-
1
-
-
77952313777
-
Differentiation of effector CD4 T cell populations (*)
-
Zhu J, Yamane H, Paul WE. Differentiation of effector CD4 T cell populations (*). Annu Rev Immunol (2010) 28:445-89. doi:10.1146/annurev-immunol-030409-101212.
-
(2010)
Annu Rev Immunol
, vol.28
, pp. 445-489
-
-
Zhu, J.1
Yamane, H.2
Paul, W.E.3
-
2
-
-
84911201387
-
Molecular regulation of effector and memory T cell differentiation
-
Chang JT, Wherry EJ, Goldrath AW. Molecular regulation of effector and memory T cell differentiation. Nat Immunol (2014) 15(12):1104-15. doi:10.1038/ni.3031.
-
(2014)
Nat Immunol
, vol.15
, Issue.12
, pp. 1104-1115
-
-
Chang, J.T.1
Wherry, E.J.2
Goldrath, A.W.3
-
3
-
-
0032981090
-
Functional differences between memory and naive CD8 T cells
-
Cho BK, Wang CY, Sugawa S, Eisen HN, Chen JZ. Functional differences between memory and naive CD8 T cells. Proc Natl Acad Sci U S A (1999) 96(6):2976-81. doi:10.1073/Pnas.96.6.2976.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, Issue.6
, pp. 2976-2981
-
-
Cho, B.K.1
Wang, C.Y.2
Sugawa, S.3
Eisen, H.N.4
Chen, J.Z.5
-
4
-
-
0034231222
-
Response of naive and memory CD8+ T cells to antigen stimulation in vivo
-
Veiga-Fernandes H, Walter U, Bourgeois C, McLean A, Rocha B. Response of naive and memory CD8+ T cells to antigen stimulation in vivo. Nat Immunol (2000) 1(1):47-53. doi:10.1038/76907.
-
(2000)
Nat Immunol
, vol.1
, Issue.1
, pp. 47-53
-
-
Veiga-Fernandes, H.1
Walter, U.2
Bourgeois, C.3
McLean, A.4
Rocha, B.5
-
5
-
-
0037074012
-
Molecular and functional profiling of memory CD8 T cell differentiation
-
Kaech SM, Hemby S, Kersh E, Ahmed R. Molecular and functional profiling of memory CD8 T cell differentiation. Cell (2002) 111(6):837-51. doi:10.1016/S0092-8674(02)01139-X.
-
(2002)
Cell
, vol.111
, Issue.6
, pp. 837-851
-
-
Kaech, S.M.1
Hemby, S.2
Kersh, E.3
Ahmed, R.4
-
6
-
-
84912096136
-
Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation
-
Russ BE, Olshanksy M, Smallwood HS, Li J, Denton AE, Prier JE, et al. Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation. Immunity (2014) 41(5):853-65. doi:10.1016/j.immuni.2014.11.001.
-
(2014)
Immunity
, vol.41
, Issue.5
, pp. 853-865
-
-
Russ, B.E.1
Olshanksy, M.2
Smallwood, H.S.3
Li, J.4
Denton, A.E.5
Prier, J.E.6
-
7
-
-
0019811465
-
Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences
-
Banerji J, Rusconi S, Schaffner W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell (1981) 27(2 Pt 1):299-308. doi:10.1016/0092-8674(81)90413-X.
-
(1981)
Cell
, vol.27
, Issue.2
, pp. 299-308
-
-
Banerji, J.1
Rusconi, S.2
Schaffner, W.3
-
8
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides T. Chromatin modifications and their function. Cell (2007) 128(4):693-705. doi:10.1016/J. Cell.2007.02.005.
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 693-705
-
-
Kouzarides, T.1
-
9
-
-
77958611660
-
Peripheral CD4+ T-cell differentiation regulated by networks of cytokines and transcription factors
-
Zhu J, Paul WE. Peripheral CD4+ T-cell differentiation regulated by networks of cytokines and transcription factors. Immunol Rev (2010) 238(1):247-62. doi:10.1111/j.1600-065X.2010.00951.x.
-
(2010)
Immunol Rev
, vol.238
, Issue.1
, pp. 247-262
-
-
Zhu, J.1
Paul, W.E.2
-
10
-
-
84879211454
-
T-cell memory differentiation: insights from transcriptional signatures and epigenetics
-
Youngblood B, Hale JS, Ahmed R. T-cell memory differentiation: insights from transcriptional signatures and epigenetics. Immunology (2013) 139(3):277-84. doi:10.1111/imm.12074.
-
(2013)
Immunology
, vol.139
, Issue.3
, pp. 277-284
-
-
Youngblood, B.1
Hale, J.S.2
Ahmed, R.3
-
11
-
-
84874296434
-
Defining the molecular blueprint that drives CD8(+) T cell differentiation in response to infection
-
Russ BE, Denton AE, Hatton L, Croom H, Olson MR, Turner SJ. Defining the molecular blueprint that drives CD8(+) T cell differentiation in response to infection. Front Immunol (2012) 3:371. doi:10.3389/fimmu.2012.00371.
-
(2012)
Front Immunol
, vol.3
, pp. 371
-
-
Russ, B.E.1
Denton, A.E.2
Hatton, L.3
Croom, H.4
Olson, M.R.5
Turner, S.J.6
-
12
-
-
84890264542
-
T cell immunity as a tool for studying epigenetic regulation of cellular differentiation
-
Russ BE, Prier JE, Rao S, Turner SJ. T cell immunity as a tool for studying epigenetic regulation of cellular differentiation. Front Genet (2013) 4:218. doi:10.3389/fgene.2013.00218.
-
(2013)
Front Genet
, vol.4
, pp. 218
-
-
Russ, B.E.1
Prier, J.E.2
Rao, S.3
Turner, S.J.4
-
13
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, et al. Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 132(5):887-98. doi:10.1016/j.cell.2008.02.022.
-
(2008)
Cell
, vol.132
, Issue.5
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.Y.4
Barski, A.5
Wang, Z.6
-
14
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, et al. Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 42(4):343-7. doi:10.1038/ng.545.
-
(2010)
Nat Genet
, vol.42
, Issue.4
, pp. 343-347
-
-
He, H.H.1
Meyer, C.A.2
Shin, H.3
Bailey, S.T.4
Wei, G.5
Wang, Q.6
-
15
-
-
0036091330
-
Nucleosome remodeling by the human SWI/SNF complex requires transient global disruption of histone-DNA interactions
-
Aoyagi S, Narlikar G, Zheng C, Sif S, Kingston RE, Hayes JJ. Nucleosome remodeling by the human SWI/SNF complex requires transient global disruption of histone-DNA interactions. Mol Cell Biol (2002) 22(11):3653-62. doi:10.1128/MCB.22.11.3653-3662.2002.
-
(2002)
Mol Cell Biol
, vol.22
, Issue.11
, pp. 3653-3662
-
-
Aoyagi, S.1
Narlikar, G.2
Zheng, C.3
Sif, S.4
Kingston, R.E.5
Hayes, J.J.6
-
16
-
-
51149107006
-
Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex
-
Lange M, Kaynak B, Forster UB, Tonjes M, Fischer JJ, Grimm C, et al. Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev (2008) 22(17):2370-84. doi:10.1101/gad.471408.
-
(2008)
Genes Dev
, vol.22
, Issue.17
, pp. 2370-2384
-
-
Lange, M.1
Kaynak, B.2
Forster, U.B.3
Tonjes, M.4
Fischer, J.J.5
Grimm, C.6
-
17
-
-
77954487796
-
Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b
-
Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou MM. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature (2010) 466(7303):258-62. doi:10.1038/nature09139.
-
(2010)
Nature
, vol.466
, Issue.7303
, pp. 258-262
-
-
Zeng, L.1
Zhang, Q.2
Li, S.3
Plotnikov, A.N.4
Walsh, M.J.5
Zhou, M.M.6
-
18
-
-
77954218952
-
Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription
-
Tang L, Nogales E, Ciferri C. Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Prog Biophys Mol Biol (2010) 102(2-3):122-8. doi:10.1016/j.pbiomolbio.2010.05.001.
-
(2010)
Prog Biophys Mol Biol
, vol.102
, Issue.2-3
, pp. 122-128
-
-
Tang, L.1
Nogales, E.2
Ciferri, C.3
-
19
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 40(7):897-903. doi:10.1038/ng.154.
-
(2008)
Nat Genet
, vol.40
, Issue.7
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
Cuddapah, S.6
-
20
-
-
84888001513
-
A new world of polycombs: unexpected partnerships and emerging functions
-
Schwartz YB, Pirrotta V. A new world of polycombs: unexpected partnerships and emerging functions. Nat Rev Genet (2013) 14(12):853-64. doi:10.1038/nrg3603.
-
(2013)
Nat Rev Genet
, vol.14
, Issue.12
, pp. 853-864
-
-
Schwartz, Y.B.1
Pirrotta, V.2
-
21
-
-
35148867907
-
UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development
-
Agger K, Cloos PA, Christensen J, Pasini D, Rose S, Rappsilber J, et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature (2007) 449(7163):731-4. doi:10.1038/nature06145.
-
(2007)
Nature
, vol.449
, Issue.7163
, pp. 731-734
-
-
Agger, K.1
Cloos, P.A.2
Christensen, J.3
Pasini, D.4
Rose, S.5
Rappsilber, J.6
-
22
-
-
43249102851
-
Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease
-
Cloos PA, Christensen J, Agger K, Helin K. Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev (2008) 22(9):1115-40. doi:10.1101/gad.1652908.
-
(2008)
Genes Dev
, vol.22
, Issue.9
, pp. 1115-1140
-
-
Cloos, P.A.1
Christensen, J.2
Agger, K.3
Helin, K.4
-
23
-
-
58149214356
-
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells
-
Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity (2009) 30(1):155-67. doi:10.1016/j.immuni.2008.12.009.
-
(2009)
Immunity
, vol.30
, Issue.1
, pp. 155-167
-
-
Wei, G.1
Wei, L.2
Zhu, J.3
Zang, C.4
Hu-Li, J.5
Yao, Z.6
-
24
-
-
30044440799
-
Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin
-
Intlekofer AM, Takemoto N, Wherry EJ, Longworth SA, Northrup JT, Palanivel VR, et al. Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin. Nat Immunol (2005) 6(12):1236-44. doi:10.1038/ni1268.
-
(2005)
Nat Immunol
, vol.6
, Issue.12
, pp. 1236-1244
-
-
Intlekofer, A.M.1
Takemoto, N.2
Wherry, E.J.3
Longworth, S.A.4
Northrup, J.T.5
Palanivel, V.R.6
-
25
-
-
84874194072
-
DNA methylation: roles in mammalian development
-
Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet (2013) 14(3):204-20. doi:10.1038/nrg3354.
-
(2013)
Nat Rev Genet
, vol.14
, Issue.3
, pp. 204-220
-
-
Smith, Z.D.1
Meissner, A.2
-
26
-
-
0024673303
-
CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation
-
Iguchi-Ariga SM, Schaffner W. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev (1989) 3(5):612-9. doi:10.1101/gad.3.5.612.
-
(1989)
Genes Dev
, vol.3
, Issue.5
, pp. 612-619
-
-
Iguchi-Ariga, S.M.1
Schaffner, W.2
-
27
-
-
76749133610
-
Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate
-
Zheng Y, Josefowicz S, Chaudhry A, Peng XP, Forbush K, Rudensky AY. Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. Nature (2010) 463(7282):808-12. doi:10.1038/nature08750.
-
(2010)
Nature
, vol.463
, Issue.7282
, pp. 808-812
-
-
Zheng, Y.1
Josefowicz, S.2
Chaudhry, A.3
Peng, X.P.4
Forbush, K.5
Rudensky, A.Y.6
-
28
-
-
0035312289
-
The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes
-
Feng Q, Zhang Y. The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes. Genes Dev (2001) 15(7):827-32. doi:10.1101/gad.876201.
-
(2001)
Genes Dev
, vol.15
, Issue.7
, pp. 827-832
-
-
Feng, Q.1
Zhang, Y.2
-
29
-
-
0031837109
-
Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription
-
Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet (1998) 19(2):187-91. doi:10.1038/561.
-
(1998)
Nat Genet
, vol.19
, Issue.2
, pp. 187-191
-
-
Jones, P.L.1
Veenstra, G.J.2
Wade, P.A.3
Vermaak, D.4
Kass, S.U.5
Landsberger, N.6
-
30
-
-
18944404300
-
The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes
-
Kondo E, Gu Z, Horii A, Fukushige S. The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes. Mol Cell Biol (2005) 25(11):4388-96. doi:10.1128/MCB.25.11.4388-4396.2005.
-
(2005)
Mol Cell Biol
, vol.25
, Issue.11
, pp. 4388-4396
-
-
Kondo, E.1
Gu, Z.2
Horii, A.3
Fukushige, S.4
-
31
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 459(7243):108-12. doi:10.1038/nature07829.
-
(2009)
Nature
, vol.459
, Issue.7243
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
Harp, L.F.6
-
32
-
-
84923796255
-
Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
-
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, et al. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 347(6225):1010-4. doi:10.1126/science.1259418.
-
(2015)
Science
, vol.347
, Issue.6225
, pp. 1010-1014
-
-
Arner, E.1
Daub, C.O.2
Vitting-Seerup, K.3
Andersson, R.4
Lilje, B.5
Drablos, F.6
-
33
-
-
84862489540
-
Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states
-
Pham TH, Benner C, Lichtinger M, Schwarzfischer L, Hu Y, Andreesen R, et al. Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. Blood (2012) 119(24):e161-71. doi:10.1182/blood-2012-01-402453.
-
(2012)
Blood
, vol.119
, Issue.24
, pp. e161-e171
-
-
Pham, T.H.1
Benner, C.2
Lichtinger, M.3
Schwarzfischer, L.4
Hu, Y.5
Andreesen, R.6
-
34
-
-
84860443136
-
Enhancers: emerging roles in cell fate specification
-
Ong CT, Corces VG. Enhancers: emerging roles in cell fate specification. EMBO Rep (2012) 13(5):423-30. doi:10.1038/embor.2012.52.
-
(2012)
EMBO Rep
, vol.13
, Issue.5
, pp. 423-430
-
-
Ong, C.T.1
Corces, V.G.2
-
35
-
-
84891347416
-
Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis
-
Weedon MN, Cebola I, Patch AM, Flanagan SE, De Franco E, Caswell R, et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet (2014) 46(1):61-4. doi:10.1038/ng.2826.
-
(2014)
Nat Genet
, vol.46
, Issue.1
, pp. 61-64
-
-
Weedon, M.N.1
Cebola, I.2
Patch, A.M.3
Flanagan, S.E.4
De Franco, E.5
Caswell, R.6
-
36
-
-
0025108409
-
Site-directed mutagenesis reveals a liver transcription factor essential for the albumin transcriptional enhancer
-
Zaret KS, Liu JK, DiPersio CM. Site-directed mutagenesis reveals a liver transcription factor essential for the albumin transcriptional enhancer. Proc Natl Acad Sci U S A (1990) 87(14):5469-73. doi:10.1073/pnas.87.14.5469.
-
(1990)
Proc Natl Acad Sci U S A
, vol.87
, Issue.14
, pp. 5469-5473
-
-
Zaret, K.S.1
Liu, J.K.2
DiPersio, C.M.3
-
37
-
-
0025800127
-
Site-directed mutagenesis of hepatocyte nuclear factor (HNF) binding sites in the mouse transthyretin (TTR) promoter reveal synergistic interactions with its enhancer region
-
Costa RH, Grayson DR. Site-directed mutagenesis of hepatocyte nuclear factor (HNF) binding sites in the mouse transthyretin (TTR) promoter reveal synergistic interactions with its enhancer region. Nucleic Acids Res (1991) 19(15):4139-45. doi:10.1093/nar/19.15.4139.
-
(1991)
Nucleic Acids Res
, vol.19
, Issue.15
, pp. 4139-4145
-
-
Costa, R.H.1
Grayson, D.R.2
-
38
-
-
84923786414
-
The selection and function of cell type-specific enhancers
-
Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol (2015) 16(3):144-54. doi:10.1038/nrm3949.
-
(2015)
Nat Rev Mol Cell Biol
, vol.16
, Issue.3
, pp. 144-154
-
-
Heinz, S.1
Romanoski, C.E.2
Benner, C.3
Glass, C.K.4
-
39
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 39(3):311-8. doi:10.1038/ng1966.
-
(2007)
Nat Genet
, vol.39
, Issue.3
, 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
-
40
-
-
80051564877
-
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
-
Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 21(8):1273-83. doi:10.1101/gr.122382.111.
-
(2011)
Genome Res
, vol.21
, Issue.8
, pp. 1273-1283
-
-
Zentner, G.E.1
Tesar, P.J.2
Scacheri, P.C.3
-
41
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 107(50):21931-6. doi:10.1073/pnas.1016071107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, Issue.50
, 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
-
42
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2011) 470(7333):279-83. doi:10.1038/nature09692.
-
(2011)
Nature
, vol.470
, Issue.7333
, pp. 279-283
-
-
Rada-Iglesias, A.1
Bajpai, R.2
Swigut, T.3
Brugmann, S.A.4
Flynn, R.A.5
Wysocka, J.6
-
43
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, CuffJ, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 125(2):315-26. doi:10.1016/j.cell.2006.02.041.
-
(2006)
Cell
, vol.125
, Issue.2
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
Kamal, M.4
Huebert, D.J.5
Cuff, J.6
-
44
-
-
84870027825
-
STATs shape the active enhancer landscape of T cell populations
-
Vahedi G, Takahashi H, Nakayamada S, Sun HW, Sartorelli V, Kanno Y, et al. STATs shape the active enhancer landscape of T cell populations. Cell (2012) 151(5):981-93. doi:10.1016/j.cell.2012.09.044.
-
(2012)
Cell
, vol.151
, Issue.5
, pp. 981-993
-
-
Vahedi, G.1
Takahashi, H.2
Nakayamada, S.3
Sun, H.W.4
Sartorelli, V.5
Kanno, Y.6
-
45
-
-
79952267284
-
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
-
Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2011) 21(3):456-64. doi:10.1101/gr.112656.110.
-
(2011)
Genome Res
, vol.21
, Issue.3
, pp. 456-464
-
-
Boyle, A.P.1
Song, L.2
Lee, B.K.3
London, D.4
Keefe, D.5
Birney, E.6
-
46
-
-
0018199224
-
DNAse footprinting: a simple method for the detection of protein-DNA binding specificity
-
Galas DJ, Schmitz A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res (1978) 5(9):3157-70. doi:10.1093/nar/5.9.3157.
-
(1978)
Nucleic Acids Res
, vol.5
, Issue.9
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
47
-
-
77956276383
-
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
-
Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc (2010) 2010(2):1-11. doi:10.1101/pdb.prot5384.
-
(2010)
Cold Spring Harb Protoc
, vol.2010
, Issue.2
, pp. 1-11
-
-
Song, L.1
Crawford, G.E.2
-
48
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods (2013) 10(12):1213-8. doi:10.1038/nmeth.2688.
-
(2013)
Nat Methods
, vol.10
, Issue.12
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
49
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science (2002) 295(5558):1306-11. doi:10.1126/science.1067799.
-
(2002)
Science
, vol.295
, Issue.5558
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
50
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 326(5950):289-93. doi:10.1126/science.1181369.
-
(2009)
Science
, vol.326
, Issue.5950
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
-
51
-
-
34548565667
-
Quantitative analysis of chromosome conformation capture assays (3C-qPCR)
-
Hagege H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc (2007) 2(7):1722-33. doi:10.1038/nprot.2007.243.
-
(2007)
Nat Protoc
, vol.2
, Issue.7
, pp. 1722-1733
-
-
Hagege, H.1
Klous, P.2
Braem, C.3
Splinter, E.4
Dekker, J.5
Cathala, G.6
-
52
-
-
9144233601
-
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
-
Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 100(26):15776-81. doi:10.1073/pnas.2136655100.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, Issue.26
, pp. 15776-15781
-
-
Shiraki, T.1
Kondo, S.2
Katayama, S.3
Waki, K.4
Kasukawa, T.5
Kawaji, H.6
-
53
-
-
33750465872
-
SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes
-
Cai S, Lee CC, Kohwi-Shigematsu T. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet (2006) 38(11):1278-88. doi:10.1038/ng1913.
-
(2006)
Nat Genet
, vol.38
, Issue.11
, pp. 1278-1288
-
-
Cai, S.1
Lee, C.C.2
Kohwi-Shigematsu, T.3
-
54
-
-
12344250807
-
Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions
-
Lee GR, Spilianakis CG, Flavell RA. Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. Nat Immunol (2005) 6(1):42-8. doi:10.1038/ni1148.
-
(2005)
Nat Immunol
, vol.6
, Issue.1
, pp. 42-48
-
-
Lee, G.R.1
Spilianakis, C.G.2
Flavell, R.A.3
-
55
-
-
5444237577
-
Long-range intrachromosomal interactions in the T helper type 2 cytokine locus
-
Spilianakis CG, Flavell RA. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol (2004) 5(10):1017-27. doi:10.1038/ni1115.
-
(2004)
Nat Immunol
, vol.5
, Issue.10
, pp. 1017-1027
-
-
Spilianakis, C.G.1
Flavell, R.A.2
-
56
-
-
78650304399
-
The enhancer HS2 critically regulates GATA-3-mediated Il4 transcription in T(H)2 cells
-
Tanaka S, Motomura Y, Suzuki Y, Yagi R, Inoue H, Miyatake S, et al. The enhancer HS2 critically regulates GATA-3-mediated Il4 transcription in T(H)2 cells. Nat Immunol (2011) 12(1):77-85. doi:10.1038/ni.1966.
-
(2011)
Nat Immunol
, vol.12
, Issue.1
, pp. 77-85
-
-
Tanaka, S.1
Motomura, Y.2
Suzuki, Y.3
Yagi, R.4
Inoue, H.5
Miyatake, S.6
-
57
-
-
0032412441
-
Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation
-
Agarwal S, Rao A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity (1998) 9(6):765-75. doi:10.1016/S1074-7613(00)80642-1.
-
(1998)
Immunity
, vol.9
, Issue.6
, pp. 765-775
-
-
Agarwal, S.1
Rao, A.2
-
58
-
-
0031593671
-
Th2-specific DNase I-hypersensitive sites in the murine IL-13 and IL-4 intergenic region
-
Takemoto N, Koyano-Nakagawa N, Yokota T, Arai N, Miyatake S, Arai K. Th2-specific DNase I-hypersensitive sites in the murine IL-13 and IL-4 intergenic region. Int Immunol (1998) 10(12):1981-5. doi:10.1093/intimm/10.12.1981.
-
(1998)
Int Immunol
, vol.10
, Issue.12
, pp. 1981-1985
-
-
Takemoto, N.1
Koyano-Nakagawa, N.2
Yokota, T.3
Arai, N.4
Miyatake, S.5
Arai, K.6
-
59
-
-
0033667895
-
Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo
-
Agarwal S, Avni O, Rao A. Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo. Immunity (2000) 12(6):643-52. doi:10.1016/S1074-7613(00)80215-0.
-
(2000)
Immunity
, vol.12
, Issue.6
, pp. 643-652
-
-
Agarwal, S.1
Avni, O.2
Rao, A.3
-
60
-
-
84875279735
-
Functionally distinct Gata3/Chd4 complexes coordinately establish T helper 2 (Th2) cell identity
-
Hosokawa H, Tanaka T, Suzuki Y, Iwamura C, Ohkubo S, Endoh K, et al. Functionally distinct Gata3/Chd4 complexes coordinately establish T helper 2 (Th2) cell identity. Proc Natl Acad Sci U S A (2013) 110(12):4691-6. doi:10.1073/pnas.1220865110.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.12
, pp. 4691-4696
-
-
Hosokawa, H.1
Tanaka, T.2
Suzuki, Y.3
Iwamura, C.4
Ohkubo, S.5
Endoh, K.6
-
61
-
-
84863393256
-
Interleukin-4 production by follicular helper T cells requires the conserved Il4 enhancer hypersensitivity site V
-
Vijayanand P, Seumois G, Simpson LJ, Abdul-Wajid S, Baumjohann D, Panduro M, et al. Interleukin-4 production by follicular helper T cells requires the conserved Il4 enhancer hypersensitivity site V. Immunity (2012) 36(2):175-87. doi:10.1016/j.immuni.2011.12.014.
-
(2012)
Immunity
, vol.36
, Issue.2
, pp. 175-187
-
-
Vijayanand, P.1
Seumois, G.2
Simpson, L.J.3
Abdul-Wajid, S.4
Baumjohann, D.5
Panduro, M.6
-
62
-
-
70349756895
-
CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus
-
Sekimata M, Perez-Melgosa M, Miller SA, Weinmann AS, Sabo PJ, Sandstrom R, et al. CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity (2009) 31(4):551-64. doi:10.1016/j.immuni.2009.08.021.
-
(2009)
Immunity
, vol.31
, Issue.4
, pp. 551-564
-
-
Sekimata, M.1
Perez-Melgosa, M.2
Miller, S.A.3
Weinmann, A.S.4
Sabo, P.J.5
Sandstrom, R.6
-
63
-
-
77958572323
-
Regulation of the Ifng locus in the context of T-lineage specification and plasticity
-
Balasubramani A, Mukasa R, Hatton RD, Weaver CT. Regulation of the Ifng locus in the context of T-lineage specification and plasticity. Immunol Rev (2010) 238(1):216-32. doi:10.1111/j.1600-065X.2010.00961.x.
-
(2010)
Immunol Rev
, vol.238
, Issue.1
, pp. 216-232
-
-
Balasubramani, A.1
Mukasa, R.2
Hatton, R.D.3
Weaver, C.T.4
-
64
-
-
0034677646
-
A novel transcription factor, T-bet, directs Th1 lineage commitment
-
Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG, Glimcher LH. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell (2000) 100(6):655-69. doi:10.1016/S0092-8674(00)80702-3.
-
(2000)
Cell
, vol.100
, Issue.6
, pp. 655-669
-
-
Szabo, S.J.1
Kim, S.T.2
Costa, G.L.3
Zhang, X.4
Fathman, C.G.5
Glimcher, L.H.6
-
65
-
-
84896699887
-
Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription
-
Balasubramani A, Winstead CJ, Turner H, Janowski KM, Harbour SN, Shibata Y, et al. Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription. PLoS Genet (2014) 10(1):e1003969. doi:10.1371/journal.pgen.1003969.
-
(2014)
PLoS Genet
, vol.10
, Issue.1
-
-
Balasubramani, A.1
Winstead, C.J.2
Turner, H.3
Janowski, K.M.4
Harbour, S.N.5
Shibata, Y.6
-
66
-
-
77956420485
-
Distal regions of the human IFNG locus direct cell type-specific expression
-
Collins PL, Chang S, Henderson M, Soutto M, Davis GM, McLoed AG, et al. Distal regions of the human IFNG locus direct cell type-specific expression. J Immunol (2010) 185(3):1492-501. doi:10.4049/jimmunol.1000124.
-
(2010)
J Immunol
, vol.185
, Issue.3
, pp. 1492-1501
-
-
Collins, P.L.1
Chang, S.2
Henderson, M.3
Soutto, M.4
Davis, G.M.5
McLoed, A.G.6
-
67
-
-
84856913512
-
Diverse functions of distal regulatory elements at the IFNG locus
-
Collins PL, Henderson MA, Aune TM. Diverse functions of distal regulatory elements at the IFNG locus. J Immunol (2012) 188(4):1726-33. doi:10.4049/jimmunol.1102879.
-
(2012)
J Immunol
, vol.188
, Issue.4
, pp. 1726-1733
-
-
Collins, P.L.1
Henderson, M.A.2
Aune, T.M.3
-
68
-
-
84889881019
-
Transcriptional control of CD4 and CD8 coreceptor expression during T cell development
-
Ellmeier W, Haust L, Tschismarov R. Transcriptional control of CD4 and CD8 coreceptor expression during T cell development. Cell Mol Life Sci (2013) 70(23):4537-53. doi:10.1007/s00018-013-1393-2.
-
(2013)
Cell Mol Life Sci
, vol.70
, Issue.23
, pp. 4537-4553
-
-
Ellmeier, W.1
Haust, L.2
Tschismarov, R.3
-
69
-
-
0032191963
-
Multiple developmental stage-specific enhancers regulate CD8 expression in developing thymocytes and in thymus-independent T cells
-
Ellmeier W, Sunshine MJ, Losos K, Littman DR. Multiple developmental stage-specific enhancers regulate CD8 expression in developing thymocytes and in thymus-independent T cells. Immunity (1998) 9(4):485-96. doi:10.1016/S1074-7613(00)80632-9.
-
(1998)
Immunity
, vol.9
, Issue.4
, pp. 485-496
-
-
Ellmeier, W.1
Sunshine, M.J.2
Losos, K.3
Littman, D.R.4
-
70
-
-
81055130116
-
Cd8 enhancer E8I and Runx factors regulate CD8alpha expression in activated CD8+ T cells
-
Hassan H, Sakaguchi S, Tenno M, Kopf A, Boucheron N, Carpenter AC, et al. Cd8 enhancer E8I and Runx factors regulate CD8alpha expression in activated CD8+ T cells. Proc Natl Acad Sci U S A (2011) 108(45):18330-5. doi:10.1073/pnas.1105835108.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.45
, pp. 18330-18335
-
-
Hassan, H.1
Sakaguchi, S.2
Tenno, M.3
Kopf, A.4
Boucheron, N.5
Carpenter, A.C.6
-
71
-
-
0036285006
-
Combined deletion of CD8 locus cis-regulatory elements affects initiation but not maintenance of CD8 expression
-
Ellmeier W, Sunshine MJ, Maschek R, Littman DR. Combined deletion of CD8 locus cis-regulatory elements affects initiation but not maintenance of CD8 expression. Immunity (2002) 16(5):623-34. doi:10.1016/S1074-7613(02)00309-6.
-
(2002)
Immunity
, vol.16
, Issue.5
, pp. 623-634
-
-
Ellmeier, W.1
Sunshine, M.J.2
Maschek, R.3
Littman, D.R.4
-
72
-
-
33645107299
-
Negative regulation of CD8 expression via Cd8 enhancer-mediated recruitment of the zinc finger protein MAZR
-
Bilic I, Koesters C, Unger B, Sekimata M, Hertweck A, Maschek R, et al. Negative regulation of CD8 expression via Cd8 enhancer-mediated recruitment of the zinc finger protein MAZR. Nat Immunol (2006) 7(4):392-400. doi:10.1038/ni1311.
-
(2006)
Nat Immunol
, vol.7
, Issue.4
, pp. 392-400
-
-
Bilic, I.1
Koesters, C.2
Unger, B.3
Sekimata, M.4
Hertweck, A.5
Maschek, R.6
-
73
-
-
84897459921
-
Epigenetic plasticity of Cd8a locus during CD8(+) T-cell development and effector differentiation and reprogramming
-
Harland KL, Day EB, Apte SH, Russ BE, Doherty PC, Turner SJ, et al. Epigenetic plasticity of Cd8a locus during CD8(+) T-cell development and effector differentiation and reprogramming. Nat Commun (2014) 5:3547. doi:10.1038/ncomms4547.
-
(2014)
Nat Commun
, vol.5
, pp. 3547
-
-
Harland, K.L.1
Day, E.B.2
Apte, S.H.3
Russ, B.E.4
Doherty, P.C.5
Turner, S.J.6
-
74
-
-
77954695599
-
CD8 locus nuclear dynamics during thymocyte development
-
Ktistaki E, Garefalaki A, Williams A, Andrews SR, Bell DM, Foster KE, et al. CD8 locus nuclear dynamics during thymocyte development. J Immunol (2010) 184(10):5686-95. doi:10.4049/jimmunol.1000170.
-
(2010)
J Immunol
, vol.184
, Issue.10
, pp. 5686-5695
-
-
Ktistaki, E.1
Garefalaki, A.2
Williams, A.3
Andrews, S.R.4
Bell, D.M.5
Foster, K.E.6
-
75
-
-
79953134246
-
Genomic views of STAT function in CD4+ T helper cell differentiation
-
O'Shea JJ, Lahesmaa R, Vahedi G, Laurence A, Kanno Y. Genomic views of STAT function in CD4+ T helper cell differentiation. Nat Rev Immunol (2011) 11(4):239-50. doi:10.1038/nri2958.
-
(2011)
Nat Rev Immunol
, vol.11
, Issue.4
, pp. 239-250
-
-
O'Shea, J.J.1
Lahesmaa, R.2
Vahedi, G.3
Laurence, A.4
Kanno, Y.5
-
76
-
-
34249707951
-
The chemokine and chemokine receptor superfamilies and their molecular evolution
-
Zlotnik A, Yoshie O, Nomiyama H. The chemokine and chemokine receptor superfamilies and their molecular evolution. Genome Biol (2006) 7(12):243. doi:10.1186/gb-2006-7-12-243.
-
(2006)
Genome Biol
, vol.7
, Issue.12
, pp. 243
-
-
Zlotnik, A.1
Yoshie, O.2
Nomiyama, H.3
-
77
-
-
84857781464
-
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
-
Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res (2012) 22(3):490-503. doi:10.1038/cr.2012.15.
-
(2012)
Cell Res
, vol.22
, Issue.3
, pp. 490-503
-
-
Chepelev, I.1
Wei, G.2
Wangsa, D.3
Tang, Q.4
Zhao, K.5
-
78
-
-
84862908850
-
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
-
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 148(1-2):84-98. doi:10.1016/j.cell.2011.12.014.
-
(2012)
Cell
, vol.148
, Issue.1-2
, pp. 84-98
-
-
Li, G.1
Ruan, X.2
Auerbach, R.K.3
Sandhu, K.S.4
Zheng, M.5
Wang, P.6
-
79
-
-
84904644906
-
Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility
-
Seumois G, Chavez L, Gerasimova A, Lienhard M, Omran N, Kalinke L, et al. Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. Nat Immunol (2014) 15(8):777-88. doi:10.1038/ni.2937.
-
(2014)
Nat Immunol
, vol.15
, Issue.8
, pp. 777-788
-
-
Seumois, G.1
Chavez, L.2
Gerasimova, A.3
Lienhard, M.4
Omran, N.5
Kalinke, L.6
-
80
-
-
84928560965
-
Super-enhancers delineate disease-associated regulatory nodes in T cells
-
Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SC, Erdos MR, et al. Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature (2015) 520(7548):558-62. doi:10.1038/nature14154.
-
(2015)
Nature
, vol.520
, Issue.7548
, pp. 558-562
-
-
Vahedi, G.1
Kanno, Y.2
Furumoto, Y.3
Jiang, K.4
Parker, S.C.5
Erdos, M.R.6
-
81
-
-
84925283769
-
What are super-enhancers?
-
Pott S, Lieb JD. What are super-enhancers? Nat Genet (2015) 47(1):8-12. doi:10.1038/ng.3167.
-
(2015)
Nat Genet
, vol.47
, Issue.1
, pp. 8-12
-
-
Pott, S.1
Lieb, J.D.2
-
82
-
-
84900314611
-
CRISPR-Cas systems for editing, regulating and targeting genomes
-
Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol (2014) 32(4):347-55. doi:10.1038/nbt.2842.
-
(2014)
Nat Biotechnol
, vol.32
, Issue.4
, pp. 347-355
-
-
Sander, J.D.1
Joung, J.K.2
|