메뉴 건너뛰기




Volumn 44, Issue 7, 2015, Pages 3082-3094

Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 9; COHESIN; CRISPR ASSOCIATED PROTEIN; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR CTCF; CCCTC-BINDING FACTOR; CELL CYCLE PROTEIN; CHROMATIN; NONHISTONE PROTEIN; REPRESSOR PROTEIN;

EID: 84965102334     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1358     Document Type: Article
Times cited : (53)

References (62)
  • 1
    • 0033529654 scopus 로고    scopus 로고
    • The protein CTCF is required for the enhancer blocking activity of vertebrate insulators
    • Bell, A.C., West, A.G., Felsenfeld, G. (1999) The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell, 98, 387-396.
    • (1999) Cell , vol.98 , pp. 387-396
    • Bell, A.C.1    West, A.G.2    Felsenfeld, G.3
  • 8
    • 84892715701 scopus 로고    scopus 로고
    • Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs
    • Berlivet, S., Paquette, D., Dumouchel, A., Langlais, D., Dostie, J., Kmita, M. (2013) Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet., 9, e1004018.
    • (2013) PLoS Genet , vol.9 , pp. e1004018
    • Berlivet, S.1    Paquette, D.2    Dumouchel, A.3    Langlais, D.4    Dostie, J.5    Kmita, M.6
  • 9
    • 0025107556 scopus 로고
    • A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus
    • Forrester, W.C., Epner, E., Driscoll, M.C., Enver, T., Brice, M., Papayannopoulou, T., Groudine, M. (1990) A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev., 4, 1637-1649.
    • (1990) Genes Dev , vol.4 , pp. 1637-1649
    • Forrester, W.C.1    Epner, E.2    Driscoll, M.C.3    Enver, T.4    Brice, M.5    Papayannopoulou, T.6    Groudine, M.7
  • 10
    • 49249099730 scopus 로고    scopus 로고
    • Spatial configuration of the chicken alpha-globin gene domain: Immature and active chromatin hubs
    • Gavrilov, A.A., Razin, S.V. (2008) Spatial configuration of the chicken alpha-globin gene domain: immature and active chromatin hubs. Nucleic Acids Res., 36, 4629-4640.
    • (2008) Nucleic Acids Res , vol.36 , pp. 4629-4640
    • Gavrilov, A.A.1    Razin, S.V.2
  • 11
    • 39049083467 scopus 로고    scopus 로고
    • Long-range regulation of alpha-globin gene expression
    • Higgs, D.R., Vernimmen, D., Wood, B. (2008) Long-range regulation of alpha-globin gene expression. Adv. Genet., 61, 143-173.
    • (2008) Adv. Genet , vol.61 , pp. 143-173
    • Higgs, D.R.1    Vernimmen, D.2    Wood, B.3
  • 13
    • 0242664094 scopus 로고    scopus 로고
    • A human globin enhancer causes both discrete and widespread alterations in chromatin structure
    • Kim, A., Dean, A. (2003) A human globin enhancer causes both discrete and widespread alterations in chromatin structure. Mol. Cell. Biol., 23, 8099-8109.
    • (2003) Mol. Cell. Biol , vol.23 , pp. 8099-8109
    • Kim, A.1    Dean, A.2
  • 14
    • 33748259774 scopus 로고    scopus 로고
    • CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus
    • Splinter, E., Heath, H., Kooren, J., Palstra, R.J., Klous, P., Grosveld, F., Galjart, N., de Laat, W. (2006) CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev., 20, 2349-2354.
    • (2006) Genes Dev , vol.20 , pp. 2349-2354
    • Splinter, E.1    Heath, H.2    Kooren, J.3    Palstra, R.J.4    Klous, P.5    Grosveld, F.6    Galjart, N.7    De Laat, W.8
  • 16
    • 84860847427 scopus 로고    scopus 로고
    • Transcriptional regulation of CFTR gene expression
    • Gillen, A.E., Harris, A. (2012) Transcriptional regulation of CFTR gene expression. Front. Biosci., 4, 587-592.
    • (2012) Front. Biosci , vol.4 , pp. 587-592
    • Gillen, A.E.1    Harris, A.2
  • 17
    • 84937438180 scopus 로고    scopus 로고
    • Chromatin dynamics in the regulation of CFTR expression
    • Gosalia, N., Harris, A. (2015) Chromatin dynamics in the regulation of CFTR expression. Genes, 6, 543-558.
    • (2015) Genes , vol.6 , pp. 543-558
    • Gosalia, N.1    Harris, A.2
  • 19
    • 65249131931 scopus 로고    scopus 로고
    • A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter
    • Ott, C.J., Suszko, M., Blackledge, N.P., Wright, J.E., Crawford, G.E., Harris, A. (2009) A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. J. Cell. Mol. Med., 13, 680-692.
    • (2009) J. Cell. Mol. Med , vol.13 , pp. 680-692
    • Ott, C.J.1    Suszko, M.2    Blackledge, N.P.3    Wright, J.E.4    Crawford, G.E.5    Harris, A.6
  • 21
    • 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
    • Gosalia, N., Neems, D., Kerschner, J.L., Kosak, S.T., Harris, A. (2014) Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus. Nucleic Acids Res., 42, 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
  • 22
    • 84865174240 scopus 로고    scopus 로고
    • Transcriptional networks driving enhancer function in the CFTR gene
    • Kerschner, J.L., Harris, A. (2012) Transcriptional networks driving enhancer function in the CFTR gene. Biochem. J., 446, 203-212.
    • (2012) Biochem. J , vol.446 , pp. 203-212
    • Kerschner, J.L.1    Harris, A.2
  • 23
    • 84899132703 scopus 로고    scopus 로고
    • Chromatin remodeling mediated by the FOXA1/A2 transcription factors activates CFTR expression in intestinal epithelial cells
    • Kerschner, J.L., Gosalia, N., Leir, S.H., Harris, A. (2014) Chromatin remodeling mediated by the FOXA1/A2 transcription factors activates CFTR expression in intestinal epithelial cells. Epigenetics, 9, 557-565.
    • (2014) Epigenetics , vol.9 , pp. 557-565
    • Kerschner, J.L.1    Gosalia, N.2    Leir, S.H.3    Harris, A.4
  • 24
    • 84861534368 scopus 로고    scopus 로고
    • Molecular mechanisms controlling CFTR gene expression in the airway
    • Zhang, Z., Ott, C.J., Lewandowska, M.A., Leir, S.H., Harris, A. (2012) Molecular mechanisms controlling CFTR gene expression in the airway. J. Cell. Mol. Med., 16, 1321-1330.
    • (2012) J. Cell. Mol. Med , vol.16 , pp. 1321-1330
    • Zhang, Z.1    Ott, C.J.2    Lewandowska, M.A.3    Leir, S.H.4    Harris, A.5
  • 25
    • 84880675359 scopus 로고    scopus 로고
    • Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer
    • Zhang, Z., Leir, S.H., Harris, A. (2013) Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer. Mol. Cell. Biol., 33, 2843-2853.
    • (2013) Mol. Cell. Biol , vol.33 , pp. 2843-2853
    • Zhang, Z.1    Leir, S.H.2    Harris, A.3
  • 26
    • 84924120741 scopus 로고    scopus 로고
    • Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element
    • Zhang, Z., Leir, S.H., Harris, A. (2015) Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element. Am. J. Respir. Cell Mol. Biol., 52, 387-396.
    • (2015) Am. J. Respir. Cell Mol. Biol , vol.52 , pp. 387-396
    • Zhang, Z.1    Leir, S.H.2    Harris, A.3
  • 27
    • 0017332809 scopus 로고
    • Absence of HeLa cell contamination in 169 cell lines derived from human tumors
    • Fogh, J., Wright, W.C., Loveless, J.D. (1977) Absence of HeLa cell contamination in 169 cell lines derived from human tumors. J. Natl. Cancer Inst., 58, 209-214.
    • (1977) J. Natl. Cancer Inst , vol.58 , pp. 209-214
    • Fogh, J.1    Wright, W.C.2    Loveless, J.D.3
  • 28
    • 0028307695 scopus 로고
    • Calu-3: A human airway epithelial cell line that shows cAMP-dependent Cl-secretion
    • Shen, B.Q., Finkbeiner, W.E., Wine, J.J., Mrsny, R.J., Widdicombe, J.H. (1994) Calu-3: a human airway epithelial cell line that shows cAMP-dependent Cl-secretion. Am. J. Physiol., 266, L493-L501.
    • (1994) Am. J. Physiol , vol.266 , pp. L493-L501
    • Shen, B.Q.1    Finkbeiner, W.E.2    Wine, J.J.3    Mrsny, R.J.4    Widdicombe, J.H.5
  • 30
    • 84961291524 scopus 로고    scopus 로고
    • Characterization of primary cultures of adult human epididymis epithelial cells
    • Leir, S.H., Browne, J.A., Eggener, S.E., Harris, A. (2015) Characterization of primary cultures of adult human epididymis epithelial cells. Fertil. Steril., 103, 647-654.
    • (2015) Fertil. Steril , vol.103 , pp. 647-654
    • Leir, S.H.1    Browne, J.A.2    Eggener, S.E.3    Harris, A.4
  • 31
    • 0025946280 scopus 로고
    • Lymphocyte mRNA as a resource for detection of mutations and polymorphisms in the CF gene
    • Chalkley, G., Harris, A. (1991) Lymphocyte mRNA as a resource for detection of mutations and polymorphisms in the CF gene. J. Med. Genet., 28, 777-780.
    • (1991) J. Med. Genet , vol.28 , pp. 777-780
    • Chalkley, G.1    Harris, A.2
  • 32
    • 84859856764 scopus 로고    scopus 로고
    • A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function
    • Bischof, J.M., Ott, C.J., Leir, S.H., Gosalia, N., Song, L., London, D., Furey, T.S., Cotton, C.U., Crawford, G.E., Harris, A. (2012) A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Thorax, 67, 385-391.
    • (2012) Thorax , vol.67 , pp. 385-391
    • Bischof, J.M.1    Ott, C.J.2    Leir, S.H.3    Gosalia, N.4    Song, L.5    London, D.6    Furey, T.S.7    Cotton, C.U.8    Crawford, G.E.9    Harris, A.10
  • 34
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 35
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., Glass, C.K. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6    Cheng, J.X.7    Murre, C.8    Singh, H.9    Glass, C.K.10
  • 36
    • 84870310006 scopus 로고    scopus 로고
    • Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation
    • Splinter, E., de Wit, E., van de Werken, H.J., Klous, P., de Laat, W. (2012) Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods, 58, 221-230.
    • (2012) Methods , vol.58 , pp. 221
    • Splinter, E.1    De Wit, E.2    Van De Werken, H.J.3    Klous, P.4    De Laat, W.5
  • 41
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., 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
  • 43
    • 84874773773 scopus 로고    scopus 로고
    • Coordinate regulation of the gel-forming mucin genes at chromosome 11p15.5
    • Gosalia, N., Leir, S.H., Harris, A. (2013) Coordinate regulation of the gel-forming mucin genes at chromosome 11p15.5. J. Biol. Chem., 288, 6717-6725.
    • (2013) J. Biol. Chem , vol.288 , pp. 6717-6725
    • Gosalia, N.1    Leir, S.H.2    Harris, A.3
  • 44
    • 0028272099 scopus 로고
    • Analysis of mutations and alternative splicing patterns in the CFTR gene using mRNA derived from nasal epithelial cells
    • Hull, J., Shackleton, S., Harris, A. (1994) Analysis of mutations and alternative splicing patterns in the CFTR gene using mRNA derived from nasal epithelial cells. Hum. Mol. Genet., 3, 1141-1146.
    • (1994) Hum. Mol. Genet , vol.3 , pp. 1141-1146
    • Hull, J.1    Shackleton, S.2    Harris, A.3
  • 45
    • 64349088929 scopus 로고    scopus 로고
    • Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA
    • Sekiya, T., Muthurajan, U.M., Luger, K., Tulin, A.V., Zaret, K.S. (2009) Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA. Genes Dev., 23, 804-809.
    • (2009) Genes Dev , vol.23 , pp. 804-809
    • Sekiya, T.1    Muthurajan, U.M.2    Luger, K.3    Tulin, A.V.4    Zaret, K.S.5
  • 46
    • 84936162207 scopus 로고    scopus 로고
    • FOXA2 regulates a network of genes involved in critical functions of human intestinal epithelia cells
    • Gosalia, N., Yang, R., Kerschner, J.L., Harris, A. (2015) FOXA2 regulates a network of genes involved in critical functions of human intestinal epithelia cells. Physiol. Genomics, 47, 290-297.
    • (2015) Physiol. Genomics , vol.47 , pp. 290-297
    • Gosalia, N.1    Yang, R.2    Kerschner, J.L.3    Harris, A.4
  • 48
    • 77649261872 scopus 로고    scopus 로고
    • Cell type specificity of chromatin organization mediated by CTCF and cohesin
    • Hou, C., Dale, R., Dean, A. (2010) Cell type specificity of chromatin organization mediated by CTCF and cohesin. Proc. Natl. Acad. Sci. U.S.A., 107, 3651-3656.
    • (2010) Proc. Natl. Acad. Sci. U.S.A , vol.107 , pp. 3651-3656
    • Hou, C.1    Dale, R.2    Dean, A.3
  • 49
    • 33746063711 scopus 로고    scopus 로고
    • CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2
    • Kurukuti, S., Tiwari, V.K., Tavoosidana, G., Pugacheva, E., Murrell, A., Zhao, Z., Lobanenkov, V., Reik, W., Ohlsson, R. (2006) 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., 103, 10684-10689.
    • (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
  • 52
    • 39449111307 scopus 로고    scopus 로고
    • Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators
    • Stedman, W., Kang, H., Lin, S., Kissil, J.L., Bartolomei, M.S., Lieberman, P.M. (2008) Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators. EMBO J., 27, 654-666.
    • (2008) EMBO J , vol.27 , pp. 654-666
    • Stedman, W.1    Kang, H.2    Lin, S.3    Kissil, J.L.4    Bartolomei, M.S.5    Lieberman, P.M.6
  • 53
    • 84923771297 scopus 로고    scopus 로고
    • Transcription CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation
    • Narendra, V., Rocha, P.P., An, D., Raviram, R., Skok, J.A., Mazzoni, E.O., Reinberg, D. (2015) Transcription. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science, 347, 1017-1021.
    • (2015) Science , vol.347 , pp. 1017-1021
    • Narendra, V.1    Rocha, P.P.2    An, D.3    Raviram, R.4    Skok, J.A.5    Mazzoni, E.O.6    Reinberg, D.7
  • 54
    • 58149498240 scopus 로고    scopus 로고
    • CTCF-dependent enhancer-blocking by alternative chromatin loop formation
    • Hou, C., Zhao, H., Tanimoto, K., Dean, A. (2008) CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc. Natl. Acad. Sci. U.S.A., 105, 20398-20403.
    • (2008) Proc. Natl. Acad. Sci. U.S.A , vol.105 , pp. 20398-20403
    • Hou, C.1    Zhao, H.2    Tanimoto, K.3    Dean, A.4
  • 57
    • 0024544576 scopus 로고
    • Ductal epithelial cells cultured from human foetal epididymis and vas deferens: Relevance to sterility in cystic fibrosis
    • Harris, A., Coleman, L. (1989) Ductal epithelial cells cultured from human foetal epididymis and vas deferens: relevance to sterility in cystic fibrosis. J. Cell Sci., 92, 687-690.
    • (1989) J. Cell Sci , vol.92 , pp. 687-690
    • Harris, A.1    Coleman, L.2
  • 58
    • 78149485097 scopus 로고    scopus 로고
    • Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2
    • Verzi, M.P., Shin, H., He, H.H., Sulahian, R., Meyer, C.A., Montgomery, R.K., Fleet, J.C., Brown, M., Liu, X.S., Shivdasani, R.A. (2010) Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev. Cell, 19, 713-726.
    • (2010) Dev. Cell , vol.19 , pp. 713-726
    • Verzi, M.P.1    Shin, H.2    He, H.H.3    Sulahian, R.4    Meyer, C.A.5    Montgomery, R.K.6    Fleet, J.C.7    Brown, M.8    Liu, X.S.9    Shivdasani, R.A.10
  • 61
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.