-
1
-
-
0020534915
-
Enhancer elements
-
COI: 1:CAS:528:DyaL3sXksVynsrc%3D, PID: 6305503
-
Khoury G, Gruss P (1983) Enhancer elements. Cell 33:313–314
-
(1983)
Cell
, vol.33
, pp. 313-314
-
-
Khoury, G.1
Gruss, P.2
-
2
-
-
0019811465
-
Expression of a β-globin gene is enhanced by remote SV40 DNA sequences
-
COI: 1:CAS:528:DyaL38XotVOhsQ%3D%3D, PID: 6277502
-
Banerji J, Rusconi S, Schaffner W (1981) Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell 27:299–308
-
(1981)
Cell
, vol.27
, pp. 299-308
-
-
Banerji, J.1
Rusconi, S.2
Schaffner, W.3
-
3
-
-
0020611791
-
A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes
-
COI: 1:CAS:528:DyaL3sXltFOjtLg%3D, PID: 6409418
-
Banerji J, Olson L, Schaffner W (1983) A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes. Cell 33:729–740
-
(1983)
Cell
, vol.33
, pp. 729-740
-
-
Banerji, J.1
Olson, L.2
Schaffner, W.3
-
4
-
-
0020567861
-
A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene
-
COI: 1:CAS:528:DyaL3sXltFOjtLs%3D, PID: 6409417
-
Gillies SD, Morrison SL, Oi VT, Tonegawa S (1983) A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. Cell 33:717–728
-
(1983)
Cell
, vol.33
, pp. 717-728
-
-
Gillies, S.D.1
Morrison, S.L.2
Oi, V.T.3
Tonegawa, S.4
-
5
-
-
0021071029
-
Cell-specific expression controlled by the 5′-flanking region of insulin and chymotrypsin genes
-
COI: 1:CAS:528:DyaL2cXmt1Ohsw%3D%3D, PID: 6358900
-
Walker MD, Edlund T, Boulet AM, Rutter WJ (1983) Cell-specific expression controlled by the 5′-flanking region of insulin and chymotrypsin genes. Nature 306:557–561
-
(1983)
Nature
, vol.306
, pp. 557-561
-
-
Walker, M.D.1
Edlund, T.2
Boulet, A.M.3
Rutter, W.J.4
-
6
-
-
0022377642
-
Cell-specific expression of the rat insulin gene: evidence for role of two distinct 5′ flanking elements
-
COI: 1:CAS:528:DyaL28XivFKqsA%3D%3D, PID: 3904002
-
Edlund T, Walker MD, Barr PJ, Rutter WJ (1985) Cell-specific expression of the rat insulin gene: evidence for role of two distinct 5′ flanking elements. Science 230:912–916
-
(1985)
Science
, vol.230
, pp. 912-916
-
-
Edlund, T.1
Walker, M.D.2
Barr, P.J.3
Rutter, W.J.4
-
7
-
-
0022350323
-
Human β-interferon gene expression is regulated by an inducible enhancer element
-
COI: 1:CAS:528:DyaL2MXks1Gqt7Y%3D, PID: 3986910
-
Goodbourn S, Zinn K, Maniatis T (1985) Human β-interferon gene expression is regulated by an inducible enhancer element. Cell 41:509–520
-
(1985)
Cell
, vol.41
, pp. 509-520
-
-
Goodbourn, S.1
Zinn, K.2
Maniatis, T.3
-
8
-
-
84977751309
-
Cell type-specific transcriptional enhancement in vitro requires the presence of trans-acting factors
-
Schöler HR, Gruss P (1985) Cell type-specific transcriptional enhancement in vitro requires the presence of trans-acting factors. EMBO J 4:3305–3313
-
(1985)
EMBO J
, vol.4
, pp. 3305-3313
-
-
Schöler, H.R.1
Gruss, P.2
-
9
-
-
0025127307
-
The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates
-
COI: 1:CAS:528:DyaK3cXls1Khurw%3D, PID: 2167833
-
Ko MSH, Nakauchi H, Takahashi N (1990) The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J 9:2835–2842
-
(1990)
EMBO J
, vol.9
, pp. 2835-2842
-
-
Ko, M.S.H.1
Nakauchi, H.2
Takahashi, N.3
-
10
-
-
0029155607
-
Enhancers increase the probability but not the level of gene expression
-
COI: 1:CAS:528:DyaK2MXntVSkurk%3D, PID: 7624382
-
Walters MC, Fiering S, Eidemiller J, Magis W, Groudine M, Martin DIK (1995) Enhancers increase the probability but not the level of gene expression. Proc Natl Acad Sci USA 92:7125–7129
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 7125-7129
-
-
Walters, M.C.1
Fiering, S.2
Eidemiller, J.3
Magis, W.4
Groudine, M.5
Martin, D.I.K.6
-
11
-
-
0031018481
-
A globin enhancer acts by increasing the proportion of erythrocytes expressing a linked transgene
-
Sutherland HGE, Martin DIK, Whitelaw E (1997) A globin enhancer acts by increasing the proportion of erythrocytes expressing a linked transgene. Mol Cell Biol 3:1607–1614
-
(1997)
Mol Cell Biol
, vol.3
, pp. 1607-1614
-
-
Sutherland, H.G.E.1
Martin, D.I.K.2
Whitelaw, E.3
-
12
-
-
0033539575
-
Mechanism by which the IFN-β enhanceosome activates transcription
-
COI: 1:CAS:528:DyaK1MXns1GmsL4%3D, PID: 10557281
-
Yie J, Senger K, Thanos D (1999) Mechanism by which the IFN-β enhanceosome activates transcription. Proc Natl Acad Sci USA 96:13108–13113
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 13108-13113
-
-
Yie, J.1
Senger, K.2
Thanos, D.3
-
13
-
-
0031972647
-
Heat shock increases the reinitiation rate from potentiated chromatin templates
-
COI: 1:CAS:528:DyaK1cXivFyntw%3D%3D, PID: 9418883
-
Sandaltzopoulos R, Becker PB (1998) Heat shock increases the reinitiation rate from potentiated chromatin templates. Mol Cell Biol 18:361–367
-
(1998)
Mol Cell Biol
, vol.18
, pp. 361-367
-
-
Sandaltzopoulos, R.1
Becker, P.B.2
-
14
-
-
84857781464
-
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
-
COI: 1:CAS:528:DC%2BC38Xjt1Wjur4%3D, PID: 22270183
-
Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K (2012) Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res 22:490–503
-
(2012)
Cell Res
, vol.22
, pp. 490-503
-
-
Chepelev, I.1
Wei, G.2
Wangsa, D.3
Tang, Q.4
Zhao, K.5
-
15
-
-
79551655285
-
Functional and mechanistic diversity of distal transcription enhancers
-
COI: 1:CAS:528:DC%2BC3MXhsFOhtL0%3D, PID: 21295696
-
Bulger M, Groudine M (2011) Functional and mechanistic diversity of distal transcription enhancers. Cell 144:327–339
-
(2011)
Cell
, vol.144
, pp. 327-339
-
-
Bulger, M.1
Groudine, M.2
-
16
-
-
79952901680
-
Enhancer function: new insights into the regulation of tissue-specific gene expression
-
COI: 1:CAS:528:DC%2BC3MXjsVGkt7w%3D, PID: 21358745
-
Ong CT, Corces VG (2011) Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet 12:283–293
-
(2011)
Nat Rev Genet
, vol.12
, pp. 283-293
-
-
Ong, C.T.1
Corces, V.G.2
-
17
-
-
84886853624
-
Topology of mammalian developmental enhancers and their regulatory landscapes
-
PID: 24153303
-
De Laat W, Duboule D (2013) Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502:499–506
-
(2013)
Nature
, vol.502
, pp. 499-506
-
-
De Laat, W.1
Duboule, D.2
-
18
-
-
84876836223
-
Modification of enhancer chromatin: what, how and why?
-
COI: 1:CAS:528:DC%2BC3sXktVOqu7g%3D, PID: 23473601
-
Calo E, Wysocka J (2013) Modification of enhancer chromatin: what, how and why? Mol Cell 49:825–837
-
(2013)
Mol Cell
, vol.49
, pp. 825-837
-
-
Calo, E.1
Wysocka, J.2
-
19
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
COI: 1:CAS:528:DC%2BD2sXitVOksbc%3D, PID: 17277777
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311–318
-
(2007)
Nat Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
-
20
-
-
66549085342
-
ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
-
COI: 1:CAS:528:DC%2BD1MXjvV2ltL8%3D, PID: 19339991
-
Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN et al (2009) ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J 28:1418–1428
-
(2009)
EMBO J
, vol.28
, pp. 1418-1428
-
-
Welboren, W.J.1
van Driel, M.A.2
Janssen-Megens, E.M.3
van Heeringen, S.J.4
Sweep, F.C.5
Span, P.N.6
-
21
-
-
84870058502
-
Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome
-
COI: 1:CAS:528:DC%2BC38Xhs12gtbrL, PID: 23159369
-
Soufi A, Donahue G, Zaret KS (2012) Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151:994–1004
-
(2012)
Cell
, vol.151
, pp. 994-1004
-
-
Soufi, A.1
Donahue, G.2
Zaret, K.S.3
-
22
-
-
84865249952
-
Transcription factors: from enhancer binding to developmental control
-
COI: 1:CAS:528:DC%2BC38XhtFCrtrbM, PID: 22868264
-
Spitz F, Furlong EE (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13:613–626
-
(2012)
Nat Rev Genet
, vol.13
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.2
-
23
-
-
84937532893
-
Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming
-
COI: 1:CAS:528:DC%2BC2MXms1yns7Y%3D, PID: 25892221
-
Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS (2015) Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 161:555–568
-
(2015)
Cell
, vol.161
, pp. 555-568
-
-
Soufi, A.1
Garcia, M.F.2
Jaroszewicz, A.3
Osman, N.4
Pellegrini, M.5
Zaret, K.S.6
-
24
-
-
17644397256
-
Transcriptional enhancers: intelligent enhanceosomes or flexible billboards?
-
COI: 1:CAS:528:DC%2BD2MXivFGltLk%3D, PID: 15696541
-
Arnosti DN, Kulkarni MM (2005) Transcriptional enhancers: intelligent enhanceosomes or flexible billboards? J Cell Biochem 94:890–898
-
(2005)
J Cell Biochem
, vol.94
, pp. 890-898
-
-
Arnosti, D.N.1
Kulkarni, M.M.2
-
25
-
-
0031604766
-
Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription
-
COI: 1:CAS:528:DyaK1cXhs1yju78%3D, PID: 9659924
-
Merika M, Williams AJ, Chen G, Collins T, Thanos D (1998) Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. Mol Cell 1:277–287
-
(1998)
Mol Cell
, vol.1
, pp. 277-287
-
-
Merika, M.1
Williams, A.J.2
Chen, G.3
Collins, T.4
Thanos, D.5
-
26
-
-
41949113742
-
The enhaceosome
-
COI: 1:CAS:528:DC%2BD1cXkvFClsLw%3D, PID: 18206362
-
Panne D (2008) The enhaceosome. Curr Opin Struct Biol 18:236–242
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 236-242
-
-
Panne, D.1
-
27
-
-
33750336243
-
Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites
-
PID: 16961928
-
Vega VB, Lin CY, Lai KS, Kong SL, Xie M, Su X et al (2006) Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites. Genome Biol 7:R82
-
(2006)
Genome Biol
, vol.7
, pp. R82
-
-
Vega, V.B.1
Lin, C.Y.2
Lai, K.S.3
Kong, S.L.4
Xie, M.5
Su, X.6
-
28
-
-
78650638953
-
Integrative model of genomic factors for determining binding site selection by estrogen receptor-α
-
PID: 21179027
-
Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L et al (2010) Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol 6:456
-
(2010)
Mol Syst Biol
, vol.6
, pp. 456
-
-
Joseph, R.1
Orlov, Y.L.2
Huss, M.3
Sun, W.4
Kong, S.L.5
Ukil, L.6
-
29
-
-
80455144479
-
Pioneer transcription factors: establishing competence for gene expression
-
COI: 1:CAS:528:DC%2BC3MXhsFaktLzN, PID: 22056668
-
Zaret KS, Carroll JS (2011) Pioneer transcription factors: establishing competence for gene expression. Genes Dev 25:2227–2241
-
(2011)
Genes Dev
, vol.25
, pp. 2227-2241
-
-
Zaret, K.S.1
Carroll, J.S.2
-
30
-
-
84902302671
-
Transcription factor cooperativity in early adipogenic hotspots and super-enhancers
-
PID: 24857652
-
Siersbæk R, Rabiee A, Nielsen R, Sidoli S, Traynor S, Loft A et al (2014) Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell Rep 7:1443–1455
-
(2014)
Cell Rep
, vol.7
, pp. 1443-1455
-
-
Siersbæk, R.1
Rabiee, A.2
Nielsen, R.3
Sidoli, S.4
Traynor, S.5
Loft, A.6
-
31
-
-
0028872728
-
Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative
-
COI: 1:CAS:528:DyaK2MXjsl2rt7o%3D, PID: 7862134
-
Adams CC, Workman JL (1995) Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol Cell Biol 15:1405–1421
-
(1995)
Mol Cell Biol
, vol.15
, pp. 1405-1421
-
-
Adams, C.C.1
Workman, J.L.2
-
32
-
-
79960563344
-
Determinants and dynamics of genome accessibility
-
COI: 1:CAS:528:DC%2BC3MXovFyjtbo%3D, PID: 21747402
-
Bell O, Tiwari VK, Thomä NH, Schübeler D (2011) Determinants and dynamics of genome accessibility. Nat Rev Genet 12:554–564
-
(2011)
Nat Rev Genet
, vol.12
, pp. 554-564
-
-
Bell, O.1
Tiwari, V.K.2
Thomä, N.H.3
Schübeler, D.4
-
33
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A
-
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A et al (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
-
34
-
-
33747195353
-
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
-
COI: 1:CAS:528:DC%2BD28Xpt1aktbs%3D, PID: 16904174
-
Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–676
-
(2006)
Cell
, vol.126
, pp. 663-676
-
-
Takahashi, K.1
Yamanaka, S.2
-
35
-
-
84918527386
-
Pioneer transcription factors in cell reprogramming
-
PID: 25512556
-
Iwafuchi-Doi M, Zaret KS (2014) Pioneer transcription factors in cell reprogramming. Genes Dev 28:2679–2692
-
(2014)
Genes Dev
, vol.28
, pp. 2679-2692
-
-
Iwafuchi-Doi, M.1
Zaret, K.S.2
-
36
-
-
80052284848
-
OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes
-
COI: 1:CAS:528:DC%2BC3MXhtFCltbnK, PID: 21844352
-
You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, Jones PA (2011) OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc Natl Acad Sci USA 108:14497–14502
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 14497-14502
-
-
You, J.S.1
Kelly, T.K.2
De Carvalho, D.D.3
Taberlay, P.C.4
Liang, G.5
Jones, P.A.6
-
37
-
-
84922374664
-
TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
-
PID: 25391375
-
Sammons MA, Zhu J, Drake AM, Berger SL (2014) TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity. Genome Res 25:179–188
-
(2014)
Genome Res
, vol.25
, pp. 179-188
-
-
Sammons, M.A.1
Zhu, J.2
Drake, A.M.3
Berger, S.L.4
-
38
-
-
84895887720
-
Enhancer biology and enhanceropathies
-
COI: 1:CAS:528:DC%2BC2cXjsFGksb8%3D, PID: 24599251
-
Smith E, Shilatifard A (2014) Enhancer biology and enhanceropathies. Nat Struct Mol Biol 21:210–219
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 210-219
-
-
Smith, E.1
Shilatifard, A.2
-
39
-
-
83255188897
-
Polycomb-repressed genes have permissive enhancers that initiate reprogramming
-
COI: 1:CAS:528:DC%2BC3MXhs1SgtrzL, PID: 22153073
-
Taberlay PC, Kelly TK, Liu CC, You JS, De Carvalho DD, Miranda TB et al (2011) Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell 147:1283–1294
-
(2011)
Cell
, vol.147
, pp. 1283-1294
-
-
Taberlay, P.C.1
Kelly, T.K.2
Liu, C.C.3
You, J.S.4
De Carvalho, D.D.5
Miranda, T.B.6
-
40
-
-
18844394569
-
Dynamic regulation of Pol II transcription by the mammalian Mediator complex
-
COI: 1:CAS:528:DC%2BD2MXktFGjsLg%3D, PID: 15896744
-
Malik S, Roeder RG (2005) Dynamic regulation of Pol II transcription by the mammalian Mediator complex. Trends Biochem Sci 30:256–263
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 256-263
-
-
Malik, S.1
Roeder, R.G.2
-
41
-
-
77952569347
-
Inducible gene expression: diverse regulatory mechanisms
-
COI: 1:CAS:528:DC%2BC3cXmtFCjtL4%3D, PID: 20421872
-
Weake VM, Workman JL (2010) Inducible gene expression: diverse regulatory mechanisms. Nat Rev Genet 11:426–437
-
(2010)
Nat Rev Genet
, vol.11
, pp. 426-437
-
-
Weake, V.M.1
Workman, J.L.2
-
43
-
-
0034912714
-
Transcriptional coactivator complexes
-
PID: 11395415
-
Näär AM, Lemon BD, Tijan R (2001) Transcriptional coactivator complexes. Annu Rev Biochem 70:475–501
-
(2001)
Annu Rev Biochem
, vol.70
, pp. 475-501
-
-
Näär, A.M.1
Lemon, B.D.2
Tijan, R.3
-
44
-
-
0035997356
-
ATP-dependent nucleosome remodeling
-
COI: 1:CAS:528:DC%2BD38Xos1Cltr8%3D, PID: 12045097
-
Becker PB, Hörz W (2002) ATP-dependent nucleosome remodeling. Annu Rev Biochem 71:247–273
-
(2002)
Annu Rev Biochem
, vol.71
, pp. 247-273
-
-
Becker, P.B.1
Hörz, W.2
-
45
-
-
34250305146
-
Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project
-
ENCODE Project Consortium 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
-
-
ENCODE Project Consortium1
-
46
-
-
0033529565
-
Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome
-
COI: 1:CAS:528:DyaK1MXlt1Cgt7o%3D, PID: 10458604
-
Kornberg RD, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294
-
(1999)
Cell
, vol.98
, pp. 285-294
-
-
Kornberg, R.D.1
Lorch, Y.2
-
47
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
COI: 1:CAS:528:DC%2BD2sXmtFKjsro%3D, PID: 17512414
-
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z 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
Wang, Z.6
-
48
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
COI: 1:CAS:528:DC%2BD1cXnslKktL0%3D, PID: 18552846
-
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S et al (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40:897–903
-
(2008)
Nat Genet
, vol.40
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
Cuddapah, S.6
-
49
-
-
84855180224
-
Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity
-
PID: 22223044
-
Koch F, Andrau JC (2011) Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity. Transcription 2:263–268
-
(2011)
Transcription
, vol.2
, pp. 263-268
-
-
Koch, F.1
Andrau, J.C.2
-
50
-
-
80054910846
-
H3K4 tri-methylation provides an epigenetic signature of active enhancers
-
COI: 1:CAS:528:DC%2BC3MXhtVWrtLzP, PID: 21847099
-
Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H et al (2011) H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J 30:4198–4210
-
(2011)
EMBO J
, vol.30
, pp. 4198-4210
-
-
Pekowska, A.1
Benoukraf, T.2
Zacarias-Cabeza, J.3
Belhocine, M.4
Koch, F.5
Holota, H.6
-
51
-
-
84927559450
-
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
-
COI: 1:CAS:528:DC%2BC2cXhvFKmtbbI, PID: 25383968
-
Core LJ, Martins AL, Dank CG, Waters CT, Siepel A, Lis JT (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46:1311–1320
-
(2014)
Nat Genet
, vol.46
, pp. 1311-1320
-
-
Core, L.J.1
Martins, A.L.2
Dank, C.G.3
Waters, C.T.4
Siepel, A.5
Lis, J.T.6
-
52
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
COI: 1:CAS:528:DC%2BC3cXhsFKlsr%2FO, PID: 21160473
-
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470:279–283
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
Bajpai, R.2
Swigut, T.3
Brugmann, S.A.4
Flynn, R.A.5
Wysocka, J.6
-
53
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
COI: 1:CAS:528:DC%2BC3cXhs1Wjs7bP, PID: 21106759
-
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ et al (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107:21931–21936
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
Cheng, A.W.2
Welstead, G.G.3
Kooistra, T.4
Carey, B.W.5
Steine, E.J.6
-
54
-
-
80051564877
-
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
-
COI: 1:CAS:528:DC%2BC3MXpvFeqs7s%3D, PID: 21632746
-
Zentner GE, Tesar PJ, Scacheri PC (2011) Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 21:1273–1283
-
(2011)
Genome Res
, vol.21
, pp. 1273-1283
-
-
Zentner, G.E.1
Tesar, P.J.2
Scacheri, P.C.3
-
55
-
-
84867158452
-
Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
-
COI: 1:CAS:528:DC%2BC38XhsVKhsrjI, PID: 22593555
-
Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I et al (2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res 22:2043–2053
-
(2012)
Genome Res
, vol.22
, pp. 2043-2053
-
-
Bogdanovic, O.1
Fernandez-Miñán, A.2
Tena, J.J.3
de la Calle-Mustienes, E.4
Hidalgo, C.5
van Kruysbergen, I.6
-
56
-
-
84856239091
-
Tissue specific analysis of chromatin states identifies temporal signatures of enhancer activity during embryonic development
-
COI: 1:CAS:528:DC%2BC38XlsFyltw%3D%3D, PID: 22231485
-
Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N et al (2012) Tissue specific analysis of chromatin states identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44:148–156
-
(2012)
Nat Genet
, vol.44
, pp. 148-156
-
-
Bonn, S.1
Zinzen, R.P.2
Girardot, C.3
Gustafson, E.H.4
Perez-Gonzalez, A.5
Delhomme, N.6
-
57
-
-
84856962477
-
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation
-
COI: 1:CAS:528:DC%2BC38Xhs1Cqt7k%3D, PID: 22297846
-
Whyte WA, Bilodeau S, Orlando DA, Hoke HA, Frampton GM, Foster CT et al (2012) Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482:221–225
-
(2012)
Nature
, vol.482
, pp. 221-225
-
-
Whyte, W.A.1
Bilodeau, S.2
Orlando, D.A.3
Hoke, H.A.4
Frampton, G.M.5
Foster, C.T.6
-
58
-
-
77952364528
-
NuA4-dependent acetylation of nucleosomal histones H4 and H2A directly stimulates incorporation of H2A.Z by the SWR1 complex
-
COI: 1:CAS:528:DC%2BC3cXmtVyktr0%3D, PID: 20332092
-
Altaf M, Auger A, Monnet-Saksouk J, Brodeur J, Piquet S, Cramet M et al (2010) NuA4-dependent acetylation of nucleosomal histones H4 and H2A directly stimulates incorporation of H2A.Z by the SWR1 complex. J Biol Chem 285:15966–15977
-
(2010)
J Biol Chem
, vol.285
, pp. 15966-15977
-
-
Altaf, M.1
Auger, A.2
Monnet-Saksouk, J.3
Brodeur, J.4
Piquet, S.5
Cramet, M.6
-
59
-
-
82955198464
-
Recognition of enhancer element-specific histone methylation by TIP60 in transcriptional activation
-
COI: 1:CAS:528:DC%2BC3MXhsVKjtr7P, PID: 22081016
-
Jeong KW, Kim K, Situ AJ, Ulmer TS, An W, Stallcup MR (2011) Recognition of enhancer element-specific histone methylation by TIP60 in transcriptional activation. Nat Struct Mol Biol 18:1358–1365
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 1358-1365
-
-
Jeong, K.W.1
Kim, K.2
Situ, A.J.3
Ulmer, T.S.4
An, W.5
Stallcup, M.R.6
-
60
-
-
34547793043
-
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression
-
Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X et al (2007) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 488:718–722
-
(2007)
Nature
, vol.488
, pp. 718-722
-
-
Lan, F.1
Collins, R.E.2
De Cegli, R.3
Alpatov, R.4
Horton, J.R.5
Shi, X.6
-
61
-
-
34547725157
-
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
-
COI: 1:CAS:528:DC%2BD2sXos1yksL8%3D, PID: 17687327
-
Ooi SKT, Qiu C, Bernstein E, Li K, Jia D, Yang Z et al (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448:714–717
-
(2007)
Nature
, vol.448
, pp. 714-717
-
-
Ooi, S.K.T.1
Qiu, C.2
Bernstein, E.3
Li, K.4
Jia, D.5
Yang, Z.6
-
63
-
-
0031841947
-
A human RNA polymerase II complex containing factors that modify chromatin structure
-
COI: 1:CAS:528:DyaK1cXls1Sgtbg%3D, PID: 9710619
-
Cho H, Orphanides G, Sun X, Yang X-J, Ogryzko V, Lees E et al (1998) A human RNA polymerase II complex containing factors that modify chromatin structure. Mol Cell Biol 18:5355–5363
-
(1998)
Mol Cell Biol
, vol.18
, pp. 5355-5363
-
-
Cho, H.1
Orphanides, G.2
Sun, X.3
Yang, X.-J.4
Ogryzko, V.5
Lees, E.6
-
64
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
COI: 1:CAS:528:DC%2BD1MXhslCntLg%3D, PID: 19212405
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854–858
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
Holt, A.6
-
65
-
-
17644445419
-
Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300
-
COI: 1:CAS:528:DyaK1cXjtFCjtLo%3D, PID: 9590171
-
Yao TP, Oh SP, Fuchs M, Zhou ND, Ch’ng LE, Newsome D et al (1998) Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell 93:361–372
-
(1998)
Cell
, vol.93
, pp. 361-372
-
-
Yao, T.P.1
Oh, S.P.2
Fuchs, M.3
Zhou, N.D.4
Ch’ng, L.E.5
Newsome, D.6
-
66
-
-
70350031643
-
CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing
-
COI: 1:CAS:528:DC%2BD1MXhtlSisbfF, PID: 19700617
-
Tie F, Banerjee R, Stratton CA, Prasad-Sinha J, Stepanik V, Zlobin A et al (2009) CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development 136:3131–3141
-
(2009)
Development
, vol.136
, pp. 3131-3141
-
-
Tie, F.1
Banerjee, R.2
Stratton, C.A.3
Prasad-Sinha, J.4
Stepanik, V.5
Zlobin, A.6
-
67
-
-
78751611793
-
Distinct roles of GCN5/PCAF-mediated H3K9ac and CB/p300-mediated H3K18/27ac in nuclear receptor transactivation
-
COI: 1:CAS:528:DC%2BC3cXhsFSrsr3E, PID: 21131905
-
Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE et al (2011) Distinct roles of GCN5/PCAF-mediated H3K9ac and CB/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J 30:249–262
-
(2011)
EMBO J
, vol.30
, pp. 249-262
-
-
Jin, Q.1
Yu, L.R.2
Wang, L.3
Zhang, Z.4
Kasper, L.H.5
Lee, J.E.6
-
68
-
-
84872198371
-
Genomic occupancy of the transcriptional co-activators p300 and CBP
-
PID: 23131664
-
Holmqvist P-H, Mannervik M (2013) Genomic occupancy of the transcriptional co-activators p300 and CBP. Transcription 4:18–23
-
(2013)
Transcription
, vol.4
, pp. 18-23
-
-
Holmqvist, P.-H.1
Mannervik, M.2
-
69
-
-
84904042103
-
Transcriptional coregulators: fine-tuning metabolism
-
COI: 1:CAS:528:DC%2BC2cXntl2jurw%3D, PID: 24794975
-
Mouchiroud L, Eichner LJ, Shaw RJ, Auwerx J (2014) Transcriptional coregulators: fine-tuning metabolism. Cell Metab 20:26–40
-
(2014)
Cell Metab
, vol.20
, pp. 26-40
-
-
Mouchiroud, L.1
Eichner, L.J.2
Shaw, R.J.3
Auwerx, J.4
-
70
-
-
79955960768
-
Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes
-
COI: 1:CAS:528:DC%2BC3MXmsVChtL4%3D, PID: 21596309
-
Cai L, Sutter BM, Li B, Tu BP (2011) Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol Cell 42:426–437
-
(2011)
Mol Cell
, vol.42
, pp. 426-437
-
-
Cai, L.1
Sutter, B.M.2
Li, B.3
Tu, B.P.4
-
71
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
COI: 1:CAS:528:DC%2BC3cXkslartL8%3D, PID: 20393465
-
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J et al (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465:182–187
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
Wu, J.6
-
72
-
-
80555156095
-
SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers
-
COI: 1:CAS:528:DC%2BC3MXhsVaqtLvL, PID: 22055187
-
Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L (2011) SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell 44:410–423
-
(2011)
Mol Cell
, vol.44
, pp. 410-423
-
-
Krebs, A.R.1
Karmodiya, K.2
Lindahl-Allen, M.3
Struhl, K.4
Tora, L.5
-
73
-
-
80052968080
-
Regulation of FoxO transcription factors by acetylation and protein–protein interactions
-
Daitoku H, Sakamaki J, Fukamizu A (2001) Regulation of FoxO transcription factors by acetylation and protein–protein interactions. Biochem Biophys Acta 1813:1954–1960
-
(2001)
Biochem Biophys Acta
, vol.1813
, pp. 1954-1960
-
-
Daitoku, H.1
Sakamaki, J.2
Fukamizu, A.3
-
74
-
-
84958643027
-
Touch, act and go: landing and operating on nucleosomes
-
COI: 1:CAS:528:DC%2BC28XovFegsg%3D%3D, PID: 26787641
-
Speranzini V, Pilotto S, Sixma TK, Mattevi A (2016) Touch, act and go: landing and operating on nucleosomes. EMBO J 35:376–388
-
(2016)
EMBO J
, vol.35
, pp. 376-388
-
-
Speranzini, V.1
Pilotto, S.2
Sixma, T.K.3
Mattevi, A.4
-
75
-
-
84864012602
-
Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27
-
COI: 1:CAS:528:DC%2BC38XoslShs7s%3D, PID: 22493065
-
Tie F, Banerjee R, Conrad PA, Scacheri PC, Harte PJ (2012) Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27. Mol Cell Biol 32:2323–2334
-
(2012)
Mol Cell Biol
, vol.32
, pp. 2323-2334
-
-
Tie, F.1
Banerjee, R.2
Conrad, P.A.3
Scacheri, P.C.4
Harte, P.J.5
-
76
-
-
84870558596
-
Transcription in the absence of histone H3.2 and H3K4 methylation
-
PID: 23142044
-
Hödl M, Basler K (2012) Transcription in the absence of histone H3.2 and H3K4 methylation. Curr Biol 22:2253–2257
-
(2012)
Curr Biol
, vol.22
, pp. 2253-2257
-
-
Hödl, M.1
Basler, K.2
-
77
-
-
84873513937
-
A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb
-
COI: 1:CAS:528:DC%2BC3sXhvFOktr8%3D, PID: 23393264
-
Pengelly AR, Copur Ö, Jäckle H, Herzig A, Müller J (2013) A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb. Science 339:698–699
-
(2013)
Science
, vol.339
, pp. 698-699
-
-
Pengelly, A.R.1
Copur, Ö.2
Jäckle, H.3
Herzig, A.4
Müller, J.5
-
78
-
-
84862662420
-
Dynamics and memory of heterochromatin in living cells
-
COI: 1:CAS:528:DC%2BC38XoslGqs7s%3D, PID: 22704655
-
Hathaway NA, Bell O, Hodges C, Miller EL, Neel DS, Crabtree GR (2012) Dynamics and memory of heterochromatin in living cells. Cell 149:1447–1460
-
(2012)
Cell
, vol.149
, pp. 1447-1460
-
-
Hathaway, N.A.1
Bell, O.2
Hodges, C.3
Miller, E.L.4
Neel, D.S.5
Crabtree, G.R.6
-
79
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
COI: 1:CAS:528:DC%2BD1cXhvVSrtbY%3D, PID: 18243105
-
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z et al (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
-
80
-
-
33745416080
-
Genome-scale mapping of DNase I sensitivity in vivo using DNA microarrays
-
COI: 1:CAS:528:DC%2BD28XmtVSnsbc%3D, PID: 16791208
-
Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H et al (2006) Genome-scale mapping of DNase I sensitivity in vivo using DNA microarrays. Nat Methods 3:511–518
-
(2006)
Nat Methods
, vol.3
, pp. 511-518
-
-
Sabo, P.J.1
Kuehn, M.S.2
Thurman, R.3
Johnson, B.E.4
Johnson, E.M.5
Cao, H.6
-
81
-
-
84865755978
-
The accessible chromatin landscape of human genome
-
COI: 1:CAS:528:DC%2BC38XhtlGns7bL, PID: 22955617
-
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E et al (2012) The accessible chromatin landscape of human genome. Nature 489:75–82
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurano, M.T.5
Haugen, E.6
-
82
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
COI: 1:CAS:528:DC%2BC3cXivVCiu7o%3D, PID: 20208536
-
He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q et al (2010) Nucleosome dynamics define transcriptional enhancers. Nat Genet 42:343–347
-
(2010)
Nat Genet
, vol.42
, pp. 343-347
-
-
He, H.H.1
Meyer, C.A.2
Shin, H.3
Bailey, S.T.4
Wei, G.5
Wang, Q.6
-
83
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
COI: 1:CAS:528:DC%2BD1cXlvV2qtLY%3D, PID: 18408708
-
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ et al (2008) Nucleosome organization in the Drosophila genome. Nature 453:358–364
-
(2008)
Nature
, vol.453
, pp. 358-364
-
-
Mavrich, T.N.1
Jiang, C.2
Ioshikhes, I.P.3
Li, X.4
Venters, B.J.5
Zanton, S.J.6
-
84
-
-
0029026719
-
Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
-
COI: 1:CAS:528:DyaK2MXmsVOjsLw%3D, PID: 7781610
-
Iyer V, Struhl K (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
-
85
-
-
0034999881
-
Poly (dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites
-
COI: 1:CAS:528:DC%2BD3MXjs1yjsr0%3D, PID: 11340174
-
Anderson JD, Widom J (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
-
86
-
-
67650725820
-
The biology of chromatin remodeling complexes
-
COI: 1:CAS:528:DC%2BD1MXos1Ghtbg%3D, PID: 19355820
-
Clapier CR, Cairns BR (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
-
87
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Shones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z et al (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887–898
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Shones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.Y.4
Barski, A.5
Wang, Z.6
-
88
-
-
0037057668
-
SATB1 targets chromatin remodelling to regulate genes over long distances
-
COI: 1:CAS:528:DC%2BD38Xns1Ont74%3D, PID: 12374985
-
Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T (2002) SATB1 targets chromatin remodelling to regulate genes over long distances. Nature 419:641–645
-
(2002)
Nature
, vol.419
, pp. 641-645
-
-
Yasui, D.1
Miyano, M.2
Cai, S.3
Varga-Weisz, P.4
Kohwi-Shigematsu, T.5
-
89
-
-
84872509787
-
Olig2 targets chromatin remodelers to enhancers to initiate oligodendrocyte differentiation
-
COI: 1:CAS:528:DC%2BC3sXht1ygtbg%3D, PID: 23332759
-
Yu Y, Chen Y, Kim B, Wang H, Zhao C, He X et al (2013) Olig2 targets chromatin remodelers to enhancers to initiate oligodendrocyte differentiation. Cell 152:248–261
-
(2013)
Cell
, vol.152
, pp. 248-261
-
-
Yu, Y.1
Chen, Y.2
Kim, B.3
Wang, H.4
Zhao, C.5
He, X.6
-
90
-
-
4444239112
-
Mutations in a new member of the chromodomain gene family cause CHARGE syndrome
-
COI: 1:CAS:528:DC%2BD2cXntFSkuro%3D, PID: 15300250
-
Vissers LE, van Ravenswaaij CM, Admiraal R, Hurst JA, de Vries BB et al (2004) Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat Genet 36:955–957
-
(2004)
Nat Genet
, vol.36
, pp. 955-957
-
-
Vissers, L.E.1
van Ravenswaaij, C.M.2
Admiraal, R.3
Hurst, J.A.4
de Vries, B.B.5
-
91
-
-
77957344798
-
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression
-
PID: 20657823
-
Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG et al (2010) CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet 6:e1001023
-
(2010)
PLoS Genet
, vol.6
, pp. e1001023
-
-
Schnetz, M.P.1
Handoko, L.2
Akhtar-Zaidi, B.3
Bartels, C.F.4
Pereira, C.F.5
Fisher, A.G.6
-
92
-
-
37849044154
-
GATA-1 modulates the chromatin structure and activity of the chicken α-globin 3′ enhancer
-
COI: 1:CAS:528:DC%2BD1cXkslGgsA%3D%3D, PID: 17984219
-
Escamilla-Del-Arenal M, Recillas-Targa F (2008) GATA-1 modulates the chromatin structure and activity of the chicken α-globin 3′ enhancer. Mol Cell Biol 28:575–586
-
(2008)
Mol Cell Biol
, vol.28
, pp. 575-586
-
-
Escamilla-Del-Arenal, M.1
Recillas-Targa, F.2
-
93
-
-
84907829329
-
A regulatory element affects the activity and chromatin structure of the chicken α-globin 3′ enhancer
-
PID: 25239823
-
García-González E, Recillas-Targa F (2014) A regulatory element affects the activity and chromatin structure of the chicken α-globin 3′ enhancer. Biochim Biophys Acta 1839:1233–1241
-
(2014)
Biochim Biophys Acta
, vol.1839
, pp. 1233-1241
-
-
García-González, E.1
Recillas-Targa, F.2
-
94
-
-
33750010410
-
Recruitment of the SWI/SNF protein Brg1 by a multiprotein complex effects transcriptional repression in murine erythroid progenitors
-
COI: 1:CAS:528:DC%2BD28XhtVajsbvM, PID: 16800816
-
Xu Z, Meng X, Cai Y, Koury MJ, Brandt SJ (2006) Recruitment of the SWI/SNF protein Brg1 by a multiprotein complex effects transcriptional repression in murine erythroid progenitors. Biochem J 399:297–304
-
(2006)
Biochem J
, vol.399
, pp. 297-304
-
-
Xu, Z.1
Meng, X.2
Cai, Y.3
Koury, M.J.4
Brandt, S.J.5
-
95
-
-
70350672529
-
BRG1 directly regulates nucleosome structure and chromatin looping of the alpha globin locus to activate transcription
-
COI: 1:CAS:528:DC%2BD1MXhtlWlt7bM, PID: 19696073
-
Kim SI, Bresnick EH, Bultman SJ (2009) BRG1 directly regulates nucleosome structure and chromatin looping of the alpha globin locus to activate transcription. Nucleic Acids Res 37:6019–6027
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 6019-6027
-
-
Kim, S.I.1
Bresnick, E.H.2
Bultman, S.J.3
-
96
-
-
0022799080
-
Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction release additional upstream activating DNA elements
-
COI: 1:CAS:528:DyaL28Xmt1Sjtbo%3D, PID: 3536481
-
Almer A, Rudolph H, Hinnen A, Hörz W (1986) Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction release additional upstream activating DNA elements. EMBO J 5:2689–2696
-
(1986)
EMBO J
, vol.5
, pp. 2689-2696
-
-
Almer, A.1
Rudolph, H.2
Hinnen, A.3
Hörz, W.4
-
97
-
-
1842314454
-
Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter
-
COI: 1:CAS:528:DyaL1cXltVansw%3D%3D, PID: 2822386
-
Richard-Foy H, Hager GL (1987) Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J 6:2321–2328
-
(1987)
EMBO J
, vol.6
, pp. 2321-2328
-
-
Richard-Foy, H.1
Hager, G.L.2
-
98
-
-
0033615717
-
DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
-
COI: 1:CAS:528:DyaK1MXnt1Gqsrc%3D, PID: 10555141
-
Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247–257
-
(1999)
Cell
, vol.99
, pp. 247-257
-
-
Okano, M.1
Bell, D.W.2
Haber, D.A.3
Li, E.4
-
99
-
-
84905052378
-
DNA methylation dynamics of the human preimplantation embryo
-
COI: 1:CAS:528:DC%2BC2cXht1ChurfJ, PID: 25079558
-
Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A et al (2014) DNA methylation dynamics of the human preimplantation embryo. Nature 511:611–615
-
(2014)
Nature
, vol.511
, pp. 611-615
-
-
Smith, Z.D.1
Chan, M.M.2
Humm, K.C.3
Karnik, R.4
Mekhoubad, S.5
Regev, A.6
-
100
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
COI: 1:CAS:528:DC%2BC3MXhs1aisb%2FN, PID: 22170606
-
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A et al (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480:490–495
-
(2011)
Nature
, vol.480
, pp. 490-495
-
-
Stadler, M.B.1
Murr, R.2
Burger, L.3
Ivanek, R.4
Lienert, F.5
Schöler, A.6
-
101
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
COI: 1:CAS:528:DC%2BC38XhtlGnsLzL, PID: 22955618
-
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B et al (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489:83–90
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
Vierstra, J.2
Stergachis, A.B.3
Reynolds, A.P.4
Haugen, E.5
Vernot, B.6
-
102
-
-
84865369147
-
DNA methylation dynamics during in vivo differentiation of blood and skin stem cells
-
COI: 1:CAS:528:DC%2BC38XhtFahsbbP, PID: 22841485
-
Bock C, Beerman I, Lien W-H, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A (2012) DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell 47:633–647
-
(2012)
Mol Cell
, vol.47
, pp. 633-647
-
-
Bock, C.1
Beerman, I.2
Lien, W.-H.3
Smith, Z.D.4
Gu, H.5
Boyle, P.6
Gnirke, A.7
Fuchs, E.8
Rossi, D.J.9
Meissner, A.10
-
103
-
-
84876946045
-
Genome-wide analysis reveals TET-and TDG-dependent 5-methylcytosine oxidation dynamics
-
COI: 1:CAS:528:DC%2BC3sXmt1CktLs%3D, PID: 23602152
-
Shen L, Wu H, Diep D, Yamaguchi S, D’Alessio AC, Fung HL et al (2013) Genome-wide analysis reveals TET-and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153:692–706
-
(2013)
Cell
, vol.153
, pp. 692-706
-
-
Shen, L.1
Wu, H.2
Diep, D.3
Yamaguchi, S.4
D’Alessio, A.C.5
Fung, H.L.6
-
104
-
-
84874771985
-
Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives
-
COI: 1:CAS:528:DC%2BC3sXjtVShtbY%3D, PID: 23434322
-
Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C et al (2013) Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152:1146–1159
-
(2013)
Cell
, vol.152
, pp. 1146-1159
-
-
Spruijt, C.G.1
Gnerlich, F.2
Smits, A.H.3
Pfaffeneder, T.4
Jansen, P.W.5
Bauer, C.6
-
105
-
-
79953319002
-
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers
-
PID: 21233399
-
Sérandour AA, Avner S, Percevault F, Demay F, Bizot M, Lucchetti-Miganeh C et al (2011) Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers. Genome Res 21:555–565
-
(2011)
Genome Res
, vol.21
, pp. 555-565
-
-
Sérandour, A.A.1
Avner, S.2
Percevault, F.3
Demay, F.4
Bizot, M.5
Lucchetti-Miganeh, C.6
-
106
-
-
79959209733
-
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
-
COI: 1:CAS:528:DC%2BC3MXotVWnsr0%3D, PID: 21689397
-
Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE (2011) 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol 12:R54
-
(2011)
Genome Biol
, vol.12
, pp. R54
-
-
Stroud, H.1
Feng, S.2
Morey Kinney, S.3
Pradhan, S.4
Jacobsen, S.E.5
-
107
-
-
84861990517
-
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome
-
COI: 1:CAS:528:DC%2BC38Xntlylu7s%3D, PID: 22608086
-
Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A et al (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149:1368–1380
-
(2012)
Cell
, vol.149
, pp. 1368-1380
-
-
Yu, M.1
Hon, G.C.2
Szulwach, K.E.3
Song, C.X.4
Zhang, L.5
Kim, A.6
-
108
-
-
79956308473
-
Genome wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
-
COI: 1:CAS:528:DC%2BC3MXlvVahu7c%3D, PID: 21552279
-
Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M et al (2011) Genome wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473:394–397
-
(2011)
Nature
, vol.473
, pp. 394-397
-
-
Pastor, W.A.1
Pape, U.J.2
Huang, Y.3
Henderson, H.R.4
Lister, R.5
Ko, M.6
-
109
-
-
79954457998
-
Genome wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells
-
COI: 1:CAS:528:DC%2BC3MXkvFCrtb8%3D, PID: 21460036
-
Wu H, D’Alessio AC, Ito S, Wang Z, Cui K, Zhao K et al (2011) Genome wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev 25:679–684
-
(2011)
Genes Dev
, vol.25
, pp. 679-684
-
-
Wu, H.1
D’Alessio, A.C.2
Ito, S.3
Wang, Z.4
Cui, K.5
Zhao, K.6
-
110
-
-
79959431845
-
Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain
-
COI: 1:CAS:528:DC%2BC3MXotF2nsr8%3D, PID: 21731699
-
Frauer C, Hoffmann T, Bultmann S, Casa V, Cardoso MC, Antes I et al (2011) Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One 6:e21306
-
(2011)
PLoS One
, vol.6
, pp. e21306
-
-
Frauer, C.1
Hoffmann, T.2
Bultmann, S.3
Casa, V.4
Cardoso, M.C.5
Antes, I.6
-
111
-
-
84871563384
-
MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system
-
PID: 23260135
-
Mellén M, Ayata P, Dewell S, Kriaucionis S, Heintz N (2012) MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151:1417–1430
-
(2012)
Cell
, vol.151
, pp. 1417-1430
-
-
Mellén, M.1
Ayata, P.2
Dewell, S.3
Kriaucionis, S.4
Heintz, N.5
-
112
-
-
84888057006
-
DNMT1-interacting RNAs block gene-specific DNA methylation
-
PID: 24107992
-
Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J et al (2013) DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 503:371–376
-
(2013)
Nature
, vol.503
, pp. 371-376
-
-
Di Ruscio, A.1
Ebralidze, A.K.2
Benoukraf, T.3
Amabile, G.4
Goff, L.A.5
Terragni, J.6
-
113
-
-
84906791043
-
Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A
-
COI: 1:CAS:528:DC%2BC2cXht1Oqs7fM, PID: 25087872
-
Arab K, Park YT, Lindroth AM, Schäfer A, Oakes C et al (2014) Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol Cell 55:604–614
-
(2014)
Mol Cell
, vol.55
, pp. 604-614
-
-
Arab, K.1
Park, Y.T.2
Lindroth, A.M.3
Schäfer, A.4
Oakes, C.5
-
114
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
PID: 20485488
-
De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK et al (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8:e1000384
-
(2010)
PLoS Biol
, vol.8
, pp. e1000384
-
-
De Santa, F.1
Barozzi, I.2
Mietton, F.3
Ghisletti, S.4
Polletti, S.5
Tusi, B.K.6
-
115
-
-
84870182699
-
Noncoding transcription at enhancers: general principles and functional models
-
COI: 1:CAS:528:DC%2BC38XhvVyktbjF, PID: 22905871
-
Natoli G, Andrau JC (2012) Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 46:1–19
-
(2012)
Annu Rev Genet
, vol.46
, pp. 1-19
-
-
Natoli, G.1
Andrau, J.C.2
-
116
-
-
84896845300
-
The emerging roles of eRNAs in transcriptional regulatory networks
-
COI: 1:CAS:528:DC%2BC2cXht1KrtrjK, PID: 24525859
-
Mousavi K, Zare H, Koulnis M, Sartorelli V (2014) The emerging roles of eRNAs in transcriptional regulatory networks. RNA Biol 11:106–110
-
(2014)
RNA Biol
, vol.11
, pp. 106-110
-
-
Mousavi, K.1
Zare, H.2
Koulnis, M.3
Sartorelli, V.4
-
117
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
COI: 1:CAS:528:DC%2BD1MXptVWjsr0%3D, PID: 19571010
-
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106:11667–11672
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
Rivea Morales, D.6
-
118
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
PID: 20887892
-
Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:46–58
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Ørom, U.A.1
Derrien, T.2
Beringer, M.3
Gumireddy, K.4
Gardini, A.5
Bussotti, G.6
-
119
-
-
33746069681
-
Dosage compensation in mammals: fine-tuning the expression of the X chromosome
-
COI: 1:CAS:528:DC%2BD28XnsVyjtrk%3D, PID: 16847345
-
Heard E, Disteche CM (2006) Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20:1848–1867
-
(2006)
Genes Dev
, vol.20
, pp. 1848-1867
-
-
Heard, E.1
Disteche, C.M.2
-
120
-
-
84861904178
-
Genome regulation by long noncoding RNAs
-
COI: 1:CAS:528:DC%2BC38XhtVGls7bO, PID: 22663078
-
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166
-
(2012)
Annu Rev Biochem
, vol.81
, pp. 145-166
-
-
Rinn, J.L.1
Chang, H.Y.2
-
121
-
-
84874368349
-
Activating RNAs associate with mediator to enhance chromatin architecture and transcription
-
COI: 1:CAS:528:DC%2BC3sXjtFWjur8%3D, PID: 23417068
-
Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA et al (2013) Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature 494:497–501
-
(2013)
Nature
, vol.494
, pp. 497-501
-
-
Lai, F.1
Orom, U.A.2
Cesaroni, M.3
Beringer, M.4
Taatjes, D.J.5
Blobel, G.A.6
-
122
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
COI: 1:CAS:528:DC%2BD1cXhtV2qsr3N, PID: 18562676
-
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB et al (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18:1433–1445
-
(2008)
Genome Res
, vol.18
, pp. 1433-1445
-
-
Dinger, M.E.1
Amaral, P.P.2
Mercer, T.R.3
Pang, K.C.4
Bruce, S.J.5
Gardiner, B.B.6
-
123
-
-
79955836460
-
A rapid, extensive and transient transcriptional response to estrogen signaling in breast cancer cells
-
COI: 1:CAS:528:DC%2BC3MXmtFGmtb8%3D, PID: 21549415
-
Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT et al (2011) A rapid, extensive and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145:622–634
-
(2011)
Cell
, vol.145
, pp. 622-634
-
-
Hah, N.1
Danko, C.G.2
Core, L.3
Waterfall, J.J.4
Siepel, A.5
Lis, J.T.6
-
124
-
-
84879694221
-
Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
-
COI: 1:CAS:528:DC%2BC3sXosFWktL0%3D, PID: 23728303
-
Lam MTY, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y et al (2013) Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498:511–515
-
(2013)
Nature
, vol.498
, pp. 511-515
-
-
Lam, M.T.Y.1
Cho, H.2
Lesch, H.P.3
Gosselin, D.4
Heinz, S.5
Tanaka-Oishi, Y.6
-
125
-
-
84879695128
-
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
-
COI: 1:CAS:528:DC%2BC3sXosFahtro%3D, PID: 23728302
-
Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY et al (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498:516–520
-
(2013)
Nature
, vol.498
, pp. 516-520
-
-
Li, W.1
Notani, D.2
Ma, Q.3
Tanasa, B.4
Nunez, E.5
Chen, A.Y.6
-
126
-
-
84883756441
-
eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci
-
COI: 1:CAS:528:DC%2BC3sXhtlGqsrrE, PID: 23993744
-
Mousavi K, Zare H, Dell’Orso S, Grontved L, Gutierrez-Cruz G, Derfoul A et al (2013) eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 51:606–617
-
(2013)
Mol Cell
, vol.51
, pp. 606-617
-
-
Mousavi, K.1
Zare, H.2
Dell’Orso, S.3
Grontved, L.4
Gutierrez-Cruz, G.5
Derfoul, A.6
-
127
-
-
84873456575
-
eRNAs are required for p53-dependent enhancer activity and gene transcription
-
COI: 1:CAS:528:DC%2BC3sXnvVyi, PID: 23273978
-
Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA et al (2013) eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 49:524–535
-
(2013)
Mol Cell
, vol.49
, pp. 524-535
-
-
Melo, C.A.1
Drost, J.2
Wijchers, P.J.3
van de Werken, H.4
de Wit, E.5
Oude Vrielink, J.A.6
-
128
-
-
84897446230
-
Enhancer RNAs and regulated transcriptional programs
-
COI: 1:CAS:528:DC%2BC2cXkvV2rurw%3D, PID: 24674738
-
Lam MTY, Li W, Rosenfeld MG, Glass CK (2014) Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 39:170–182
-
(2014)
Trends Biochem Sci
, vol.39
, pp. 170-182
-
-
Lam, M.T.Y.1
Li, W.2
Rosenfeld, M.G.3
Glass, C.K.4
-
129
-
-
84865757142
-
Landscape of transcription in human cells
-
COI: 1:CAS:528:DC%2BC38XhtlGnt73M, PID: 22955620
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A et al (2012) Landscape of transcription in human cells. Nature 489:101–108
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.6
-
130
-
-
84881526410
-
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
-
COI: 1:CAS:528:DC%2BC3sXht1Gmtb3L, PID: 23932714
-
Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD et al (2013) Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 51:310–325
-
(2013)
Mol Cell
, vol.51
, pp. 310-325
-
-
Kaikkonen, M.U.1
Spann, N.J.2
Heinz, S.3
Romanoski, C.E.4
Allison, K.A.5
Stender, J.D.6
-
131
-
-
84922391291
-
Enhancer RNA facilitates NELF release from immediate early genes
-
COI: 1:CAS:528:DC%2BC2cXhs1agtrnE, PID: 25263592
-
Schaukowitch K, Joo JY, Liu X et al (2014) Enhancer RNA facilitates NELF release from immediate early genes. Mol Cell 56:29–41
-
(2014)
Mol Cell
, vol.56
, pp. 29-41
-
-
Schaukowitch, K.1
Joo, J.Y.2
Liu, X.3
-
132
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
COI: 1:CAS:528:DC%2BC2cXkvV2mt7g%3D, PID: 24670763
-
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J et al (2014) An atlas of active enhancers across human cell types and tissues. Nature 507:455–461
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
-
133
-
-
60349089645
-
Nucleosome positioning and gene regulation: advances through genomics
-
COI: 1:CAS:528:DC%2BD1MXhvFGlu7Y%3D, PID: 19204718
-
Jiang C, Pugh F (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161–172
-
(2009)
Nat Rev Genet
, vol.10
, pp. 161-172
-
-
Jiang, C.1
Pugh, F.2
-
134
-
-
79958077283
-
Nucleosome positioning in Saccharomyces cerevisiae
-
COI: 1:CAS:528:DC%2BC3MXpslOitrg%3D, PID: 21646431
-
Jansen A, Verstrepen KJ (2011) Nucleosome positioning in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 75:301–320
-
(2011)
Microbiol Mol Biol Rev
, vol.75
, pp. 301-320
-
-
Jansen, A.1
Verstrepen, K.J.2
-
135
-
-
84886704313
-
Nucleosome distribution near the 3′ ends of genes in the human genome
-
COI: 1:CAS:528:DC%2BC3sXhslGhtb3F, PID: 24096667
-
Huang H, Liu H, Sun X (2013) Nucleosome distribution near the 3′ ends of genes in the human genome. Biosci Biotechnol Biochem 77:2051–2055
-
(2013)
Biosci Biotechnol Biochem
, vol.77
, pp. 2051-2055
-
-
Huang, H.1
Liu, H.2
Sun, X.3
-
136
-
-
84923997553
-
Human promoters are intrinsically directional
-
COI: 1:CAS:528:DC%2BC2MXhvVOqtro%3D, PID: 25639469
-
Duttke SH, Lacadie SA, Ibrahaim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U (2015) Human promoters are intrinsically directional. Mol Cell 57:674–684
-
(2015)
Mol Cell
, vol.57
, pp. 674-684
-
-
Duttke, S.H.1
Lacadie, S.A.2
Ibrahaim, M.M.3
Glass, C.K.4
Corcoran, D.L.5
Benner, C.6
Heinz, S.7
Kadonaga, J.T.8
Ohler, U.9
-
137
-
-
84923333199
-
Integrative analysis of haplotype-resolved epigenomes across human tissues
-
COI: 1:CAS:528:DC%2BC2MXjtVSktb0%3D, PID: 25693566
-
Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY et al (2015) Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature 518:350–354
-
(2015)
Nature
, vol.518
, pp. 350-354
-
-
Leung, D.1
Jung, I.2
Rajagopal, N.3
Schmitt, A.4
Selvaraj, S.5
Lee, A.Y.6
-
138
-
-
84862778066
-
Intragenic enhancers act as alternative promoters
-
COI: 1:CAS:528:DC%2BC38XjtFWgurs%3D, PID: 22264824
-
Kowalczyk MS, Hughes JR, Garrick D, Lynch MD, Sharpe JA, Sloane-Stanley JA et al (2012) Intragenic enhancers act as alternative promoters. Mol Cell 45:447–458
-
(2012)
Mol Cell
, vol.45
, pp. 447-458
-
-
Kowalczyk, M.S.1
Hughes, J.R.2
Garrick, D.3
Lynch, M.D.4
Sharpe, J.A.5
Sloane-Stanley, J.A.6
-
139
-
-
77957139539
-
Mediator and cohesin connect gene expression and chromatin architecture
-
COI: 1:CAS:528:DC%2BC3cXhtVCmtLzP, PID: 20720539
-
Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL et al (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467:430–435
-
(2010)
Nature
, vol.467
, pp. 430-435
-
-
Kagey, M.H.1
Newman, J.J.2
Bilodeau, S.3
Zhan, Y.4
Orlando, D.A.5
van Berkum, N.L.6
-
140
-
-
77953020027
-
The Mediator complex protein Med31 is required for embryonic growth and cell proliferation during mammalian development
-
COI: 1:CAS:528:DC%2BC3cXmsVekur4%3D, PID: 20347762
-
Risley MD, Clowes C, Yu M, Mitchell K, Hentges KE (2010) The Mediator complex protein Med31 is required for embryonic growth and cell proliferation during mammalian development. Dev Biol 342:146–156
-
(2010)
Dev Biol
, vol.342
, pp. 146-156
-
-
Risley, M.D.1
Clowes, C.2
Yu, M.3
Mitchell, K.4
Hentges, K.E.5
-
141
-
-
84876216563
-
Master transcription factors and mediator establish super-enhancers at key cell identity genes
-
COI: 1:CAS:528:DC%2BC3sXlvVCrtbg%3D, PID: 23582322
-
Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH et al (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153:307–319
-
(2013)
Cell
, vol.153
, pp. 307-319
-
-
Whyte, W.A.1
Orlando, D.A.2
Hnisz, D.3
Abraham, B.J.4
Lin, C.Y.5
Kagey, M.H.6
-
142
-
-
77958111633
-
The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation
-
COI: 1:CAS:528:DC%2BC3cXhtlShsLrP, PID: 20940737
-
Malik S, Roeder RG (2010) The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet 11:761–772
-
(2010)
Nat Rev Genet
, vol.11
, pp. 761-772
-
-
Malik, S.1
Roeder, R.G.2
-
143
-
-
0033898468
-
p300-mediated acetylation facilitates the transfer of histone H2A–H2B dimers from nucleosomes to a histone chaperone
-
COI: 1:CAS:528:DC%2BD3cXls1yqtro%3D, PID: 10921904
-
Ito T, Ikehara T, Nakagawa T, Kraus WL, Muramatsu M (2000) p300-mediated acetylation facilitates the transfer of histone H2A–H2B dimers from nucleosomes to a histone chaperone. Genes Dev 14:1899–1907
-
(2000)
Genes Dev
, vol.14
, pp. 1899-1907
-
-
Ito, T.1
Ikehara, T.2
Nakagawa, T.3
Kraus, W.L.4
Muramatsu, M.5
-
144
-
-
84925283769
-
What are super-enhancers?
-
COI: 1:CAS:528:DC%2BC2cXitFygtb7M, PID: 25547603
-
Pott S, Lieb JD (2015) What are super-enhancers? Nat Genet 47:8–12
-
(2015)
Nat Genet
, vol.47
, pp. 8-12
-
-
Pott, S.1
Lieb, J.D.2
-
145
-
-
84923811117
-
The Mediator complex: a central integrator of transcription
-
COI: 1:CAS:528:DC%2BC2MXjtFemsrs%3D, PID: 25693131
-
Allen BL, Taatjes DJ (2015) The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 16:155–166
-
(2015)
Nat Rev Mol Cell Biol
, vol.16
, pp. 155-166
-
-
Allen, B.L.1
Taatjes, D.J.2
-
146
-
-
0034048586
-
To be or not to be active: the stochastic nature of enhancer action
-
Fiering S, Whitelaw E, Martin DI (2000) To be or not to be active: the stochastic nature of enhancer action. BioEssays 4:381–387
-
(2000)
BioEssays
, vol.4
, pp. 381-387
-
-
Fiering, S.1
Whitelaw, E.2
Martin, D.I.3
-
147
-
-
84903697261
-
Enhancer function: mechanistic and genome-wide insights come together
-
COI: 1:CAS:528:DC%2BC2cXhtFSgtLrE, PID: 24996062
-
Plank JL, Dean A (2014) Enhancer function: mechanistic and genome-wide insights come together. Mol Cell 55:5–14
-
(2014)
Mol Cell
, vol.55
, pp. 5-14
-
-
Plank, J.L.1
Dean, A.2
-
148
-
-
84923786414
-
The selection and function of cell type-specific enhancers
-
COI: 1:CAS:528:DC%2BC2MXjtFenu7o%3D, PID: 25650801
-
Heinz S, Romanoski CE, Benner C, Glass CK (2015) The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 16:144–154
-
(2015)
Nat Rev Mol Cell Biol
, vol.16
, pp. 144-154
-
-
Heinz, S.1
Romanoski, C.E.2
Benner, C.3
Glass, C.K.4
-
149
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
COI: 1:CAS:528:DC%2BC38XlslShurw%3D, PID: 22495300
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y et al (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
-
150
-
-
84861100147
-
Spatial partitioning of the regulatory landscape of the X-inactivation centre
-
COI: 1:CAS:528:DC%2BC38XlslSisrw%3D, PID: 22495304
-
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485:381–385
-
(2012)
Nature
, vol.485
, pp. 381-385
-
-
Nora, E.P.1
Lajoie, B.R.2
Schulz, E.G.3
Giorgetti, L.4
Okamoto, I.5
Servant, N.6
-
151
-
-
84856747483
-
Three-dimensional folding and functional organization principles of the Drosophila genome
-
COI: 1:CAS:528:DC%2BC38XhvFehsLo%3D, PID: 22265598
-
Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M et al (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458–472
-
(2012)
Cell
, vol.148
, pp. 458-472
-
-
Sexton, T.1
Yaffe, E.2
Kenigsberg, E.3
Bantignies, F.4
Leblanc, B.5
Hoichman, M.6
-
152
-
-
84939802036
-
Getting the genome in shape: the formation of loops, domain and compartments
-
PID: 26257189
-
Bouwman BA, de Laat W (2015) Getting the genome in shape: the formation of loops, domain and compartments. Genome Biol 16:154
-
(2015)
Genome Biol
, vol.16
, pp. 154
-
-
Bouwman, B.A.1
de Laat, W.2
-
153
-
-
84905642951
-
Genome-scale functional characterization of Drosophila developmental enhancers in vivo
-
COI: 1:CAS:528:DC%2BC2cXpslGiu74%3D, PID: 24896182
-
Kvon EZ, Kazmar T, Stampfel G, Yáñez-Cuna JO, Pagani M, Schernhuber K et al (2014) Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512:91–95
-
(2014)
Nature
, vol.512
, pp. 91-95
-
-
Kvon, E.Z.1
Kazmar, T.2
Stampfel, G.3
Yáñez-Cuna, J.O.4
Pagani, M.5
Schernhuber, K.6
-
154
-
-
84930092058
-
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
-
COI: 1:CAS:528:DC%2BC2MXht1Wltb%2FL, PID: 25938943
-
Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L et al (2015) Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet 47:598–606
-
(2015)
Nat Genet
, vol.47
, pp. 598-606
-
-
Mifsud, B.1
Tavares-Cadete, F.2
Young, A.N.3
Sugar, R.4
Schoenfelder, S.5
Ferreira, L.6
-
155
-
-
84887620842
-
A high-resolution map of the three-dimensional chromatin interactome in human cells
-
COI: 1:CAS:528:DC%2BC3sXhslSnsLfK, PID: 24141950
-
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY et al (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503:290–294
-
(2013)
Nature
, vol.503
, pp. 290-294
-
-
Jin, F.1
Li, Y.2
Dixon, J.R.3
Selvaraj, S.4
Ye, Z.5
Lee, A.Y.6
-
156
-
-
84927763931
-
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
-
COI: 1:CAS:528:DC%2BC2MXmvFCgu7c%3D, PID: 25752748
-
Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM et al (2015) The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res 25:582–597
-
(2015)
Genome Res
, vol.25
, pp. 582-597
-
-
Schoenfelder, S.1
Furlan-Magaril, M.2
Mifsud, B.3
Tavares-Cadete, F.4
Sugar, R.5
Javierre, B.M.6
-
157
-
-
84905593782
-
Enhancer loops appear stable during development and are associated with paused polymerase
-
COI: 1:CAS:528:DC%2BC2cXht12ms77L, PID: 25043061
-
Ghavi-Helm Y, Klein FA, Pakodzi T, Ciglar L, Noordermeer D, Huber W et al (2014) Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512:96–100
-
(2014)
Nature
, vol.512
, pp. 96-100
-
-
Ghavi-Helm, Y.1
Klein, F.A.2
Pakodzi, T.3
Ciglar, L.4
Noordermeer, D.5
Huber, W.6
-
158
-
-
84939246295
-
CRISPR inversion of CTCF sites alters genome topology an enhancer/promoter function
-
COI: 1:CAS:528:DC%2BC2MXhtlCisLnI, PID: 26276636
-
Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU et al (2015) CRISPR inversion of CTCF sites alters genome topology an enhancer/promoter function. Cell 162:900–910
-
(2015)
Cell
, vol.162
, pp. 900-910
-
-
Guo, Y.1
Xu, Q.2
Canzio, D.3
Shou, J.4
Li, J.5
Gorkin, D.U.6
-
159
-
-
84930091577
-
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions
-
PID: 25959774
-
Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E et al (2015) Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161:1012–1025
-
(2015)
Cell
, vol.161
, pp. 1012-1025
-
-
Lupiáñez, D.G.1
Kraft, K.2
Heinrich, V.3
Krawitz, P.4
Brancati, F.5
Klopocki, E.6
-
160
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
COI: 1:CAS:528:DC%2BC38XhtlGnsLnM, PID: 22955621
-
Sanyal A, Lajoie BR, Jain G, Dekker J (2012) The long-range interaction landscape of gene promoters. Nature 489:109–113
-
(2012)
Nature
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
Lajoie, B.R.2
Jain, G.3
Dekker, J.4
|