-
2
-
-
3543023310
-
Evidence for nucleosome depletion at active regulatory regions genome-wide
-
Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 36: 900-905.
-
(2004)
Nat Genet
, vol.36
, pp. 900-905
-
-
Lee, C.K.1
Shibata, Y.2
Rao, B.3
Strahl, B.D.4
Lieb, J.D.5
-
3
-
-
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.
-
(2005)
Mol Cell
, vol.18
, pp. 735-748
-
-
Sekinger, E.A.1
Moqtaderi, Z.2
Struhl, K.3
-
5
-
-
48249107863
-
-
Society for General Microbiology. Symposium (50th: 1993: UMIST), Oliver SG, Broda P, Sims PFG (1993) The eukaryotic genome: organisation and regulation. Cambridge, New York: Cambridge University Press. pp xii, 395.
-
Society for General Microbiology. Symposium (50th: 1993: UMIST), Oliver SG, Broda P, Sims PFG (1993) The eukaryotic genome: organisation and regulation. Cambridge, New York: Cambridge University Press. pp xii, 395.
-
-
-
-
6
-
-
0022650876
-
Chromatin Fibers Are Left-Handed Double Helices with Diameter and Mass Per Unit Length That Depend on Linker Length
-
Williams SP, Athey BD, Muglia LJ, Schappe RS, Gough AH, et al. (1986) Chromatin Fibers Are Left-Handed Double Helices with Diameter and Mass Per Unit Length That Depend on Linker Length. Biophysical Journal 49: 233-248.
-
(1986)
Biophysical Journal
, vol.49
, pp. 233-248
-
-
Williams, S.P.1
Athey, B.D.2
Muglia, L.J.3
Schappe, R.S.4
Gough, A.H.5
-
7
-
-
29144531244
-
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning
-
Guillemette B, Bataille AR, Gevry N, Adam M, Blanchette M, et al. (2005) Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol 3: e384.
-
(2005)
PLoS Biol
, vol.3
-
-
Guillemette, B.1
Bataille, A.R.2
Gevry, N.3
Adam, M.4
Blanchette, M.5
-
8
-
-
29444454191
-
Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling
-
Li B, Pattenden SG, Lee D, Gutierrez J, Chen J, et al. (2005) Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc Natl Acad Sci U S A 102: 18385-18390.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 18385-18390
-
-
Li, B.1
Pattenden, S.G.2
Lee, D.3
Gutierrez, J.4
Chen, J.5
-
9
-
-
26844511498
-
Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin
-
Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, et al. (2005) Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123: 233-248.
-
(2005)
Cell
, vol.123
, pp. 233-248
-
-
Raisner, R.M.1
Hartley, P.D.2
Meneghini, M.D.3
Bao, M.Z.4
Liu, C.L.5
-
10
-
-
26844489856
-
Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss
-
Zhang H, Roberts DN, Cairns BR (2005) Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123: 219-231.
-
(2005)
Cell
, vol.123
, pp. 219-231
-
-
Zhang, H.1
Roberts, D.N.2
Cairns, B.R.3
-
11
-
-
22744432660
-
Genome-scale identification of nucleosome positions in S. cerevisiae
-
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, et al. (2005) Genome-scale 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
-
12
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
Lee W, Tillo D, Bray N, Morse RH, Davis RW, et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
-
(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
-
13
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, et al. (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
-
14
-
-
33846862405
-
High-throughput mapping of the chromatin structure of human promoters
-
Ozsolak F, Song JS, Liu XS, Fisher DE (2007) High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 25: 244-248.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 244-248
-
-
Ozsolak, F.1
Song, J.S.2
Liu, X.S.3
Fisher, D.E.4
-
15
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, et al. (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
-
16
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
-
17
-
-
33947201809
-
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
-
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, et al. (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128: 1231-1245.
-
(2007)
Cell
, vol.128
, pp. 1231-1245
-
-
Kim, T.H.1
Abdullaev, Z.K.2
Smith, A.D.3
Ching, K.A.4
Loukinov, D.I.5
-
18
-
-
30344478870
-
A global map of p53 transcription-factor binding sites in the human genome
-
Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell 124: 207-219.
-
(2006)
Cell
, vol.124
, pp. 207-219
-
-
Wei, C.L.1
Wu, Q.2
Vega, V.B.3
Chiu, K.P.4
Ng, P.5
-
19
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
20
-
-
48249137262
-
High-resolution mapping and characterization of open chromatin across the genome
-
In press
-
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, et al. (2007) High-resolution mapping and characterization of open chromatin across the genome. Cell In press.
-
(2007)
Cell
-
-
Boyle, A.P.1
Davis, S.2
Shulha, H.P.3
Meltzer, P.4
Margulies, E.H.5
-
21
-
-
0037453015
-
Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of imprinting?
-
Lee JT (2003) Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of imprinting? Curr Biol 13: R242-254.
-
(2003)
Curr Biol
, vol.13
-
-
Lee, J.T.1
-
22
-
-
0031029141
-
Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF
-
Burcin M, Arnold R, Lutz M, Kaiser B, Runge D, et al. (1997) Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF. Mol Cell Biol 17: 1281-1288.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 1281-1288
-
-
Burcin, M.1
Arnold, R.2
Lutz, M.3
Kaiser, B.4
Runge, D.5
-
23
-
-
0027362621
-
CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms
-
Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, et al. (1993) CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol 13: 7612-7624.
-
(1993)
Mol Cell Biol
, vol.13
, pp. 7612-7624
-
-
Klenova, E.M.1
Nicolas, R.H.2
Paterson, H.F.3
Carne, A.F.4
Heath, C.M.5
-
24
-
-
0035451090
-
CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
-
Ohlsson R, Renkawitz R, Lobanenkov V (2001) CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 17: 520-527.
-
(2001)
Trends Genet
, vol.17
, pp. 520-527
-
-
Ohlsson, R.1
Renkawitz, R.2
Lobanenkov, V.3
-
25
-
-
36348985646
-
Critical DNA binding interactions of the insulator protein CTCF: A small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci
-
Renda M, Baglivo I, Burgess-Beusse B, Esposito S, Fattorusso R, et al. (2007) Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci. J Biol Chem 282: 33336-33345.
-
(2007)
J Biol Chem
, vol.282
, pp. 33336-33345
-
-
Renda, M.1
Baglivo, I.2
Burgess-Beusse, B.3
Esposito, S.4
Fattorusso, R.5
-
26
-
-
0029929793
-
An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes
-
Filippova GN, Fagerlie S, Klenova EM, Myers C, Dehner Y, et al. (1996) An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol 16: 2802-2813.
-
(1996)
Mol Cell Biol
, vol.16
, pp. 2802-2813
-
-
Filippova, G.N.1
Fagerlie, S.2
Klenova, E.M.3
Myers, C.4
Dehner, Y.5
-
27
-
-
0033215443
-
Looping versus linking: Toward a model for long-distance gene activation
-
Bulger M, Groudine M (1999) Looping versus linking: toward a model for long-distance gene activation. Genes Dev 13: 2465-2477.
-
(1999)
Genes Dev
, vol.13
, pp. 2465-2477
-
-
Bulger, M.1
Groudine, M.2
-
28
-
-
33746063711
-
CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2
-
Kurukuti S, Tiwari VK, Tavoosidana G, Pugacheva E, Murrell A, et al. (2006) CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc Natl Acad Sci U S A 103: 10684-10689.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 10684-10689
-
-
Kurukuti, S.1
Tiwari, V.K.2
Tavoosidana, G.3
Pugacheva, E.4
Murrell, A.5
-
29
-
-
0025675441
-
A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5′-flanking sequence of the chicken c-myc gene
-
Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, et al. (1990) A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5′-flanking sequence of the chicken c-myc gene. Oncogene 5: 1743-1753.
-
(1990)
Oncogene
, vol.5
, pp. 1743-1753
-
-
Lobanenkov, V.V.1
Nicolas, R.H.2
Adler, V.V.3
Paterson, H.4
Klenova, E.M.5
-
30
-
-
0842310349
-
CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species
-
Yusufzai TM, Tagami H, Nakatani Y, Felsenfeld G (2004) CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell 13: 291-298.
-
(2004)
Mol Cell
, vol.13
, pp. 291-298
-
-
Yusufzai, T.M.1
Tagami, H.2
Nakatani, Y.3
Felsenfeld, G.4
-
31
-
-
33749155924
-
Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA
-
Segal DJ, Crotty JW, Bhakta MS, Barbas CF 3rd, Horton NC (2006) Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J Mol Biol 363: 405-421.
-
(2006)
J Mol Biol
, vol.363
, pp. 405-421
-
-
Segal, D.J.1
Crotty, J.W.2
Bhakta, M.S.3
Barbas 3rd, C.F.4
Horton, N.C.5
-
32
-
-
33747500567
-
A genomic code for nucleosome positioning
-
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, et al. (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
Thastrom, A.4
Field, Y.5
-
33
-
-
34548441932
-
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome
-
Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, et al. (2007) Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet 3: e136.
-
(2007)
PLoS Genet
, vol.3
-
-
Xi, H.1
Shulha, H.P.2
Lin, J.M.3
Vales, T.R.4
Fu, Y.5
-
35
-
-
8644230848
-
DNA instructed displacement of histones H2A and H2B at an inducible promoter
-
Vicent GP, Nacht AS, Smith CL, Peterson CL, Dimitrov S, et al. (2004) DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol Cell 16: 439-452.
-
(2004)
Mol Cell
, vol.16
, pp. 439-452
-
-
Vicent, G.P.1
Nacht, A.S.2
Smith, C.L.3
Peterson, C.L.4
Dimitrov, S.5
-
36
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu YT, Ching CW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics 39: 311-318.
-
(2007)
Nature Genetics
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.T.4
Ching, C.W.5
-
37
-
-
0034935016
-
CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus
-
Filippova GN, Thienes CP, Penn BH, Cho DH, Hu YJ, et al. (2001) CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus. Nat Genet 28: 335-343.
-
(2001)
Nat Genet
, vol.28
, pp. 335-343
-
-
Filippova, G.N.1
Thienes, C.P.2
Penn, B.H.3
Cho, D.H.4
Hu, Y.J.5
-
38
-
-
0036240062
-
Multiple nucleosome positioning sites regulate the CTCF-mediated insulator function of the H19 imprinting control region
-
Kanduri M, Kanduri C, Mariano P, Vostrov AA, Quitschke W, et al. (2002) Multiple nucleosome positioning sites regulate the CTCF-mediated insulator function of the H19 imprinting control region. Mol Cell Biol 22: 3339-3344.
-
(2002)
Mol Cell Biol
, vol.22
, pp. 3339-3344
-
-
Kanduri, M.1
Kanduri, C.2
Mariano, P.3
Vostrov, A.A.4
Quitschke, W.5
-
39
-
-
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.
-
(1988)
Nucleic Acids Res
, vol.16
, pp. 6677-6690
-
-
Kornberg, R.D.1
Stryer, L.2
-
40
-
-
33947137710
-
Dynamics of replication-independent histone turnover in budding yeast
-
Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, et al. (2007) Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408.
-
(2007)
Science
, vol.315
, pp. 1405-1408
-
-
Dion, M.F.1
Kaplan, T.2
Kim, M.3
Buratowski, S.4
Friedman, N.5
-
41
-
-
33947098453
-
Histone replacement marks the boundaries of cis-regulatory domains
-
Mito Y, Henikoff JG, Henikoff S (2007) Histone replacement marks the boundaries of cis-regulatory domains. Science 315: 1408-1411.
-
(2007)
Science
, vol.315
, pp. 1408-1411
-
-
Mito, Y.1
Henikoff, J.G.2
Henikoff, S.3
-
42
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
-
43
-
-
0033976586
-
TRANSFAC: An integrated system for gene expression regulation
-
Wingender E, Chen X, Hehl R, Karas H, Liebich I, et al. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28: 316-319.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 316-319
-
-
Wingender, E.1
Chen, X.2
Hehl, R.3
Karas, H.4
Liebich, I.5
-
44
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
-
45
-
-
0033289822
-
Expression and purification of recombinant histones and nucleosome reconstitution
-
Luger K, Rechsteiner TJ, Richmond TJ (1999) Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol Biol 119: 1-16.
-
(1999)
Methods Mol Biol
, vol.119
, pp. 1-16
-
-
Luger, K.1
Rechsteiner, T.J.2
Richmond, T.J.3
|