-
1
-
-
0025675441
-
A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene
-
Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. Oncogene. 1990;5:1743-53.
-
(1990)
Oncogene
, vol.5
, pp. 1743-1753
-
-
Lobanenkov, V.V.1
Nicolas, R.H.2
Adler, V.V.3
Paterson, H.4
Klenova, E.M.5
Polotskaja, A.V.6
Goodwin, G.H.7
-
2
-
-
67549119096
-
CTCF: master weaver of the genome
-
Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell. 2009;137: 1194-211.
-
(2009)
Cell
, vol.137
, pp. 1194-1211
-
-
Phillips, J.E.1
Corces, V.G.2
-
3
-
-
0033529654
-
The protein CTCF is required for the enhancer blocking activity of vertebrate insulators
-
Bell AC, West AG, Felsenfeld G. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell. 1999;98:387-96.
-
(1999)
Cell
, vol.98
, pp. 387-396
-
-
Bell, A.C.1
West, A.G.2
Felsenfeld, G.3
-
4
-
-
0037076316
-
Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities
-
Recillas-Targa F, Pikaart MJ, Burgess-Beusse B, Bell AC, Litt MD, West AG, Gaszner M, Felsenfeld G. Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities. Proc Natl Acad Sci USA. 2002;99:6883-8.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 6883-6888
-
-
Recillas-Targa, F.1
Pikaart, M.J.2
Burgess-Beusse, B.3
Bell, A.C.4
Litt, M.D.5
West, A.G.6
Gaszner, M.7
Felsenfeld, G.8
-
5
-
-
84878188440
-
Chromatin insulators: linking genome organization to cellular function
-
Phillips-Cremins JE, Corces VG. Chromatin insulators: linking genome organization to cellular function. Mol Cell. 2013;50:461-74.
-
(2013)
Mol Cell
, vol.50
, pp. 461-474
-
-
Phillips-Cremins, J.E.1
Corces, V.G.2
-
6
-
-
33746063711
-
CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2
-
Kurukuti S, Tiwari VK, Tavoosidana G, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W, Ohlsson R. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc Natl Acad Sci U S A. 2006;103:10684-9.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 10684-10689
-
-
Kurukuti, S.1
Tiwari, V.K.2
Tavoosidana, G.3
Pugacheva, E.4
Murrell, A.5
Zhao, Z.6
Lobanenkov, V.7
Reik, W.8
Ohlsson, R.9
-
7
-
-
84856619909
-
CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement
-
Feeney AJ, Verma-Gaur J. CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement. Cell Res. 2012;22:280-2.
-
(2012)
Cell Res
, vol.22
, pp. 280-282
-
-
Feeney, A.J.1
Verma-Gaur, J.2
-
8
-
-
77956645612
-
CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus
-
Majumder P, Boss JM. CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus. Mol Cell Biol. 2010;30:4211-23.
-
(2010)
Mol Cell Biol
, vol.30
, pp. 4211-4223
-
-
Majumder, P.1
Boss, J.M.2
-
9
-
-
35649000946
-
Evidence that homologous Xchromosome pairing requires transcription and Ctcf protein
-
Xu N, Donohoe ME, Silva SS, Lee JT. Evidence that homologous Xchromosome pairing requires transcription and Ctcf protein. Nat Genet. 2007;39:1390-6.
-
(2007)
Nat Genet
, vol.39
, pp. 1390-1396
-
-
Xu, N.1
Donohoe, M.E.2
Silva, S.S.3
Lee, J.T.4
-
10
-
-
80455176999
-
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
-
Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature. 2011;479: 74-9.
-
(2011)
Nature
, vol.479
, pp. 74-79
-
-
Shukla, S.1
Kavak, E.2
Gregory, M.3
Imashimizu, M.4
Shutinoski, B.5
Kashlev, M.6
Oberdoerffer, P.7
Sandberg, R.8
Oberdoerffer, S.9
-
11
-
-
84871398317
-
CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice
-
Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q. CTCF/cohesin-mediated DNA looping is required for protocadherin alpha promoter choice. Proc Natl Acad Sci USA. 2012;109:21081-6.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 21081-21086
-
-
Guo, Y.1
Monahan, K.2
Wu, H.3
Gertz, J.4
Varley, K.E.5
Li, W.6
Myers, R.M.7
Maniatis, T.8
Wu, Q.9
-
12
-
-
0027362621
-
CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms
-
Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol. 1993;13: 7612-24.
-
(1993)
Mol Cell Biol
, vol.13
, pp. 7612-7624
-
-
Klenova, E.M.1
Nicolas, R.H.2
Paterson, H.F.3
Carne, A.F.4
Heath, C.M.5
Goodwin, G.H.6
Neiman, P.E.7
Lobanenkov, V.V.8
-
13
-
-
79959699992
-
CTCF-mediated functional chromatin interactome in pluripotent cells
-
Handoko L, Xu H, Li G, Ngan CY, ChewE, SchnappM, Lee CW, Ye C, Ping JL, Mulawadi F, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 2011;43:630-8.
-
(2011)
Nat Genet
, vol.43
, pp. 630-638
-
-
Handoko, L.1
Xu, H.2
Li, G.3
Ngan, C.Y.4
Chew, E.5
Schnapp, M.6
Lee, C.W.7
Ye, C.8
Ping, J.L.9
Mulawadi, F.10
-
14
-
-
70449103609
-
An oestrogen-receptor-alpha-bound human chromatin interactome
-
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009;462:58-64.
-
(2009)
Nature
, vol.462
, pp. 58-64
-
-
Fullwood, M.J.1
Liu, M.H.2
Pan, Y.F.3
Liu, J.4
Xu, H.5
Mohamed, Y.B.6
Orlov, Y.L.7
Velkov, S.8
Ho, A.9
Mei, P.H.10
-
15
-
-
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, Barrera LO, Van Calcar S, Qu C, Ching KA, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39:311-8.
-
(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
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
-
16
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010;107:21931-6.
-
(2010)
Proc Natl Acad Sci U S A
, 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
Hanna, J.7
Lodato, M.A.8
Frampton, G.M.9
Sharp, P.A.10
-
17
-
-
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;470:279-83.
-
(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
-
18
-
-
84878860751
-
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
-
Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 2013; 153:1281-95.
-
(2013)
Cell
, vol.153
, pp. 1281-1295
-
-
Phillips-Cremins, J.E.1
Sauria, M.E.2
Sanyal, A.3
Gerasimova, T.I.4
Lajoie, B.R.5
Bell, J.S.6
Ong, C.T.7
Hookway, T.A.8
Guo, C.9
Sun, Y.10
-
19
-
-
84880286574
-
De novo mutations in the genome organizer CTCF cause intellectual disability
-
Gregor A, Oti M, Kouwenhoven EN, Hoyer J, Sticht H, Ekici AB, Kjaergaard S, Rauch A, Stunnenberg HG, Uebe S, et al. De novo mutations in the genome organizer CTCF cause intellectual disability. Am J Hum Genet. 2013;93:124-31.
-
(2013)
Am J Hum Genet
, vol.93
, pp. 124-131
-
-
Gregor, A.1
Oti, M.2
Kouwenhoven, E.N.3
Hoyer, J.4
Sticht, H.5
Ekici, A.B.6
Kjaergaard, S.7
Rauch, A.8
Stunnenberg, H.G.9
Uebe, S.10
-
20
-
-
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, Poh HM, Goh Y, Lim J, Zhang J, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148:84-98.
-
(2012)
Cell
, vol.148
, pp. 84-98
-
-
Li, G.1
Ruan, X.2
Auerbach, R.K.3
Sandhu, K.S.4
Zheng, M.5
Wang, P.6
Poh, H.M.7
Goh, Y.8
Lim, J.9
Zhang, J.10
-
21
-
-
84887620842
-
A high-resolution map of the three-dimensional chromatin interactome in human cells
-
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013;503:290-4.
-
(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
Yen, C.A.7
Schmitt, A.D.8
Espinoza, C.A.9
Ren, B.10
-
22
-
-
84864008380
-
Dynamic reconfiguration of long human genes during one transcription cycle
-
Larkin JD, Cook PR, Papantonis A. Dynamic reconfiguration of long human genes during one transcription cycle. Mol Cell Biol. 2012;32:2738-47.
-
(2012)
Mol Cell Biol
, vol.32
, pp. 2738-2747
-
-
Larkin, J.D.1
Cook, P.R.2
Papantonis, A.3
-
23
-
-
84890432056
-
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations
-
Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013;504:306-10.
-
(2013)
Nature
, vol.504
, pp. 306-310
-
-
Zhang, Y.1
Wong, C.H.2
Birnbaum, R.Y.3
Li, G.4
Favaro, R.5
Ngan, C.Y.6
Lim, J.7
Tai, E.8
Poh, H.M.9
Wong, E.10
-
24
-
-
84905593782
-
Enhancer loops appear stable during development and are associated with paused polymerase
-
Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Enhancer loops appear stable during development and are associated with paused polymerase. Nature. 2014;512:96-100.
-
(2014)
Nature
, vol.512
, pp. 96-100
-
-
Ghavi-Helm, Y.1
Klein, F.A.2
Pakozdi, T.3
Ciglar, L.4
Noordermeer, D.5
Huber, W.6
Furlong, E.E.7
-
25
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
26
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665-80.
-
(2014)
Cell
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.1
Huntley, M.H.2
Durand, N.C.3
Stamenova, E.K.4
Bochkov, I.D.5
Robinson, J.T.6
Sanborn, A.L.7
Machol, I.8
Omer, A.D.9
Lander, E.S.10
Aiden, E.L.11
-
27
-
-
84924533047
-
Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture
-
Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 2015;10:1297-309.
-
(2015)
Cell Rep
, vol.10
, pp. 1297-1309
-
-
Vietri Rudan, M.1
Barrington, C.2
Henderson, S.3
Ernst, C.4
Odom, D.T.5
Tanay, A.6
-
28
-
-
70450222694
-
A model for all genomes: the role of transcription factories
-
Cook PR. A model for all genomes: the role of transcription factories. J Mol Biol. 2010;395:1-10.
-
(2010)
J Mol Biol
, vol.395
, pp. 1-10
-
-
Cook, P.R.1
-
29
-
-
84873581550
-
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
-
Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell. 2013;12:180-92.
-
(2013)
Cell Stem Cell
, vol.12
, pp. 180-192
-
-
Hu, G.1
Cui, K.2
Northrup, D.3
Liu, C.4
Wang, C.5
Tang, Q.6
Ge, K.7
Levens, D.8
Crane-Robinson, C.9
Zhao, K.10
-
30
-
-
84857707318
-
ChromHMM: automating chromatin-state discovery and characterization
-
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215-6.
-
(2012)
Nat Methods
, vol.9
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
31
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473: 43-9.
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
-
32
-
-
33845631171
-
'Genome design' model and multicellular complexity: golden middle
-
Vinogradov AE. 'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res. 2006;34:5906-14.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5906-5914
-
-
Vinogradov, A.E.1
-
33
-
-
84874253819
-
Gene Ontology annotations and resources
-
Gene Ontology C, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, et al. Gene Ontology annotations and resources. Nucleic Acids Res. 2013;41:D530-5.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D530-D535
-
-
Gene Ontology, C.1
Blake, J.A.2
Dolan, M.3
Drabkin, H.4
Hill, D.P.5
Li, N.6
Sitnikov, D.7
Bridges, S.8
Burgess, S.9
Buza, T.10
-
34
-
-
84884416048
-
Human housekeeping genes, revisited
-
Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet. 2013;29:569-74.
-
(2013)
Trends Genet
, vol.29
, pp. 569-574
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
35
-
-
84951567954
-
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
-
Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, et al. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell. 2015;163: 1611-27.
-
(2015)
Cell
, vol.163
, pp. 1611-1627
-
-
Tang, Z.1
Luo, O.J.2
Li, X.3
Zheng, M.4
Zhu, J.J.5
Szalaj, P.6
Trzaskoma, P.7
Magalska, A.8
Wlodarczyk, J.9
Ruszczycki, B.10
-
36
-
-
84891808382
-
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42:D142-7.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
Buchman, S.7
Chen, C.Y.8
Chou, A.9
Ienasescu, H.10
-
37
-
-
84865836579
-
Widespread plasticity in CTCF occupancy linked to DNA methylation
-
Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 2012;22:1680-8.
-
(2012)
Genome Res
, vol.22
, pp. 1680-1688
-
-
Wang, H.1
Maurano, M.T.2
Qu, H.3
Varley, K.E.4
Gertz, J.5
Pauli, F.6
Lee, K.7
Canfield, T.8
Weaver, M.9
Sandstrom, R.10
-
38
-
-
84941021874
-
Role of DNA Methylation in Modulating Transcription Factor Occupancy
-
Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA. Role of DNA Methylation in Modulating Transcription Factor Occupancy. Cell Rep. 2015;12:1184-95.
-
(2015)
Cell Rep
, vol.12
, pp. 1184-1195
-
-
Maurano, M.T.1
Wang, H.2
John, S.3
Shafer, A.4
Canfield, T.5
Lee, K.6
Stamatoyannopoulos, J.A.7
-
39
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-80.
-
(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
Hu, M.7
Liu, J.S.8
Ren, B.9
-
40
-
-
84892934183
-
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
-
Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, Brouwer RW, van de Corput MP, van de Werken HJ, Knoch TA, van IWF, et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci USA. 2014;111:996-1001.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 996-1001
-
-
Zuin, J.1
Dixon, J.R.2
van der Reijden, M.I.3
Ye, Z.4
Kolovos, P.5
Brouwer, R.W.6
van de Corput, M.P.7
van de Werken, H.J.8
Knoch, T.A.9
van, I.W.F.10
-
41
-
-
84867912686
-
The chromatin insulator CTCF and the emergence of metazoan diversity
-
Heger P, Marin B, Bartkuhn M, Schierenberg E, Wiehe T. The chromatin insulator CTCF and the emergence of metazoan diversity. Proc Natl Acad Sci USA. 2012;109:17507-12.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 17507-17512
-
-
Heger, P.1
Marin, B.2
Bartkuhn, M.3
Schierenberg, E.4
Wiehe, T.5
-
44
-
-
84939246295
-
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
-
Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell. 2015;162:900-10.
-
(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
Jung, I.7
Wu, H.8
Zhai, Y.9
Tang, Y.10
-
45
-
-
84927711843
-
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
-
Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome Res. 2015; 25:504-13.
-
(2015)
Genome Res
, vol.25
, pp. 504-513
-
-
Ing-Simmons, E.1
Seitan, V.C.2
Faure, A.J.3
Flicek, P.4
Carroll, T.5
Dekker, J.6
Fisher, A.G.7
Lenhard, B.8
Merkenschlager, M.9
-
46
-
-
84939240549
-
A CTCF Code for 3D Genome Architecture
-
Nichols MH, Corces VG. A CTCF Code for 3D Genome Architecture. Cell. 2015;162:703-5.
-
(2015)
Cell
, vol.162
, pp. 703-705
-
-
Nichols, M.H.1
Corces, V.G.2
-
47
-
-
84948403758
-
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
-
Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A. 2015;112:E6456-65.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, pp. E6456-E6465
-
-
Sanborn, A.L.1
Rao, S.S.2
Huang, S.C.3
Durand, N.C.4
Huntley, M.H.5
Jewett, A.I.6
Bochkov, I.D.7
Chinnappan, D.8
Cutkosky, A.9
Li, J.10
-
48
-
-
79952259195
-
Fixing the model for transcription: the DNA moves, not the polymerase
-
Papantonis A, Cook PR. Fixing the model for transcription: the DNA moves, not the polymerase. Transcription. 2011;2:41-4.
-
(2011)
Transcription
, vol.2
, pp. 41-44
-
-
Papantonis, A.1
Cook, P.R.2
-
49
-
-
33847200412
-
CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide
-
Chernukhin I, Shamsuddin S, Kang SY, Bergstrom R, Kwon YW, Yu W, Whitehead J, Mukhopadhyay R, Docquier F, Farrar D, et al. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol. 2007;27:1631-48.
-
(2007)
Mol Cell Biol
, vol.27
, pp. 1631-1648
-
-
Chernukhin, I.1
Shamsuddin, S.2
Kang, S.Y.3
Bergstrom, R.4
Kwon, Y.W.5
Yu, W.6
Whitehead, J.7
Mukhopadhyay, R.8
Docquier, F.9
Farrar, D.10
-
50
-
-
84878590595
-
A genome-wide map of CTCF multivalency redefines the CTCF code
-
Nakahashi H, Kwon KR, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, et al. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep. 2013;3:1678-89.
-
(2013)
Cell Rep
, vol.3
, pp. 1678-1689
-
-
Nakahashi, H.1
Kwon, K.R.2
Resch, W.3
Vian, L.4
Dose, M.5
Stavreva, D.6
Hakim, O.7
Pruett, N.8
Nelson, S.9
Yamane, A.10
-
51
-
-
70849129503
-
A wave of nascent transcription on activated human genes
-
Wada Y, Ohta Y, Xu M, Tsutsumi S, Minami T, Inoue K, Komura D, Kitakami J, Oshida N, Papantonis A, et al. A wave of nascent transcription on activated human genes. Proc Natl Acad Sci USA. 2009;106:18357-61.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 18357-18361
-
-
Wada, Y.1
Ohta, Y.2
Xu, M.3
Tsutsumi, S.4
Minami, T.5
Inoue, K.6
Komura, D.7
Kitakami, J.8
Oshida, N.9
Papantonis, A.10
-
52
-
-
84868325694
-
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
-
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Res. 2012;22:2163-75.
-
(2012)
Genome Res
, vol.22
, pp. 2163-2175
-
-
Faure, A.J.1
Schmidt, D.2
Watt, S.3
Schwalie, P.C.4
Wilson, M.D.5
Xu, H.6
Ramsay, R.G.7
Odom, D.T.8
Flicek, P.9
-
53
-
-
84890566970
-
Cohesin-mediated interactions organize chromosomal domain architecture
-
Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J. 2013;32: 3119-29.
-
(2013)
EMBO J
, vol.32
, pp. 3119-3129
-
-
Sofueva, S.1
Yaffe, E.2
Chan, W.C.3
Georgopoulou, D.4
Vietri Rudan, M.5
Mira-Bontenbal, H.6
Pollard, S.M.7
Schroth, G.P.8
Tanay, A.9
Hadjur, S.10
-
54
-
-
38849121606
-
Cohesins functionally associate with CTCF on mammalian chromosome arms
-
Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell. 2008;132:422-33.
-
(2008)
Cell
, vol.132
, pp. 422-433
-
-
Parelho, V.1
Hadjur, S.2
Spivakov, M.3
Leleu, M.4
Sauer, S.5
Gregson, H.C.6
Jarmuz, A.7
Canzonetta, C.8
Webster, Z.9
Nesterova, T.10
-
55
-
-
84889005653
-
Transcription factories: genome organization and gene regulation
-
Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev. 2013;113:8683-705.
-
(2013)
Chem Rev
, vol.113
, pp. 8683-8705
-
-
Papantonis, A.1
Cook, P.R.2
-
56
-
-
84906877432
-
Functional interplay between MyoD and CTCF in regulating long-range chromatin interactions during differentiation
-
Battistelli C, Busanello A, Maione R. Functional interplay between MyoD and CTCF in regulating long-range chromatin interactions during differentiation. J Cell Sci. 2014;127:3757-67.
-
(2014)
J Cell Sci
, vol.127
, pp. 3757-3767
-
-
Battistelli, C.1
Busanello, A.2
Maione, R.3
-
57
-
-
84891771466
-
The UCSC Genome Browser database: 2014 update
-
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42:D764-70.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D764-D770
-
-
Karolchik, D.1
Barber, G.P.2
Casper, J.3
Clawson, H.4
Cline, M.S.5
Diekhans, M.6
Dreszer, T.R.7
Fujita, P.A.8
Guruvadoo, L.9
Haeussler, M.10
-
58
-
-
78650638953
-
Integrative model of genomic factors for determining binding site selection by estrogen receptor-alpha
-
Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, Pan YF, Li G, Lim M, Thomsen JS, et al. Integrative model of genomic factors for determining binding site selection by estrogen receptor-alpha. Mol Syst Biol. 2010;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
Pan, Y.F.7
Li, G.8
Lim, M.9
Thomsen, J.S.10
-
59
-
-
84891768365
-
Ensembl 2014
-
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. Ensembl 2014. Nucleic Acids Res. 2014;42:D749-55.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D749-D755
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
-
60
-
-
61649083057
-
BioMart-biological queries made easy
-
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart-biological queries made easy. BMC Genomics. 2009;10:22.
-
(2009)
BMC Genomics
, vol.10
, pp. 22
-
-
Smedley, D.1
Haider, S.2
Ballester, B.3
Holland, R.4
London, D.5
Thorisson, G.6
Kasprzyk, A.7
-
61
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760-74.
-
(2012)
Genome Res
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
-
62
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
65
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
-
(2004)
Genome Biol
, vol.5
, pp. R80
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
-
66
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics. 2005;21:650-9.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
Chalifa-Caspi, V.4
Shklar, M.5
Ophir, R.6
Bar-Even, A.7
Horn-Saban, S.8
Safran, M.9
Domany, E.10
-
67
-
-
79953300078
-
FIMO: scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27:1017-8.
-
(2011)
Bioinformatics
, vol.27
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
68
-
-
67849122320
-
MEME SUITE: tools for motif discovery and searching
-
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202-8.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
69
-
-
85007514436
-
CTCF loop analysis and prediction scripts and datasets
-
Oti M. CTCF loop analysis and prediction scripts and datasets. Zenodo. 2015. doi:10.5281/zenodo.29423.
-
(2015)
Zenodo
-
-
Oti, M.1
|