메뉴 건너뛰기




Volumn 155, Issue 7, 2013, Pages 1507-1520

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

(26)  Kieffer Kwon, Kyong Rim a   Tang, Zhonghui b   Mathe, Ewy a   Qian, Jason a   Sung, Myong Hee c   Li, Guoliang b   Resch, Wolfgang a   Baek, Songjoon c   Pruett, Nathanael a   Grøntved, Lars c   Vian, Laura a   Nelson, Steevenson a   Zare, Hossein a   Hakim, Ofir d   Reyon, Deepak e,f   Yamane, Arito a   Nakahashi, Hirotaka a   Kovalchuk, Alexander L g   Zou, Jizhong a   Joung, J Keith e,f   more..


Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; MYC PROTEIN; PROTEIN KINASE PIM 1; TRANSCRIPTOME; LONG UNTRANSLATED RNA; TRANSCRIPTION FACTOR;

EID: 84894589713     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.11.039     Document Type: Article
Times cited : (259)

References (64)
  • 1
    • 84855878190 scopus 로고    scopus 로고
    • Quantitative analysis of genome-wide chromatin remodeling
    • S. Baek, M.H. Sung, and G.L. Hager Quantitative analysis of genome-wide chromatin remodeling Methods Mol. Biol. 833 2012 433 441
    • (2012) Methods Mol. Biol. , vol.833 , pp. 433-441
    • Baek, S.1    Sung, M.H.2    Hager, G.L.3
  • 2
    • 84875200257 scopus 로고    scopus 로고
    • Long noncoding RNAs: Cellular address codes in development and disease
    • P.J. Batista, and H.Y. Chang Long noncoding RNAs: cellular address codes in development and disease Cell 152 2013 1298 1307
    • (2013) Cell , vol.152 , pp. 1298-1307
    • Batista, P.J.1    Chang, H.Y.2
  • 3
    • 84861529303 scopus 로고    scopus 로고
    • Enhancers as information integration hubs in development: Lessons from genomics
    • C. Buecker, and J. Wysocka Enhancers as information integration hubs in development: lessons from genomics Trends Genet. 28 2012 276 284
    • (2012) Trends Genet. , vol.28 , pp. 276-284
    • Buecker, C.1    Wysocka, J.2
  • 4
    • 84863201964 scopus 로고    scopus 로고
    • Targeted transcriptional activation of silent oct4 pluripotency gene by combining designer TALEs and inhibition of epigenetic modifiers
    • S. Bultmann, R. Morbitzer, C.S. Schmidt, K. Thanisch, F. Spada, J. Elsaesser, T. Lahaye, and H. Leonhardt Targeted transcriptional activation of silent oct4 pluripotency gene by combining designer TALEs and inhibition of epigenetic modifiers Nucleic Acids Res. 40 2012 5368 5377
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5368-5377
    • Bultmann, S.1    Morbitzer, R.2    Schmidt, C.S.3    Thanisch, K.4    Spada, F.5    Elsaesser, J.6    Lahaye, T.7    Leonhardt, H.8
  • 5
    • 0037031604 scopus 로고    scopus 로고
    • OcaB is required for normal transcription and V(D)J recombination of a subset of immunoglobulin kappa genes
    • R. Casellas, M. Jankovic, G. Meyer, A. Gazumyan, Y. Luo, R. Roeder, and M. Nussenzweig OcaB is required for normal transcription and V(D)J recombination of a subset of immunoglobulin kappa genes Cell 110 2002 575 585
    • (2002) Cell , vol.110 , pp. 575-585
    • Casellas, R.1    Jankovic, M.2    Meyer, G.3    Gazumyan, A.4    Luo, Y.5    Roeder, R.6    Nussenzweig, M.7
  • 6
    • 59449102152 scopus 로고    scopus 로고
    • Restricting activation-induced cytidine deaminase tumorigenic activity in B lymphocytes
    • R. Casellas, A. Yamane, A.L. Kovalchuk, and M. Potter Restricting activation-induced cytidine deaminase tumorigenic activity in B lymphocytes Immunology 126 2009 316 328
    • (2009) Immunology , vol.126 , pp. 316-328
    • Casellas, R.1    Yamane, A.2    Kovalchuk, A.L.3    Potter, M.4
  • 7
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • X. Chen, H. Xu, P. Yuan, F. Fang, M. Huss, V.B. Vega, E. Wong, Y.L. Orlov, W. Zhang, and J. Jiang et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells Cell 133 2008 1106 1117
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1    Xu, H.2    Yuan, P.3    Fang, F.4    Huss, M.5    Vega, V.B.6    Wong, E.7    Orlov, Y.L.8    Zhang, W.9    Jiang, J.10
  • 11
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • ENCODE Project Consortium B.E. Bernstein, E. Birney, I. Dunham, E.D. Green, C. Gunter, and M. Snyder An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3    Green, E.D.4    Gunter, C.5    Snyder, M.6
  • 13
    • 0035115847 scopus 로고    scopus 로고
    • Two distal downstream enhancers direct expression of the human apolipoprotein e gene to astrocytes in the brain
    • S. Grehan, E. Tse, and J.M. Taylor Two distal downstream enhancers direct expression of the human apolipoprotein E gene to astrocytes in the brain J. Neurosci. 21 2001 812 822
    • (2001) J. Neurosci. , vol.21 , pp. 812-822
    • Grehan, S.1    Tse, E.2    Taylor, J.M.3
  • 14
    • 84869052718 scopus 로고    scopus 로고
    • Cis-acting noncoding RNAs: Friends and foes
    • S. Guil, and M. Esteller Cis-acting noncoding RNAs: friends and foes Nat. Struct. Mol. Biol. 19 2012 1068 1075
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 1068-1075
    • Guil, S.1    Esteller, M.2
  • 16
    • 0034892132 scopus 로고    scopus 로고
    • X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2
    • D.B. Huang, Y.Q. Chen, M. Ruetsche, C.B. Phelps, and G. Ghosh X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2 Structure 9 2001 669 678
    • (2001) Structure , vol.9 , pp. 669-678
    • Huang, D.B.1    Chen, Y.Q.2    Ruetsche, M.3    Phelps, C.B.4    Ghosh, G.5
  • 17
    • 84876183774 scopus 로고    scopus 로고
    • In vivo analysis of Aicda gene regulation: A critical balance between upstream enhancers and intronic silencers governs appropriate expression
    • T. Huong, M. Kobayashi, M. Nakata, G. Shioi, H. Miyachi, T. Honjo, and H. Nagaoka In vivo analysis of Aicda gene regulation: a critical balance between upstream enhancers and intronic silencers governs appropriate expression PLoS ONE 8 2013 e61433
    • (2013) PLoS ONE , vol.8 , pp. 61433
    • Huong, T.1    Kobayashi, M.2    Nakata, M.3    Shioi, G.4    Miyachi, H.5    Honjo, T.6    Nagaoka, H.7
  • 20
    • 84860379799 scopus 로고    scopus 로고
    • Enhancer and promoter interactions-long distance calls
    • I. Krivega, and A. Dean Enhancer and promoter interactions-long distance calls Curr. Opin. Genet. Dev. 22 2012 79 85
    • (2012) Curr. Opin. Genet. Dev. , vol.22 , pp. 79-85
    • Krivega, I.1    Dean, A.2
  • 22
    • 84862908850 scopus 로고    scopus 로고
    • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    • G. Li, X. Ruan, R.K. Auerbach, K.S. Sandhu, M. Zheng, P. Wang, H.M. Poh, Y. Goh, J. Lim, and J. Zhang et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation Cell 148 2012 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
  • 23
    • 0025951891 scopus 로고
    • Sites of specific B cell activation in primary and secondary responses to T cell-dependent and T cell-independent antigens
    • Y.J. Liu, J. Zhang, P.J. Lane, E.Y. Chan, and I.C. MacLennan Sites of specific B cell activation in primary and secondary responses to T cell-dependent and T cell-independent antigens Eur. J. Immunol. 21 1991 2951 2962
    • (1991) Eur. J. Immunol. , vol.21 , pp. 2951-2962
    • Liu, Y.J.1    Zhang, J.2    Lane, P.J.3    Chan, E.Y.4    Maclennan, I.C.5
  • 24
    • 0037031831 scopus 로고    scopus 로고
    • Chromatin structural analyses of the mouse Igkappa gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer
    • Z.M. Liu, J.B. George-Raizen, S. Li, K.C. Meyers, M.Y. Chang, and W.T. Garrard Chromatin structural analyses of the mouse Igkappa gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer J. Biol. Chem. 277 2002 32640 32649
    • (2002) J. Biol. Chem. , vol.277 , pp. 32640-32649
    • Liu, Z.M.1    George-Raizen, J.B.2    Li, S.3    Meyers, K.C.4    Chang, M.Y.5    Garrard, W.T.6
  • 25
    • 0024461826 scopus 로고
    • The immunoglobulin kappa locus contains a second, stronger B-cell-specific enhancer which is located downstream of the constant region
    • K.B. Meyer, and M.S. Neuberger The immunoglobulin kappa locus contains a second, stronger B-cell-specific enhancer which is located downstream of the constant region EMBO J. 8 1989 1959 1964
    • (1989) EMBO J. , vol.8 , pp. 1959-1964
    • Meyer, K.B.1    Neuberger, M.S.2
  • 26
    • 0030069150 scopus 로고    scopus 로고
    • High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells
    • M. Nakamura, S. Kondo, M. Sugai, M. Nazarea, S. Imamura, and T. Honjo High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells Int. Immunol. 8 1996 193 201
    • (1996) Int. Immunol. , vol.8 , pp. 193-201
    • Nakamura, M.1    Kondo, S.2    Sugai, M.3    Nazarea, M.4    Imamura, S.5    Honjo, T.6
  • 29
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • M.A. Nobrega, I. Ovcharenko, V. Afzal, and E.M. Rubin Scanning human gene deserts for long-range enhancers Science 302 2003 413
    • (2003) Science , vol.302 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 31
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • C.P. Ponting, P.L. Oliver, and W. Reik Evolution and functions of long noncoding RNAs Cell 136 2009 629 641
    • (2009) Cell , vol.136 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 32
    • 0032168362 scopus 로고    scopus 로고
    • OCA-B integrates B cell antigen receptor-, CD40L- and IL 4-mediated signals for the germinal center pathway of B cell development
    • X.F. Qin, A. Reichlin, Y. Luo, R.G. Roeder, and M.C. Nussenzweig OCA-B integrates B cell antigen receptor-, CD40L- and IL 4-mediated signals for the germinal center pathway of B cell development EMBO J. 17 1998 5066 5075
    • (1998) EMBO J. , vol.17 , pp. 5066-5075
    • Qin, X.F.1    Reichlin, A.2    Luo, Y.3    Roeder, R.G.4    Nussenzweig, M.C.5
  • 35
    • 0038515309 scopus 로고    scopus 로고
    • E-proteins directly regulate expression of activation-induced deaminase in mature B cells
    • C.E. Sayegh, M.W. Quong, Y. Agata, and C. Murre E-proteins directly regulate expression of activation-induced deaminase in mature B cells Nat. Immunol. 4 2003 586 593
    • (2003) Nat. Immunol. , vol.4 , pp. 586-593
    • Sayegh, C.E.1    Quong, M.W.2    Agata, Y.3    Murre, C.4
  • 36
    • 0032727374 scopus 로고    scopus 로고
    • Building the heart piece by piece: Modularity of cis-elements regulating Nkx2-5 transcription
    • R.J. Schwartz, and E.N. Olson Building the heart piece by piece: modularity of cis-elements regulating Nkx2-5 transcription Development 126 1999 4187 4192
    • (1999) Development , vol.126 , pp. 4187-4192
    • Schwartz, R.J.1    Olson, E.N.2
  • 37
    • 0022481133 scopus 로고
    • Multiple nuclear factors interact with the immunoglobulin enhancer sequences
    • R. Sen, and D. Baltimore Multiple nuclear factors interact with the immunoglobulin enhancer sequences Cell 46 1986 705 716
    • (1986) Cell , vol.46 , pp. 705-716
    • Sen, R.1    Baltimore, D.2
  • 38
    • 84876946045 scopus 로고    scopus 로고
    • Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics
    • L. Shen, H. Wu, D. Diep, S. Yamaguchi, A.C. D'Alessio, H.L. Fung, K. Zhang, and Y. Zhang Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics Cell 153 2013 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    Zhang, K.7    Zhang, Y.8
  • 43
    • 77958607062 scopus 로고    scopus 로고
    • Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins
    • N. Treiber, T. Treiber, G. Zocher, and R. Grosschedl Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins Genes Dev. 24 2010 2270 2275
    • (2010) Genes Dev. , vol.24 , pp. 2270-2275
    • Treiber, N.1    Treiber, T.2    Zocher, G.3    Grosschedl, R.4
  • 45
    • 70249088327 scopus 로고    scopus 로고
    • Genomic views of distant-acting enhancers
    • A. Visel, E.M. Rubin, and L.A. Pennacchio Genomic views of distant-acting enhancers Nature 461 2009 199 205
    • (2009) Nature , vol.461 , pp. 199-205
    • Visel, A.1    Rubin, E.M.2    Pennacchio, L.A.3
  • 47
    • 36148940618 scopus 로고    scopus 로고
    • S-S synapsis during class switch recombination is promoted by distantly located transcriptional elements and activation-induced deaminase
    • R. Wuerffel, L. Wang, F. Grigera, J. Manis, E. Selsing, T. Perlot, F.W. Alt, M. Cogne, E. Pinaud, and A.L. Kenter S-S synapsis during class switch recombination is promoted by distantly located transcriptional elements and activation-induced deaminase Immunity 27 2007 711 722
    • (2007) Immunity , vol.27 , pp. 711-722
    • Wuerffel, R.1    Wang, L.2    Grigera, F.3    Manis, J.4    Selsing, E.5    Perlot, T.6    Alt, F.W.7    Cogne, M.8    Pinaud, E.9    Kenter, A.L.10
  • 48
    • 84880426365 scopus 로고    scopus 로고
    • Developmental biology. Enhancing pluripotency and lineage specification
    • W. Xie, and B. Ren Developmental biology. Enhancing pluripotency and lineage specification Science 341 2013 245 247
    • (2013) Science , vol.341 , pp. 245-247
    • Xie, W.1    Ren, B.2
  • 51
    • 84860684566 scopus 로고    scopus 로고
    • Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation
    • Y. Goh, M.J. Fullwood, H.M. Poh, S.Q. Peh, C.T. Ong, J. Zhang, X. Ruan, and Y. Ruan Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation J. Vis. Exp. 62 2012 3770
    • (2012) J. Vis. Exp. , vol.62 , pp. 3770
    • Goh, Y.1    Fullwood, M.J.2    Poh, H.M.3    Peh, S.Q.4    Ong, C.T.5    Zhang, J.6    Ruan, X.7    Ruan, Y.8
  • 52
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
    • (2009) Genome Biol. , vol.10 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 55
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • J.E. Phillips, and V.G. Corces CTCF: master weaver of the genome Cell 137 2009 1194 1211
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 56
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 59
    • 84865098750 scopus 로고    scopus 로고
    • BatMis: A fast algorithm for k-mismatch mapping
    • C. Tennakoon, R.W. Purbojati, and W.K. Sung BatMis: a fast algorithm for k-mismatch mapping Bioinformatics 28 2012 2122 2128
    • (2012) Bioinformatics , vol.28 , pp. 2122-2128
    • Tennakoon, C.1    Purbojati, R.W.2    Sung, W.K.3
  • 63
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • T.D. Wu, and S. Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 26 2010 873 881
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.