메뉴 건너뛰기




Volumn 25, Issue 4, 2015, Pages 582-597

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(24)  Schoenfelder, Stefan a   Furlan Magaril, Mayra a   Mifsud, Borbala b,c   Tavares Cadete, Filipe b,c   Sugar, Robert c,d   Javierre, Biola Maria a   Nagano, Takashi a   Katsman, Yulia e   Sakthidevi, Moorthy e   Wingett, Steven W a   Dimitrova, Emilia a   Dimond, Andrew a   Edelman, Lucas B a   Elderkin, Sarah a   Tabbada, Kristina a   Darbo, Elodie b,c   Andrews, Simon a   Herman, Bram f   Higgs, Andy f   LeProust, Emily f   more..


Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EMBRYO; GENE CLUSTER; GENE EXPRESSION; GENETIC TRANSCRIPTION; HISTONE MODIFICATION; MOUSE; NONHUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY MECHANISM; RESTRICTION FRAGMENT; ANIMAL; BINDING SITE; C57BL MOUSE; CHROMATIN; CYTOLOGY; EMBRYOLOGY; EMBRYONIC STEM CELL; ENHANCER REGION; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; LIVER; METABOLISM;

EID: 84927763931     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.185272.114     Document Type: Article
Times cited : (337)

References (79)
  • 2
    • 0037111656 scopus 로고    scopus 로고
    • Deletion of the mouse α-globin regulatory element (HS-26) has an unexpectedly mild phenotype
    • Anguita E, Sharpe JA, Sloane-Stanley JA, Tufarelli C, Higgs DR, Wood WG. 2002. Deletion of the mouse α-globin regulatory element (HS-26) has an unexpectedly mild phenotype. Blood 100: 3450-3456.
    • (2002) Blood , vol.100 , pp. 3450-3456
    • Anguita, E.1    Sharpe, J.A.2    Sloane-Stanley, J.A.3    Tufarelli, C.4    Higgs, D.R.5    Wood, W.G.6
  • 3
    • 46149115158 scopus 로고    scopus 로고
    • Virus infection induces NFKB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression
    • Apostolou E, Thanos D. 2008. Virus infection induces NFKB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell 134: 85-96.
    • (2008) Cell , vol.134 , pp. 85-96
    • Apostolou, E.1    Thanos, D.2
  • 8
    • 0035496898 scopus 로고    scopus 로고
    • Targeted deletion of 5′HS1 and 5′HS4 of the β-globin locus control region reveals additive activity of the DNase I hypersensitive sites
    • Bender MA, Roach JN, Halow J, Close J, Alami R, Bouhassira EE, Groudine M, Fiering SN. 2001. Targeted deletion of 5′HS1 and 5′HS4 of the β-globin locus control region reveals additive activity of the DNase I hypersensitive sites. Blood 98: 2022-2027.
    • (2001) Blood , vol.98 , pp. 2022-2027
    • Bender, M.A.1    Roach, J.N.2    Halow, J.3    Close, J.4    Alami, R.5    Bouhassira, E.E.6    Groudine, M.7    Fiering, S.N.8
  • 9
    • 84860323219 scopus 로고    scopus 로고
    • The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation
    • Bender MA, Ragoczy T, Lee J, Byron R, Telling A, Dean A, Groudine M. 2012. The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation. Blood 119: 3820-3827.
    • (2012) Blood , vol.119 , pp. 3820-3827
    • Bender, M.A.1    Ragoczy, T.2    Lee, J.3    Byron, R.4    Telling, A.5    Dean, A.6    Groudine, M.7
  • 10
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B 57: 289-300.
    • (1995) J R Stat Soc Series B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 11
    • 79551655285 scopus 로고    scopus 로고
    • Functional and mechanistic diversity of distal transcription enhancers
    • 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
  • 12
    • 84876836223 scopus 로고    scopus 로고
    • Modification of enhancer chromatin: What, how, and why?
    • 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
  • 14
    • 0034986652 scopus 로고    scopus 로고
    • A BAC transgenic analysis of the Mrf4/Myf5 locus reveals interdigitated elements that control activation and maintenance of gene expression during muscle development
    • Carvajal JJ, Cox D, Summerbell D, Rigby PW. 2001. A BAC transgenic analysis of the Mrf4/Myf5 locus reveals interdigitated elements that control activation and maintenance of gene expression during muscle development. Development 128: 1857-1868.
    • (2001) Development , vol.128 , pp. 1857-1868
    • Carvajal, J.J.1    Cox, D.2    Summerbell, D.3    Rigby, P.W.4
  • 15
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 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
  • 18
    • 84861964135 scopus 로고    scopus 로고
    • Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor
    • Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. 2012. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149: 1233-1244.
    • (2012) Cell , vol.149 , pp. 1233-1244
    • Deng, W.1    Lee, J.2    Wang, H.3    Miller, J.4    Reik, A.5    Gregory, P.D.6    Dean, A.7    Blobel, G.A.8
  • 19
    • 85027929606 scopus 로고    scopus 로고
    • Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization
    • Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. 2013. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell 13: 602-616.
    • (2013) Cell Stem Cell , vol.13 , pp. 602-616
    • Denholtz, M.1    Bonora, G.2    Chronis, C.3    Splinter, E.4    De Laat, W.5    Ernst, J.6    Pellegrini, M.7    Plath, K.8
  • 20
    • 84861095603 scopus 로고    scopus 로고
    • 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. 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    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 24
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 26
    • 84886777912 scopus 로고    scopus 로고
    • Chromosomal contact permits transcription between coregulated genes
    • Fanucchi S, Shibayama Y, Burd S, Weinberg MS, Mhlanga MM. 2013. Chromosomal contact permits transcription between coregulated genes. Cell 155: 606-620.
    • (2013) Cell , vol.155 , pp. 606-620
    • Fanucchi, S.1    Shibayama, Y.2    Burd, S.3    Weinberg, M.S.4    Mhlanga, M.M.5
  • 27
    • 84874705284 scopus 로고    scopus 로고
    • Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression
    • Ferreira R, Spensberger D, Silber Y, Dimond A, Li J, Green AR, Göttgens B. 2013. Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression. Mol Cell Biol 33: 1254-1266.
    • (2013) Mol Cell Biol , vol.33 , pp. 1254-1266
    • Ferreira, R.1    Spensberger, D.2    Silber, Y.3    Dimond, A.4    Li, J.5    Green, A.R.6    Göttgens, B.7
  • 28
    • 77954960062 scopus 로고    scopus 로고
    • Phenotypic robustness conferred by apparently redundant transcriptional enhancers
    • Frankel N, Davis GK, Vargas D, Wang S, Payre F, Stern DL. 2010. Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466: 490-493.
    • (2010) Nature , vol.466 , pp. 490-493
    • Frankel, N.1    Davis, G.K.2    Vargas, D.3    Wang, S.4    Payre, F.5    Stern, D.L.6
  • 30
    • 84876838711 scopus 로고    scopus 로고
    • The hierarchy of the 3D genome
    • Gibcus JH, Dekker J. 2013. The hierarchy of the 3D genome. Mol Cell 49: 773-782.
    • (2013) Mol Cell , vol.49 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 35
    • 51149097760 scopus 로고    scopus 로고
    • Shadow enhancers as a source of evolutionary novelty
    • Hong JW, Hendrix DA, Levine MS. 2008. Shadow enhancers as a source of evolutionary novelty. Science 321: 1314.
    • (2008) Science , vol.321 , pp. 1314
    • Hong, J.W.1    Hendrix, D.A.2    Levine, M.S.3
  • 37
    • 33645073400 scopus 로고    scopus 로고
    • A functional screen for sonic hedgehog regulatory elements across a 1Mbinterval identifies long-range ventral forebrain enhancers
    • Jeong Y, El-Jaick K, Roessler E, Muenke M, Epstein DJ. 2006. A functional screen for sonic hedgehog regulatory elements across a 1Mbinterval identifies long-range ventral forebrain enhancers. Development 133: 761-772.
    • (2006) Development , vol.133 , pp. 761-772
    • Jeong, Y.1    El-Jaick, K.2    Roessler, E.3    Muenke, M.4    Epstein, D.J.5
  • 43
    • 84872605250 scopus 로고    scopus 로고
    • The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation
    • Lin C, Garruss AS, Luo Z, Guo F, Shilatifard A. 2013. The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. Cell 152: 144-156.
    • (2013) Cell , vol.152 , pp. 144-156
    • Lin, C.1    Garruss, A.S.2    Luo, Z.3    Guo, F.4    Shilatifard, A.5
  • 44
    • 84875249885 scopus 로고    scopus 로고
    • An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape
    • Marinic M, Aktas T, Ruf S, Spitz F. 2013. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev Cell 24: 530-542.
    • (2013) Dev Cell , vol.24 , pp. 530-542
    • Marinic, M.1    Aktas, T.2    Ruf, S.3    Spitz, F.4
  • 46
    • 38149133051 scopus 로고    scopus 로고
    • Transcription factories are nuclear subcompartments that remain in the absence of transcription
    • Mitchell JA, Fraser P. 2008. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 22: 20-25.
    • (2008) Genes Dev , vol.22 , pp. 20-25
    • Mitchell, J.A.1    Fraser, P.2
  • 57
    • 79953176250 scopus 로고    scopus 로고
    • Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor
    • Ruf S, Symmons O, Uslu VV, Dolle D, Hot C, Ettwiller L, Spitz F. 2011. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet 43: 379-386.
    • (2011) Nat Genet , vol.43 , pp. 379-386
    • Ruf, S.1    Symmons, O.2    Uslu, V.V.3    Dolle, D.4    Hot, C.5    Ettwiller, L.6    Spitz, F.7
  • 58
    • 14844341770 scopus 로고    scopus 로고
    • Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb
    • Sagai T, Hosoya M, Mizushina Y, Tamura M, Shiroishi T. 2005. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132: 797-803.
    • (2005) Development , vol.132 , pp. 797-803
    • Sagai, T.1    Hosoya, M.2    Mizushina, Y.3    Tamura, M.4    Shiroishi, T.5
  • 59
    • 68549123708 scopus 로고    scopus 로고
    • A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings
    • Sagai T, Amano T, Tamura M, Mizushina Y, Sumiyama K, Shiroishi T. 2009. A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings. Development 136: 1665-1674.
    • (2009) Development , vol.136 , pp. 1665-1674
    • Sagai, T.1    Amano, T.2    Tamura, M.3    Mizushina, Y.4    Sumiyama, K.5    Shiroishi, T.6
  • 60
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • 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
  • 64
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    • Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. 2006. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38: 1348-1354.
    • (2006) Nat Genet , vol.38 , pp. 1348-1354
    • Simonis, M.1    Klous, P.2    Splinter, E.3    Moshkin, Y.4    Willemsen, R.5    De Wit, E.6    Van Steensel, B.7    De Laat, W.8
  • 66
    • 20444494936 scopus 로고    scopus 로고
    • Interchromosomal associations between alternatively expressed loci
    • Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. 2005. Interchromosomal associations between alternatively expressed loci. Nature 435: 637-645.
    • (2005) Nature , vol.435 , pp. 637-645
    • Spilianakis, C.G.1    Lalioti, M.D.2    Town, T.3    Lee, G.R.4    Flavell, R.A.5
  • 67
    • 0038613098 scopus 로고    scopus 로고
    • A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
    • Spitz F, Gonzalez F, Duboule D. 2003. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113: 405-417.
    • (2003) Cell , vol.113 , pp. 405-417
    • Spitz, F.1    Gonzalez, F.2    Duboule, D.3
  • 71
    • 34247272882 scopus 로고    scopus 로고
    • Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression
    • Vernimmen D, De Gobbi M, Sloane-Stanley JA, Wood WG, Higgs DR. 2007. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J 26: 2041-2051.
    • (2007) EMBO J , vol.26 , pp. 2041-2051
    • Vernimmen, D.1    De Gobbi, M.2    Sloane-Stanley, J.A.3    Wood, W.G.4    Higgs, D.R.5
  • 73
    • 84887835943 scopus 로고    scopus 로고
    • KLF4 organizes long-range chromosomal interactions with the Oct4 locus in reprogramming and pluripotency
    • Wei Z, Gao F, Kim S, Yang H, Lyu J, An W, Wang K, Lu W. 2013. KLF4 organizes long-range chromosomal interactions with the Oct4 locus in reprogramming and pluripotency. Cell Stem Cell 13: 36-47.
    • (2013) Cell Stem Cell , vol.13 , pp. 36-47
    • Wei, Z.1    Gao, F.2    Kim, S.3    Yang, H.4    Lyu, J.5    An, W.6    Wang, K.7    Lu, W.8
  • 77
    • 33750203582 scopus 로고    scopus 로고
    • Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
    • Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, et al. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38: 1341-1347.
    • (2006) Nat Genet , vol.38 , pp. 1341-1347
    • Zhao, Z.1    Tavoosidana, G.2    Sjolinder, M.3    Gondor, A.4    Mariano, P.5    Wang, S.6    Kanduri, C.7    Lezcano, M.8    Sandhu, K.S.9    Singh, U.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.