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Volumn 98, Issue 1, 2016, Pages 185-201

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

Author keywords

CFTR; chromatin looping; gene regulation; topologically associating domain

Indexed keywords

CAVEOLIN 1; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; TRANSCRIPTION FACTOR CTCF; CFTR PROTEIN, HUMAN; CHROMATIN;

EID: 84954288250     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.12.002     Document Type: Article
Times cited : (105)

References (67)
  • 1
    • 84875190221 scopus 로고    scopus 로고
    • Genome architecture: Domain organization of interphase chromosomes
    • W.A. Bickmore, and B. van Steensel Genome architecture: Domain organization of interphase chromosomes Cell 152 2013 1270 1284
    • (2013) Cell , vol.152 , pp. 1270-1284
    • Bickmore, W.A.1    Van Steensel, B.2
  • 2
    • 34249307315 scopus 로고    scopus 로고
    • Nuclear organization of the genome and the potential for gene regulation
    • P. Fraser, and W. Bickmore Nuclear organization of the genome and the potential for gene regulation Nature 447 2007 413 417
    • (2007) Nature , vol.447 , pp. 413-417
    • Fraser, P.1    Bickmore, W.2
  • 4
    • 0035316574 scopus 로고    scopus 로고
    • Chromosome territories, nuclear architecture and gene regulation in mammalian cells
    • T. Cremer, and C. Cremer Chromosome territories, nuclear architecture and gene regulation in mammalian cells Nat. Rev. Genet. 2 2001 292 301
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 292-301
    • Cremer, T.1    Cremer, C.2
  • 5
    • 33646729244 scopus 로고    scopus 로고
    • Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations
    • M.R. Branco, and A. Pombo Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations PLoS Biol. 4 2006 e138
    • (2006) PLoS Biol. , vol.4 , pp. e138
    • Branco, M.R.1    Pombo, A.2
  • 6
    • 0033553877 scopus 로고    scopus 로고
    • Differences in the localization and morphology of chromosomes in the human nucleus
    • J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague, and W.A. Bickmore Differences in the localization and morphology of chromosomes in the human nucleus J. Cell Biol. 145 1999 1119 1131
    • (1999) J. Cell Biol. , vol.145 , pp. 1119-1131
    • Croft, J.A.1    Bridger, J.M.2    Boyle, S.3    Perry, P.4    Teague, P.5    Bickmore, W.A.6
  • 13
    • 0029973080 scopus 로고    scopus 로고
    • Active RNA polymerases are localized within discrete transcription "factories" in human nuclei
    • F.J. Iborra, A. Pombo, D.A. Jackson, and P.R. Cook Active RNA polymerases are localized within discrete transcription "factories" in human nuclei J. Cell Sci. 109 1996 1427 1436
    • (1996) J. Cell Sci. , vol.109 , pp. 1427-1436
    • Iborra, F.J.1    Pombo, A.2    Jackson, D.A.3    Cook, P.R.4
  • 16
    • 58149463874 scopus 로고    scopus 로고
    • Chromosomal dynamics at the Shh locus: Limb bud-specific differential regulation of competence and active transcription
    • T. Amano, T. Sagai, H. Tanabe, Y. Mizushina, H. Nakazawa, and T. Shiroishi Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription Dev. Cell 16 2009 47 57
    • (2009) Dev. Cell , vol.16 , pp. 47-57
    • Amano, T.1    Sagai, T.2    Tanabe, H.3    Mizushina, Y.4    Nakazawa, H.5    Shiroishi, T.6
  • 20
    • 3543018516 scopus 로고    scopus 로고
    • Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops
    • A. Murrell, S. Heeson, and W. Reik Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops Nat. Genet. 36 2004 889 893
    • (2004) Nat. Genet. , vol.36 , pp. 889-893
    • Murrell, A.1    Heeson, S.2    Reik, W.3
  • 22
    • 67149111884 scopus 로고    scopus 로고
    • Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions
    • A. Miele, K. Bystricky, and J. Dekker Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions PLoS Genet. 5 2009 e1000478
    • (2009) PLoS Genet. , vol.5 , pp. e1000478
    • Miele, A.1    Bystricky, K.2    Dekker, J.3
  • 25
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • A. Sanyal, B.R. Lajoie, G. Jain, and J. Dekker The long-range interaction landscape of gene promoters Nature 489 2012 109 113
    • (2012) Nature , vol.489 , pp. 109-113
    • Sanyal, A.1    Lajoie, B.R.2    Jain, G.3    Dekker, J.4
  • 26
    • 0036923833 scopus 로고    scopus 로고
    • Looping and interaction between hypersensitive sites in the active beta-globin locus
    • B. Tolhuis, R.J. Palstra, E. Splinter, F. Grosveld, and W. de Laat Looping and interaction between hypersensitive sites in the active beta-globin locus Mol. Cell 10 2002 1453 1465
    • (2002) Mol. Cell , vol.10 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.J.2    Splinter, E.3    Grosveld, F.4    De Laat, W.5
  • 27
    • 34247272882 scopus 로고    scopus 로고
    • Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression
    • D. Vernimmen, M. De Gobbi, J.A. Sloane-Stanley, W.G. Wood, and D.R. Higgs Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression EMBO J. 26 2007 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
  • 28
    • 77749323471 scopus 로고    scopus 로고
    • Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells
    • J.B. Wright, S.J. Brown, and M.D. Cole Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells Mol. Cell. Biol. 30 2010 1411 1420
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 1411-1420
    • Wright, J.B.1    Brown, S.J.2    Cole, M.D.3
  • 29
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • D.A. Kleinjan, and V. van Heyningen Long-range control of gene expression: emerging mechanisms and disruption in disease Am. J. Hum. Genet. 76 2005 8 32
    • (2005) Am. J. Hum. Genet. , vol.76 , pp. 8-32
    • Kleinjan, D.A.1    Van Heyningen, V.2
  • 31
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • J.R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J.S. Liu, and B. Ren Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 2012 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
  • 37
    • 84988931974 scopus 로고    scopus 로고
    • Two ways to fold the genome during the cell cycle: Insights obtained with chromosome conformation capture
    • J. Dekker Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture Epigenetics Chromatin 7 2014 25
    • (2014) Epigenetics Chromatin , vol.7 , pp. 25
    • Dekker, J.1
  • 39
    • 84900297485 scopus 로고    scopus 로고
    • Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription
    • L. Giorgetti, R. Galupa, E.P. Nora, T. Piolot, F. Lam, J. Dekker, G. Tiana, and E. Heard Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription Cell 157 2014 950 963
    • (2014) Cell , vol.157 , pp. 950-963
    • Giorgetti, L.1    Galupa, R.2    Nora, E.P.3    Piolot, T.4    Lam, F.5    Dekker, J.6    Tiana, G.7    Heard, E.8
  • 40
    • 84876838711 scopus 로고    scopus 로고
    • The hierarchy of the 3D genome
    • J.H. Gibcus, and J. Dekker The hierarchy of the 3D genome Mol. Cell 49 2013 773 782
    • (2013) Mol. Cell , vol.49 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 42
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children's Hospital Oakland Research Institute
    • E. Birney, J.A. Stamatoyannopoulos, A. Dutta, R. Guigó, T.R. Gingeras, E.H. Margulies, Z. Weng, M. Snyder, E.T. Dermitzakis, R.E. Thurman, et al. ENCODE Project Consortium NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children's Hospital Oakland Research Institute Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 2007 799 816
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3    Guigó, R.4    Gingeras, T.R.5    Margulies, E.H.6    Weng, Z.7    Snyder, M.8    Dermitzakis, E.T.9    Thurman, R.E.10
  • 43
    • 70349625401 scopus 로고    scopus 로고
    • My5C: Web tools for chromosome conformation capture studies
    • B.R. Lajoie, N.L. van Berkum, A. Sanyal, and J. Dekker My5C: web tools for chromosome conformation capture studies Nat. Methods 6 2009 690 691
    • (2009) Nat. Methods , vol.6 , pp. 690-691
    • Lajoie, B.R.1    Van Berkum, N.L.2    Sanyal, A.3    Dekker, J.4
  • 45
    • 84870344301 scopus 로고    scopus 로고
    • Analysis of long-range chromatin interactions using Chromosome Conformation Capture
    • N. Naumova, E.M. Smith, Y. Zhan, and J. Dekker Analysis of long-range chromatin interactions using Chromosome Conformation Capture Methods 58 2012 192 203
    • (2012) Methods , vol.58 , pp. 192-203
    • Naumova, N.1    Smith, E.M.2    Zhan, Y.3    Dekker, J.4
  • 46
    • 84870310396 scopus 로고    scopus 로고
    • From cells to chromatin: Capturing snapshots of genome organization with 5C technology
    • M.A. Ferraiuolo, A. Sanyal, N. Naumova, J. Dekker, and J. Dostie From cells to chromatin: capturing snapshots of genome organization with 5C technology Methods 58 2012 255 267
    • (2012) Methods , vol.58 , pp. 255-267
    • Ferraiuolo, M.A.1    Sanyal, A.2    Naumova, N.3    Dekker, J.4    Dostie, J.5
  • 47
    • 84927779326 scopus 로고    scopus 로고
    • The Hitchhiker's guide to Hi-C analysis: Practical guidelines
    • B.R. Lajoie, J. Dekker, and N. Kaplan The Hitchhiker's guide to Hi-C analysis: practical guidelines Methods 72 2015 65 75
    • (2015) Methods , vol.72 , pp. 65-75
    • Lajoie, B.R.1    Dekker, J.2    Kaplan, N.3
  • 48
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
    • J. Dekker, M.A. Marti-Renom, and L.A. Mirny Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data Nat. Rev. Genet. 14 2013 390 403
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 49
    • 84869003748 scopus 로고    scopus 로고
    • Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains
    • C. Hou, L. Li, Z.S. Qin, and V.G. Corces Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains Mol. Cell 48 2012 471 484
    • (2012) Mol. Cell , vol.48 , pp. 471-484
    • Hou, C.1    Li, L.2    Qin, Z.S.3    Corces, V.G.4
  • 50
    • 85006305723 scopus 로고    scopus 로고
    • Insulator function and topological domain border strength scale with architectural protein occupancy
    • K. Van Bortle, M.H. Nichols, L. Li, C.T. Ong, N. Takenaka, Z.S. Qin, and V.G. Corces Insulator function and topological domain border strength scale with architectural protein occupancy Genome Biol. 15 2014 R82
    • (2014) Genome Biol. , vol.15 , pp. R82
    • Van Bortle, K.1    Nichols, M.H.2    Li, L.3    Ong, C.T.4    Takenaka, N.5    Qin, Z.S.6    Corces, V.G.7
  • 53
    • 84908333387 scopus 로고    scopus 로고
    • Chromatin loops as allosteric modulators of enhancer-promoter interactions
    • B. Doyle, G. Fudenberg, M. Imakaev, and L.A. Mirny Chromatin loops as allosteric modulators of enhancer-promoter interactions PLoS Comput. Biol. 10 2014 e1003867
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003867
    • Doyle, B.1    Fudenberg, G.2    Imakaev, M.3    Mirny, L.A.4
  • 56
    • 21444440910 scopus 로고    scopus 로고
    • The CFTR gene and regulation of its expression
    • V.A. McCarthy, and A. Harris The CFTR gene and regulation of its expression Pediatr. Pulmonol. 40 2005 1 8
    • (2005) Pediatr. Pulmonol. , vol.40 , pp. 1-8
    • McCarthy, V.A.1    Harris, A.2
  • 58
    • 0033179057 scopus 로고    scopus 로고
    • Analysis of DNase-I-hypersensitive sites at the 3′ end of the cystic fibrosis transmembrane conductance regulator gene (CFTR)
    • H.N. Nuthall, D.S. Moulin, C. Huxley, and A. Harris Analysis of DNase-I-hypersensitive sites at the 3′ end of the cystic fibrosis transmembrane conductance regulator gene (CFTR) Biochem. J. 341 1999 601 611
    • (1999) Biochem. J. , vol.341 , pp. 601-611
    • Nuthall, H.N.1    Moulin, D.S.2    Huxley, C.3    Harris, A.4
  • 59
    • 84880675359 scopus 로고    scopus 로고
    • Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer
    • Z. Zhang, S.H. Leir, and A. Harris Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer Mol. Cell. Biol. 33 2013 2843 2853
    • (2013) Mol. Cell. Biol. , vol.33 , pp. 2843-2853
    • Zhang, Z.1    Leir, S.H.2    Harris, A.3
  • 60
    • 84924120741 scopus 로고    scopus 로고
    • Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element
    • Z. Zhang, S.H. Leir, and A. Harris Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element Am. J. Respir. Cell Mol. Biol. 52 2015 387 396
    • (2015) Am. J. Respir. Cell Mol. Biol. , vol.52 , pp. 387-396
    • Zhang, Z.1    Leir, S.H.2    Harris, A.3
  • 62
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
    • (2012) Nature , vol.489 , pp. 57-74
  • 63
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • J. Ernst, and M. Kellis ChromHMM: automating chromatin-state discovery and characterization Nat. Methods 9 2012 215 216
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 66
    • 84923374968 scopus 로고    scopus 로고
    • Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus
    • N. Gosalia, D. Neems, J.L. Kerschner, S.T. Kosak, and A. Harris Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus Nucleic Acids Res. 42 2014 9612 9622
    • (2014) Nucleic Acids Res. , vol.42 , pp. 9612-9622
    • Gosalia, N.1    Neems, D.2    Kerschner, J.L.3    Kosak, S.T.4    Harris, A.5
  • 67
    • 0035668536 scopus 로고    scopus 로고
    • Making contacts on a nucleic acid polymer
    • K. Rippe Making contacts on a nucleic acid polymer Trends Biochem. Sci. 26 2001 733 740
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 733-740
    • Rippe, K.1


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