-
1
-
-
84875149194
-
Regulation of nucleosome dynamics by histone modifications
-
Zentner GE, Henikoff S. 2013 Regulation of nucleosome dynamics by histone modifications. Nat. Struct. Mol. Biol. 20, 259-266. (doi:10.1038/nsmb. 2470)
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 259-266
-
-
Zentner, G.E.1
Henikoff, S.2
-
2
-
-
79956316470
-
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
-
Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011 A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332, 977-980. (doi:10.1126/science.1200508)
-
(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
-
3
-
-
80053140931
-
A role for Snf2-related nucleosomespacing enzymes in genome-wide nucleosome organization
-
Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton GJ, Owen-Hughes T. 2011 A role for Snf2-related nucleosomespacing enzymes in genome-wide nucleosome organization. Science 333, 1758-1760. (doi:10. 1126/science.1206097)
-
(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
-
4
-
-
84868679486
-
Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription
-
Hennig BP, Bendrin K, Zhou Y, Fischer T. 2012 Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription. EMBO Rep. 13, 997-1003. (doi:10.1038/embor.2012.146)
-
(2012)
EMBO Rep.
, vol.13
, pp. 997-1003
-
-
Hennig, B.P.1
Bendrin, K.2
Zhou, Y.3
Fischer, T.4
-
5
-
-
84870510245
-
CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S
-
Pointner J 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. (doi:10.1038/emboj.2012.289)
-
(2012)
Pombe. EMBO J.
, vol.31
, pp. 4388-4403
-
-
Pointner, J.1
-
6
-
-
84870575288
-
Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin
-
Shim YS, Choi Y, Kang K, Cho K, Oh S, Lee J, Grewal SIS, Lee D. 2012 Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin. EMBO J. 31, 4375-4387. (doi:10.1038/emboj.2012.267)
-
(2012)
EMBO J.
, vol.31
, pp. 4375-4387
-
-
Shim, Y.S.1
Choi, Y.2
Kang, K.3
Cho, K.4
Oh, S.5
Lee, J.6
Grewal, S.I.S.7
Lee, D.8
-
7
-
-
77952245290
-
Divergence of nucleosome positioning between two closely related yeast species: Genetic basis and functional consequences
-
Tirosh I, Sigal N, Barkai N. 2010 Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol. Syst. Biol. 6, 365. (doi:10.1038/msb.2010.20)
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 365
-
-
Tirosh, I.1
Sigal, N.2
Barkai, N.3
-
8
-
-
0023777538
-
Statistical distributions of nucleosomes: Nonrandom locations by a stochastic mechanism
-
Kornberg RD, Stryer L. 1988 Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 16, 6677-6690. (doi:10.1093/nar/16.14.6677)
-
(1988)
Nucleic Acids Res.
, vol.16
, pp. 6677-6690
-
-
Kornberg, R.D.1
Stryer, L.2
-
9
-
-
1842411320
-
Crystal structure of the nucleosome core particle at 2.8 A resolution
-
Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997 Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-260. (doi:10.1038/38444)
-
(1997)
Nature
, vol.389
, pp. 251-260
-
-
Luger, K.1
Mäder, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
10
-
-
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. (doi:10.1038/nature01595)
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
11
-
-
0039837085
-
Sequence motifs and free energies of selected natural and nonnatural nucleosome positioning DNA sequences
-
Thåström A, Lowary PT, Widlund HR, Cao H, Kubista M, Widom J. 1999 Sequence motifs and free energies of selected natural and nonnatural nucleosome positioning DNA sequences. J. Mol. Biol. 288, 213-229. (doi:10.1006/jmbi. 1999.2686)
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 213-229
-
-
Thåström, A.1
Lowary, P.T.2
Widlund, H.R.3
Cao, H.4
Kubista, M.5
Widom, J.6
-
12
-
-
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. USA 77, 3816-3820. (doi:10.1073/pnas.77.7.3816)
-
(1980)
Proc. Natl Acad. Sci. USA
, vol.77
, pp. 3816-3820
-
-
Trifonov, E.N.1
Sussman, J.L.2
-
13
-
-
0030595138
-
Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
-
Ioshikhes I, Bolshoy A, Derenshteyn K, Borodovsky M, Trifonov EN. 1996 Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262, 129-139. (doi:10.1006/jmbi.1996.0503)
-
(1996)
J. Mol. Biol.
, vol.262
, pp. 129-139
-
-
Ioshikhes, I.1
Bolshoy, A.2
Derenshteyn, K.3
Borodovsky, M.4
Trifonov, E.N.5
-
14
-
-
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. (doi:10.1038/nature04979)
-
(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
-
15
-
-
33749153628
-
Nucleosome positions predicted through comparative genomics
-
Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. 2006 Nucleosome positions predicted through comparative genomics. Nat. Genet. 38, 1210-1215. (doi:10.1038/ng1878)
-
(2006)
Nat. Genet.
, vol.38
, pp. 1210-1215
-
-
Ioshikhes, I.P.1
Albert, I.2
Zanton, S.J.3
Pugh, B.F.4
-
16
-
-
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. (doi:10.1101/gr. 116228.110)
-
(2011)
Genome Res.
, vol.21
, pp. 1863-1871
-
-
Ioshikhes, I.1
Hosid, S.2
Pugh, B.F.3
-
17
-
-
79957929301
-
Stable and dynamic nucleosome states during a meiotic developmental process
-
Zhang L, Ma H, Pugh BF. 2011 Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res. 21, 875-884. (doi:10.1101/gr.117465.110)
-
(2011)
Genome Res.
, vol.21
, pp. 875-884
-
-
Zhang, L.1
Ma, H.2
Pugh, B.F.3
-
18
-
-
84887900495
-
Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe
-
Soriano I, Quintales L, Antequera F. 2013 Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe. BMC Genomics 14, 813. (doi:10.1186/1471-2164-14-813)
-
(2013)
BMC Genomics
, vol.14
, pp. 813
-
-
Soriano, I.1
Quintales, L.2
Antequera, F.3
-
19
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. 2007 A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39, 1235-1244. (doi:10.1038/ng2117)
-
(2007)
Nat. Genet.
, vol.39
, 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
-
20
-
-
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. (doi:10. 1101/gr.078261.108)
-
(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
-
21
-
-
83255187902
-
Evolution of nucleosome occupancy: Conservation of global properties and divergence of gene-specific patterns
-
Tsui K, Dubuis S, Gebbia M, Morse RH, Barkai N, Tirosh I, Nislow C. 2011 Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol. Cell. Biol. 31, 4348-4355. (doi:10.1128/MCB.05276-11)
-
(2011)
Mol. Cell. Biol.
, vol.31
, pp. 4348-4355
-
-
Tsui, K.1
Dubuis, S.2
Gebbia, M.3
Morse, R.H.4
Barkai, N.5
Tirosh, I.6
Nislow, C.7
-
22
-
-
80555156654
-
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
-
Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ. 2011 Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res. 21, 1851-1862. (doi:10.1101/gr. 122267.111)
-
(2011)
Genome Res.
, vol.21
, pp. 1851-1862
-
-
Tsankov, A.1
Yanagisawa, Y.2
Rhind, N.3
Regev, A.4
Rando, O.J.5
-
23
-
-
84855351444
-
Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast
-
De Castro E, Soriano I, Marín L, Serrano R, Quintales L, Antequera F. 2012 Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast. EMBO J. 31, 124-137. (doi:10.1038/emboj.2011.350)
-
(2012)
EMBO J.
, vol.31
, pp. 124-137
-
-
De Castro, E.1
Soriano, I.2
Marín, L.3
Serrano, R.4
Quintales, L.5
Antequera, F.6
-
24
-
-
76349103252
-
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
-
Lantermann AB, Straub T, Strålfors A, Yuan G-C, Ekwall K, Korber P. 2010 Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 17, 251-257. (doi:10.1038/nsmb.1741)
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 251-257
-
-
Lantermann, A.B.1
Straub, T.2
Strålfors, A.3
Yuan, G.-C.4
Ekwall, K.5
Korber, P.6
-
25
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. (doi:10.1186/gb-2009-10-3-r25)
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
26
-
-
0003833285
-
-
Philadelphia, PA: Society for Industrial and Applied Mathematics
-
Daubechies I. 1992 Ten lectures on wavelets. Philadelphia, PA: Society for Industrial and Applied Mathematics.
-
(1992)
Ten Lectures on Wavelets
-
-
Daubechies, I.1
-
27
-
-
84929952110
-
Comparative analysis of methods for genome-wide nucleosome cartography
-
In press
-
Quintales L, Vázquez E, Antequera F. In press. Comparative analysis of methods for genome-wide nucleosome cartography. Brief. Bioinform. (doi:10. 1093/bib/bbu037)
-
Brief. Bioinform
-
-
Quintales, L.1
Vázquez, E.2
Antequera, F.3
-
28
-
-
79956319465
-
Comparative functional genomics of the fission yeasts
-
Rhind N et al. 2011 Comparative functional genomics of the fission yeasts. Science 332, 930-936. (doi:10.1126/science.1203357)
-
(2011)
Science
, vol.332
, pp. 930-936
-
-
Rhind, N.1
-
29
-
-
0034577919
-
Where does fission yeast sit on the tree of life?
-
Sipiczki M. 2000 Where does fission yeast sit on the tree of life? Genome Biol. 1, reviews1011. (doi:10. 1186/gb-2000-1-2-reviews1011)
-
(2000)
Genome Biol.
, vol.1
-
-
Sipiczki, M.1
-
30
-
-
84929961336
-
Nucleosome positioning in yeasts: Methods, maps, and mechanisms
-
In press
-
Lieleg C, Krietenstein N, Walker M, Korber P. In press. Nucleosome positioning in yeasts: methods, maps, and mechanisms. Chromosoma. (doi:10.1007/s00412-014-0501-x)
-
Chromosoma
-
-
Lieleg, C.1
Krietenstein, N.2
Walker, M.3
Korber, P.4
-
31
-
-
33646190728
-
Periodicity of SNP distribution around transcription start sites
-
Higasa K, Hayashi K. 2006 Periodicity of SNP distribution around transcription start sites. BMC Genomics 7, 66. (doi:10.1186/1471-2164-7-66)
-
(2006)
BMC Genomics
, vol.7
, pp. 66
-
-
Higasa, K.1
Hayashi, K.2
-
32
-
-
56049115800
-
A novel DNA sequence periodicity decodes nucleosome positioning
-
Chen K, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, Yu J. 2008 A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res. 36, 6228-6236. (doi:10.1093/nar/gkn626)
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 6228-6236
-
-
Chen, K.1
Meng, Q.2
Ma, L.3
Liu, Q.4
Tang, P.5
Chiu, C.6
Hu, S.7
Yu, J.8
-
33
-
-
56649089682
-
Evolutionary footprints of nucleosome positions in yeast
-
Washietl S, Machné R, Goldman N. 2008 Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 24, 583-587. (doi:10.1016/j. tig.2008.09.003)
-
(2008)
Trends Genet
, vol.24
, pp. 583-587
-
-
Washietl, S.1
Machné, R.2
Goldman, N.3
-
34
-
-
75149135277
-
G + C content dominates intrinsic nucleosome occupancy
-
Tillo D, Hughes TR. 2009 G + C content dominates intrinsic nucleosome occupancy. BMC Bioinform. 10, 442. (doi:10.1186/1471-2105-10-442)
-
(2009)
BMC Bioinform.
, vol.10
, pp. 442
-
-
Tillo, D.1
Hughes, T.R.2
-
35
-
-
58449116917
-
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
-
Sasaki S et al. 2009 Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323, 401-404. (doi:10.1126/science.1163183)
-
(2009)
Science
, vol.323
, pp. 401-404
-
-
Sasaki, S.1
-
36
-
-
84890280929
-
Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning
-
Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J, Wang J-P. 2013 Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proc. Natl Acad. Sci. USA 110, 20 158-20 163. (doi:10.1073/pnas.1315809110)
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 20158-20163
-
-
Moyle-Heyrman, G.1
Zaichuk, T.2
Xi, L.3
Zhang, Q.4
Uhlenbeck, O.C.5
Holmgren, R.6
Widom, J.7
Wang, J.-P.8
-
37
-
-
76949093375
-
Nucleosome positioning: How is it established, and why does it matter?
-
Radman-Livaja M, Rando OJ. 2010 Nucleosome positioning: how is it established, and why does it matter? Dev. Biol. 339, 258-266. (doi:10.1016/j. ydbio.2009.06.012)
-
(2010)
Dev. Biol.
, vol.339
, pp. 258-266
-
-
Radman-Livaja, M.1
Rando, O.J.2
-
39
-
-
80555156662
-
Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
-
Prendergast JGD, Semple C A M. 2011 Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res. 21, 1777-1787. (doi:10.1101/gr.122275.111)
-
(2011)
Genome Res.
, vol.21
, pp. 1777-1787
-
-
Prendergast, J.G.D.1
Semple, C.A.M.2
-
40
-
-
57149100569
-
The impact of the nucleosome code on protein-coding sequence evolution in yeast
-
Warnecke T, Batada NN, Hurst LD. 2008 The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet. 4, e1000250. (doi:10.1371/journal.pgen. 1000250)
-
(2008)
PLoS Genet.
, vol.4
, pp. e1000250
-
-
Warnecke, T.1
Batada, N.N.2
Hurst, L.D.3
-
41
-
-
59649112972
-
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome
-
Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT, Wang MD. 2009 High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat. Struct. Mol. Biol. 16, 124-129. (doi:10.1038/nsmb.1526)
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 124-129
-
-
Hall, M.A.1
Shundrovsky, A.2
Bai, L.3
Fulbright, R.M.4
Lis, J.T.5
Wang, M.D.6
-
42
-
-
0026513573
-
Species specific protein-DNA interactions may determine the chromatin units of genes in S. Cerevisiae and in S. Pombe
-
Bernardi F, Zatchej M, Thoma F. 1992 Species specific protein-DNA interactions may determine the chromatin units of genes in S. cerevisiae and in S. pombe. EMBO J. 11, 1177-1185.
-
(1992)
EMBO J.
, vol.11
, pp. 1177-1185
-
-
Bernardi, F.1
Zatchej, M.2
Thoma, F.3
-
43
-
-
84867371116
-
A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern
-
Hughes AL, Jin Y, Rando OJ, Struhl K. 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. (doi:10.1016/j.molcel. 2012.07.003)
-
(2012)
Mol. Cell
, vol.48
, pp. 5-15
-
-
Hughes, A.L.1
Jin, Y.2
Rando, O.J.3
Struhl, K.4
-
44
-
-
0028196622
-
Unusual chromosome structure of fission yeast DNA in mouse cells
-
McManus J, Perry P, Sumner AT, Wright DM, Thomson EJ, Allshire RC, Hastie ND, Bickmore WA. 1994 Unusual chromosome structure of fission yeast DNA in mouse cells. J. Cell Sci. 107, 469-486.
-
(1994)
J. Cell Sci.
, vol.107
, pp. 469-486
-
-
McManus, J.1
Perry, P.2
Sumner, A.T.3
Wright, D.M.4
Thomson, E.J.5
Allshire, R.C.6
Hastie, N.D.7
Bickmore, W.A.8
-
45
-
-
20444403749
-
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
-
Sekinger EA, Moqtaderi Z, Struhl K. 2005 Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18, 735-748. (doi:10.1016/j.molcel.2005.05.003)
-
(2005)
Mol. Cell
, vol.18
, pp. 735-748
-
-
Sekinger, E.A.1
Moqtaderi, Z.2
Struhl, K.3
-
46
-
-
79958038927
-
Working the kinks out of nucleosomal DNA
-
Olson WK, Zhurkin VB. 2011 Working the kinks out of nucleosomal DNA. Curr. Opin. Struct. Biol. 21, 348-357. (doi:10.1016/j.sbi.2011.03.006)
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 348-357
-
-
Olson, W.K.1
Zhurkin, V.B.2
|