메뉴 건너뛰기




Volumn 47, Issue 6, 2015, Pages 598-606

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(18)  Mifsud, Borbala a,b   Tavares Cadete, Filipe a,g   Young, Alice N c   Sugar, Robert a   Schoenfelder, Stefan c   Ferreira, Lauren c   Wingett, Steven W c   Andrews, Simon c   Grey, William d   Ewels, Philip A c   Herman, Bram e   Happe, Scott e   Higgs, Andy e   Leproust, Emily e,g,h   Follows, George A f   Fraser, Peter c   Luscombe, Nicholas M a,b,g   Osborne, Cameron S c,d  


Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLOOD CELL; CAPTURE HI C; CELLS BY BODY ANATOMY; CONTROLLED STUDY; ENHANCER REGION; GENE CONTROL; GENE INTERACTION; GENE LOCUS; GENE MAPPING; GENETIC PROCEDURES; HISTONE MODIFICATION; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION INITIATION; CELL LINE; CHROMOSOME MAP; EPISTASIS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; HUMAN GENOME;

EID: 84930092058     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3286     Document Type: Article
Times cited : (723)

References (38)
  • 1
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
    • Dekker, J., Marti-Renom, M.A. & Mirny, L.A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390-403 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 2
    • 84862908850 scopus 로고    scopus 로고
    • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    • Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84-98 (2012).
    • (2012) Cell , vol.148 , pp. 84-98
    • Li, G.1
  • 3
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • Sanyal, A., Lajoie, B.R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012).
    • (2012) Nature , vol.489 , pp. 109-113
    • Sanyal, A.1    Lajoie, B.R.2    Jain, G.3    Dekker, J.4
  • 4
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 5
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identifed by analysis of chromatin interactions
    • Dixon, J.R. et al. Topological domains in mammalian genomes identifed by analysis of chromatin interactions. Nature 485, 376-380 (2012).
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1
  • 6
    • 84887620842 scopus 로고    scopus 로고
    • A high-resolution map of the three-dimensional chromatin interactome in human cells
    • Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-294 (2013).
    • (2013) Nature , vol.503 , pp. 290-294
    • Jin, F.1
  • 7
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182-189 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 182-189
    • Gnirke, A.1
  • 8
    • 84895832107 scopus 로고    scopus 로고
    • Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment
    • Hughes, J.R. et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat. Genet. 46, 205-212 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 205-212
    • Hughes, J.R.1
  • 9
    • 84868193627 scopus 로고    scopus 로고
    • Gene loops enhance transcriptional directionality
    • Tan-Wong, S.M. et al. Gene loops enhance transcriptional directionality. Science 338, 671-675 (2012).
    • (2012) Science , vol.338 , pp. 671-675
    • Tan-Wong, S.M.1
  • 10
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • Phillips, J.E. & Corces, V.G. CTCF: master weaver of the genome. Cell 137, 1194-1211 (2009).
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 11
    • 38849121606 scopus 로고    scopus 로고
    • Cohesins functionally associate with CTCF on mammalian chromosome arms
    • Parelho, V. et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422-433 (2008).
    • (2008) Cell , vol.132 , pp. 422-433
    • Parelho, V.1
  • 12
    • 39149121436 scopus 로고    scopus 로고
    • Cohesin mediates transcriptional insulation by CCCTC-binding factor
    • Wendt, K.S. et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796-801 (2008).
    • (2008) Nature , vol.451 , pp. 796-801
    • Wendt, K.S.1
  • 13
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    • Giresi, P.G., Kim, J., McDaniell, R.M., Iyer, V.R. & Lieb, J.D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17, 877-885 (2007).
    • (2007) Genome Res. , vol.17 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3    Iyer, V.R.4    Lieb, J.D.5
  • 14
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
    • (2012) Nature , vol.489 , pp. 75-82
    • Thurman, R.E.1
  • 15
    • 23044431656 scopus 로고    scopus 로고
    • Histone H3 lysine 9 methylation and HP1y are associated with transcription elongation through mammalian chromatin
    • Vakoc, C.R., Mandat, S.A., Olenchock, B.A. & Blobel, G.A. Histone H3 lysine 9 methylation and HP1y are associated with transcription elongation through mammalian chromatin. Mol. Cell 19, 381-391 (2005).
    • (2005) Mol. Cell , vol.19 , pp. 381-391
    • Vakoc, C.R.1    Mandat, S.A.2    Olenchock, B.A.3    Blobel, G.A.4
  • 16
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 17
    • 84926177361 scopus 로고    scopus 로고
    • Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
    • Ma, W. et al. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat. Methods 12, 71-78 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 71-78
    • Ma, W.1
  • 18
    • 59949085939 scopus 로고    scopus 로고
    • H3K27me3 forms BLOCs over silent genes and intergenic regions and specifes a histone banding pattern on a mouse autosomal chromosome
    • Pauler, F.M. et al. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifes a histone banding pattern on a mouse autosomal chromosome. Genome Res. 19, 221-233 (2009).
    • (2009) Genome Res. , vol.19 , pp. 221-233
    • Pauler, F.M.1
  • 19
    • 0034175837 scopus 로고    scopus 로고
    • Identifcation and characterization of human ZNF274 cDNA, which encodes a novel kruppel-type zinc-fnger protein having nucleolar targeting ability
    • Yano, K. et al. Identifcation and characterization of human ZNF274 cDNA, which encodes a novel kruppel-type zinc-fnger protein having nucleolar targeting ability. Genomics 65, 75-80 (2000).
    • (2000) Genomics , vol.65 , pp. 75-80
    • Yano, K.1
  • 20
    • 0037325402 scopus 로고    scopus 로고
    • P300/cAMP-response-element-binding-protein ('CREB')-binding protein (CBP) modulates co-operation between myocyte enhancer factor 2A (MEF2A) and thyroid hormone receptor-retinoid X receptor
    • De Luca, A. et al. p300/cAMP-response-element-binding-protein ('CREB')-binding protein (CBP) modulates co-operation between myocyte enhancer factor 2A (MEF2A) and thyroid hormone receptor-retinoid X receptor. Biochem. J. 369, 477-484 (2003).
    • (2003) Biochem. J. , vol.369 , pp. 477-484
    • De Luca, A.1
  • 21
    • 0030803279 scopus 로고    scopus 로고
    • Interaction and functional collaboration of p300 and C/EBPp
    • Mink, S., Haenig, B. & Klempnauer, K.H. Interaction and functional collaboration of p300 and C/EBPp. Mol. Cell. Biol. 17, 6609-6617 (1997).
    • (1997) Mol. Cell. Biol. , vol.17 , pp. 6609-6617
    • Mink, S.1    Haenig, B.2    Klempnauer, K.H.3
  • 22
    • 5444243359 scopus 로고    scopus 로고
    • Active genes dynamically colocalize to shared sites of ongoing transcription
    • Osborne, C.S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36, 1065-1071 (2004).
    • (2004) Nat. Genet. , vol.36 , pp. 1065-1071
    • Osborne, C.S.1
  • 23
    • 34548210885 scopus 로고    scopus 로고
    • Myc dynamically and preferentially relocates to a transcription factory occupied by Igh
    • Osborne, C.S. et al. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 5, e192 (2007).
    • (2007) PLoS Biol. , vol.5 , pp. e192
    • Osborne, C.S.1
  • 24
    • 73349090560 scopus 로고    scopus 로고
    • Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
    • Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53-61 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 53-61
    • Schoenfelder, S.1
  • 25
    • 0344012605 scopus 로고    scopus 로고
    • Nucleolar clustering of dispersed tRNA genes
    • Thompson, M., Haeusler, R.A., Good, P.D. & Engelke, D.R. Nucleolar clustering of dispersed tRNA genes. Science 302, 1399-1401 (2003).
    • (2003) Science , vol.302 , pp. 1399-1401
    • Thompson, M.1    Haeusler, R.A.2    Good, P.D.3    Engelke, D.R.4
  • 26
    • 79955415754 scopus 로고    scopus 로고
    • Multiple Wnt/p-catenin responsive enhancers align with the MYC promoter through long-range chromatin loops
    • Yochum, G.S. Multiple Wnt/p-catenin responsive enhancers align with the MYC promoter through long-range chromatin loops. PLoS ONE 6, e18966 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e18966
    • Yochum, G.S.1
  • 27
    • 84870674626 scopus 로고    scopus 로고
    • Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors
    • Sur, I.K. et al. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science 338, 1360-1363 (2012).
    • (2012) Science , vol.338 , pp. 1360-1363
    • Sur, I.K.1
  • 28
    • 84890717859 scopus 로고    scopus 로고
    • Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation
    • Shi, J. et al. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 27, 2648-2662 (2013).
    • (2013) Genes Dev. , vol.27 , pp. 2648-2662
    • Shi, J.1
  • 29
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano, M.T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
    • (2012) Science , vol.337 , pp. 1190-1195
    • Maurano, M.T.1
  • 30
    • 79959216005 scopus 로고    scopus 로고
    • Genetics and pathogenesis of infammatory bowel disease
    • Khor, B., Gardet, A. & Xavier, R.J. Genetics and pathogenesis of infammatory bowel disease. Nature 474, 307-317 (2011).
    • (2011) Nature , vol.474 , pp. 307-317
    • Khor, B.1    Gardet, A.2    Xavier, R.J.3
  • 31
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 32
    • 84883163079 scopus 로고    scopus 로고
    • Distinct functions for RIP140 in development, infammation, and metabolism
    • Nautiyal, J., Christian, M. & Parker, M.G. Distinct functions for RIP140 in development, infammation, and metabolism. Trends Endocrinol. Metab. 24, 451-459 (2013).
    • (2013) Trends Endocrinol. Metab. , vol.24 , pp. 451-459
    • Nautiyal, J.1    Christian, M.2    Parker, M.G.3
  • 33
    • 84867729539 scopus 로고    scopus 로고
    • Negative regulation of IL-17-mediated signaling and infammation by the ubiquitin-specifc protease USP25
    • Zhong, B. et al. Negative regulation of IL-17-mediated signaling and infammation by the ubiquitin-specifc protease USP25. Nat Immunol. 13, 1110-1117 (2012).
    • (2012) Nat Immunol. , vol.13 , pp. 1110-1117
    • Zhong, B.1
  • 34
    • 84890432056 scopus 로고    scopus 로고
    • Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations
    • Zhang, Y. et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504, 306-310 (2013).
    • (2013) Nature , vol.504 , pp. 306-310
    • Zhang, Y.1
  • 35
    • 84899639879 scopus 로고    scopus 로고
    • Cytokines in infammatory bowel disease
    • Neurath, M.F. Cytokines in infammatory bowel disease. Nat. Rev. Immunol. 14, 329-342 (2014).
    • (2014) Nat. Rev. Immunol. , vol.14 , pp. 329-342
    • Neurath, M.F.1
  • 36
    • 84923823453 scopus 로고    scopus 로고
    • Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
    • Dryden, N.H. et al. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res. 24, 1854-1868 (2014).
    • (2014) Genome Res. , vol.24 , pp. 1854-1868
    • Dryden, N.H.1
  • 37
    • 65749102055 scopus 로고    scopus 로고
    • Chromosome conformation capture
    • pdb prot5137
    • Cope, N.F. & Fraser, P. Chromosome conformation capture. Cold Spring Harb. Protoc. 2009, pdb prot5137 (2009).
    • (2009) Cold Spring Harb. Protoc. , vol.2009
    • Cope, N.F.1    Fraser, P.2
  • 38
    • 0001921501 scopus 로고    scopus 로고
    • (eds. Beatty, B., Mai, S. & Squire, J.) Oxford University Press
    • Solovei, I. et al. in FISH: A Practical Approach (eds. Beatty, B., Mai, S. & Squire, J.) 119-157 (Oxford University Press, 2002).
    • (2002) FISH: A Practical Approach , pp. 119-157
    • Solovei, I.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.