 2012. DNASE1 sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
Pai, A.A.2
Pique-Regi, R.3
Veyrieras, J.B.4
Gaffney, D.J.5
Pickrell, J.K.6
Leon, S.D.7
Michelini, K.8
Lewellen, N.9
Crawford, G.E.10
-
7
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
8
-
-
85015069067
-
Controlling the double helix
-
Felsenfeld G, Groudine M. 2003. Controlling the double helix. Nature 421: 448-453.
-
(2003)
Nature
, vol.421
, pp. 448-453
-
-
Felsenfeld, G.1
Groudine, M.2
-
9
-
-
84870485829
-
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
-
Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza JZ, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I, et al. 2012. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res 22: 2399-2408.
-
(2012)
Genome Res
, vol.22
, pp. 2399-2408
-
-
Fenouil, R.1
Cauchy, P.2
Koch, F.3
Descostes, N.4
Cabeza, J.Z.5
Innocenti, C.6
Ferrier, P.7
Spicuglia, S.8
Gut, M.9
Gut, I.10
-
10
-
-
84870674869
-
Controls of nucleosome positioning in the human genome
-
e1003036
-
Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. 2012. Controls of nucleosome positioning in the human genome. PLoS Genet 8: e1003036.
-
(2012)
PLoS Genet
, vol.8
-
-
Gaffney, D.J.1
McVicker, G.2
Pai, A.A.3
Fondufe-Mittendorf, Y.N.4
Lewellen, N.5
Michelini, K.6
Widom, J.7
Gilad, Y.8
Pritchard, J.K.9
-
11
-
-
34250369627
-
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
-
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17: 877-885.
-
(2007)
Genome Res
, vol.17
, pp. 877-885
-
-
Giresi, P.G.1
Kim, J.2
McDaniell, R.M.3
Iyer, V.R.4
Lieb, J.D.5
-
12
-
-
0023899769
-
Nuclease hypersensitive sites in chromatin
-
Gross DS, Garrard WT. 1988. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57: 159-197.
-
(1988)
Annu Rev Biochem
, vol.57
, pp. 159-197
-
-
Gross, D.S.1
Garrard, W.T.2
-
13
-
-
80053501181
-
Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
-
Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K. 2011. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res 21: 1650-1658.
-
(2011)
Genome Res
, vol.21
, pp. 1650-1658
-
-
Hu, G.1
Schones, D.E.2
Cui, K.3
Ybarra, R.4
Northrup, D.5
Tang, Q.6
Gattinoni, L.7
Restifo, N.P.8
Huang, S.9
Zhao, K.10
-
14
-
-
80555125013
-
Variety of genomic DNA patterns for nucleosome positioning
-
Ioshikhes I, Hosid S, Pugh BF. 2011. Variety of genomic DNA patterns for nucleosome positioning. Genome Res 21: 1863-1871.
-
(2011)
Genome Res
, vol.21
, pp. 1863-1871
-
-
Ioshikhes, I.1
Hosid, S.2
Pugh, B.F.3
-
15
-
-
60349089645
-
Nucleosome positioning and gene regulation: Advances thorough genomics
-
Jiang C, Pugh BF. 2009. Nucleosome positioning and gene regulation: Advances thorough genomics. Nat Rev Genet 10: 161-172.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 161-172
-
-
Jiang, C.1
Pugh, B.F.2
-
16
-
-
62649085538
-
The DNAencoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNAencoded 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
-
17
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 6: 996-1006.
-
(2002)
Genome Res
, vol.6
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
18
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 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
-
19
-
-
77950854479
-
Heritable individual-specific and allele-specific chromatin signatures in humans
-
McDaniell R, Lee B-K, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, et al. 2010. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235-239.
-
(2010)
Science
, vol.328
, pp. 235-239
-
-
McDaniell, R.1
Lee, B.-K.2
Song, L.3
Liu, Z.4
Boyle, A.P.5
Erdos, M.R.6
Scott, L.J.7
Morken, M.A.8
Kucera, K.S.9
Battenhouse, A.10
-
20
-
-
34547418057
-
Nucleosome occupancy information improves de novo motif discovery
-
Narlikar L, Gordan R, Hartemink AJ. 2007. Nucleosome occupancy information improves de novo motif discovery. Res Comp Mol Biol 4453: 107-121.
-
(2007)
Res Comp Mol Biol
, vol.4453
, pp. 107-121
-
-
Narlikar, L.1
Gordan, R.2
Hartemink, A.J.3
-
21
-
-
0016133106
-
Internal structure of the chromatin subunit
-
Noll M. 1974. Internal structure of the chromatin subunit. Nucleic Acids Res 1: 1573-1578.
-
(1974)
Nucleic Acids Res
, vol.1
, pp. 1573-1578
-
-
Noll, M.1
-
22
-
-
77955388311
-
A preoccupied position on nucleosomes
-
Pugh BF. 2010. A preoccupied position on nucleosomes. Nat Struct Mol Biol 17: 923.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 923
-
-
Pugh, B.F.1
-
23
-
-
68049083831
-
Incorporating nucleosomes into thermodynamic models of transcription regulation
-
Raveh-Sadka T, Levo M, Segal E. 2009. Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19: 1480-1496.
-
(2009)
Genome Res
, vol.19
, pp. 1480-1496
-
-
Raveh-Sadka, T.1
Levo, M.2
Segal, E.3
-
24
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond TJ, Davey CA. 2003. The structure of DNA in the nucleosome core. Nature 423: 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
25
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell SC, Drew HR, Travers AA. 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
-
26
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, Roh T-Y, Barski A,Wang Z,Wei G, Zhao K. 2008 Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.-Y.4
Barski, A.5
Wang, Z.6
Wei, G.7
Zhao, K.8
-
27
-
-
33747500567
-
A genomic code for nucleosome positioning
-
Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang J-PZ, Widom J. 2006. A genomic code for nucleosome positioning. Nature 442: 772-778.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thåström, A.4
Field, Y.5
Moore, I.K.6
Wang, J.-P.Z.7
Widom, J.8
-
28
-
-
0018233528
-
DNase I, DNase II, and staphylococcal nuclease cut at different, yet symmetrically located, sites in the nucleosome core
-
Sollner-Webb B, Melchior W Jr, Felsenfeld G. 1978. DNase I, DNase II, and staphylococcal nuclease cut at different, yet symmetrically located, sites in the nucleosome core. Cell 14: 611-627.
-
(1978)
Cell
, vol.14
, pp. 611-627
-
-
Sollner-Webb, B.1
Melchior Jr., W.2
Felsenfeld, G.3
-
29
-
-
80053539409
-
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
-
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee B-K, Sheffield NC, Gra?f S, Huss M, Keefe D, et al. 2011. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21: 1757-1767.
-
(2011)
Genome Res
, vol.21
, pp. 1757-1767
-
-
Song, L.1
Zhang, Z.2
Grasfeder, L.L.3
Boyle, A.P.4
Giresi, P.G.5
Lee, B.-K.6
Sheffield, N.C.7
Gräf, S.8
Huss, M.9
Keefe, D.10
-
30
-
-
0034663606
-
DNase i digestion reveals alternating asymmetrical protection of the nucleosome by the higher order chromatin structure
-
Staynov DZ. 2000. DNase I digestion reveals alternating asymmetrical protection of the nucleosome by the higher order chromatin structure. Nucleic Acids Res 28: 3092-3099.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 3092-3099
-
-
Staynov, D.Z.1
-
31
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurana MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, et al. 2012. The accessible chromatin landscape of the human genome. Nature 489: 75-78.
-
(2012)
Nature
, vol.489
, pp. 75-78
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurana, M.T.5
Haugen, E.6
Sheffield, N.C.7
Stergachis, A.B.8
Wang, H.9
Vernot, B.10
-
32
-
-
33847106524
-
Higher-order structures of chromatin: The elusive 30 nm fiber
-
Tremethick DJ. 2007. Higher-order structures of chromatin: The elusive 30 nm fiber. Cell 128: 651-654.
-
(2007)
Cell
, vol.128
, pp. 651-654
-
-
Tremethick, D.J.1
-
33
-
-
0001415964
-
The pitch of chromatin DNA is reflected in its nucleotide sequence
-
Trifonov EN, Sussman JL. 1980. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci 77: 3816-3820.
-
(1980)
Proc Natl Acad Sci
, vol.77
, pp. 3816-3820
-
-
Trifonov, E.N.1
Sussman, J.L.2
-
34
-
-
79959557189
-
Determinants of nucleosome organization in primary humans cells
-
Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary humans 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
Sidow, A.6
-
35
-
-
0028935863
-
Chromatin higher order structure: Chasing a mirage?
-
van Holde K, Zlatanova J. 1995. Chromatin higher order structure: Chasing a mirage? J Bio Chem 270: 8373-8376.
-
(1995)
J Bio Chem
, vol.270
, pp. 8373-8376
-
-
Van Holde, K.1
Zlatanova, J.2
-
36
-
-
0018370487
-
Helical repeat of DNA in solution
-
Wang JC. 1979. Helical repeat of DNA in solution. Proc Natl Acad Sci 76: 200-203.
-
(1979)
Proc Natl Acad Sci
, vol.76
, pp. 200-203
-
-
Wang, J.C.1
-
37
-
-
52949092297
-
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae
-
e1000175
-
Wang J-P, Fondufe-Mittendorf Y, Xi L, Tsai G-F, Segal E, Widom J. 2008. Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Comput Biol 4: e1000175.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Wang, J.-P.1
Fondufe-Mittendorf, Y.2
Xi, L.3
Tsai, G.-F.4
Segal, E.5
Widom, J.6
-
38
-
-
0018458970
-
The chromatin structure of specific genes: 1. Evidence for higher order domain of defined DNA sequence
-
Wu C, Bingham PM, Livak KJ, Holmgren R, Elgin SCR. 1979. The chromatin structure of specific genes: 1. Evidence for higher order domain of defined DNA sequence. Cell 16: 797-806.
-
(1979)
Cell
, vol.16
, pp. 797-806
-
-
Wu, C.1
Bingham, P.M.2
Livak, K.J.3
Holmgren, R.4
Elgin, S.C.R.5
-
39
-
-
68249142923
-
Intrinsic histone-DNA interactions are not themajor determinant of nucleosome positions in vivo
-
Zhang Y,Moqtaderi Z, Rattner BP, Euskirchen G, SnyderM, Kadonaga JT, Liu XS, Struhl K. 2009. Intrinsic histone-DNA interactions are not themajor 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
|