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Volumn 7, Issue 1, 2014, Pages

Targeted Chromatin Capture (T2C): A novel high resolution high throughput method to detect genomic interactions and regulatory elements

Author keywords

Chromatin conformation capture; Enhancers; Long range interactions; Promoters

Indexed keywords


EID: 84904412804     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-7-10     Document Type: Article
Times cited : (67)

References (53)
  • 1
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • 10.1038/nature11082 22495300
    • 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, Nature 2012 485 376 380 10.1038/nature11082 22495300
    • (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
  • 2
    • 0035316574 scopus 로고    scopus 로고
    • Chromosome territories, nuclear architecture and gene regulation in mammalian cells
    • DOI 10.1038/35066075
    • Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Cremer T, Cremer C, Nat Rev Genet 2001 2 292 301 10.1038/35066075 11283701 (Pubitemid 33674777)
    • (2001) Nature Reviews Genetics , vol.2 , Issue.4 , pp. 292-301
    • Cremer, T.1    Cremer, C.2
  • 3
    • 0031306463 scopus 로고    scopus 로고
    • The effect of distance on long-range chromatin interactions
    • The effect of distance on long-range chromatin interactions. Dillon N, Trimborn T, Strouboulis J, Fraser P, Grosveld F, Mol Cell 1997 1 131 139 10.1016/S1097-2765(00)80014-3 9659910 (Pubitemid 127376400)
    • (1997) Molecular Cell , vol.1 , Issue.1 , pp. 131-139
    • Dillon, N.1    Trimbom, T.2    Strouboulis, J.3    Fraser, P.4    Grosveld, F.5
  • 4
    • 0024334963 scopus 로고
    • An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge
    • DOI 10.1016/0092-8674(89)90110-4
    • An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge. Mueller-Storm HP, Sogo JM, Schaffner W, Cell 1989 58 767 777 10.1016/0092-8674(89)90110-4 2548735 (Pubitemid 19210968)
    • (1989) Cell , vol.58 , Issue.4 , pp. 767-777
    • Muller, H.-P.1    Sogo, J.M.2    Schaffner, W.3
  • 5
    • 41949121201 scopus 로고    scopus 로고
    • The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions
    • DOI 10.1016/j.cell.2008.03.024, PII S0092867408004406
    • The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Jhunjhunwala S, van Zelm MC, Peak MM, Cutchin S, Riblet R, van Dongen JJ, Grosveld FG, Knoch TA, Murre C, Cell 2008 133 265 279 10.1016/j.cell.2008.03.024 18423198 (Pubitemid 351512300)
    • (2008) Cell , vol.133 , Issue.2 , pp. 265-279
    • Jhunjhunwala, S.1    Van Zelm, M.C.2    Peak, M.M.3    Cutchin, S.4    Riblet, R.5    Van Dongen, J.J.M.6    Grosveld, F.G.7    Knoch, T.A.8    Murre, C.9
  • 7
    • 79551655285 scopus 로고    scopus 로고
    • Functional and mechanistic diversity of distal transcription enhancers
    • 10.1016/j.cell.2011.01.024 21295696
    • Functional and mechanistic diversity of distal transcription enhancers. Bulger M, Groudine M, Cell 2011 144 327 339 10.1016/j.cell.2011.01.024 21295696
    • (2011) Cell , vol.144 , pp. 327-339
    • Bulger, M.1    Groudine, M.2
  • 8
    • 79953162491 scopus 로고    scopus 로고
    • Gene expression in time and space: Additive vs hierarchical organization of cis-regulatory regions
    • 10.1016/j.gde.2011.01.021 21349696
    • Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions. Maeda RK, Karch F, Curr Opin Genet Dev 2011 21 187 193 10.1016/j.gde.2011.01.021 21349696
    • (2011) Curr Opin Genet Dev , vol.21 , pp. 187-193
    • Maeda, R.K.1    Karch, F.2
  • 9
    • 84855508402 scopus 로고    scopus 로고
    • Enhancers and silencers: An integrated and simple model for their function
    • 10.1186/1756-8935-5-1 22230046
    • Enhancers and silencers: an integrated and simple model for their function. Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A, Epigenetics Chromatin 2012 5 1 10.1186/1756-8935-5-1 22230046
    • (2012) Epigenetics Chromatin , vol.5 , pp. 1
    • Kolovos, P.1    Knoch, T.A.2    Grosveld, F.G.3    Cook, P.R.4    Papantonis, A.5
  • 10
    • 12344299320 scopus 로고    scopus 로고
    • Single base pair change in the long-range Sonic hedgehog limb-specific enhancer is a genetic basis for preaxial polydactyly
    • DOI 10.1002/dvdy.20254
    • Single base pair change in the long-range Sonic hedgehog limb-specific enhancer is a genetic basis for preaxial polydactyly. Maas SA, Fallon JF, Dev Dyn 2005 232 345 348 10.1002/dvdy.20254 15637698 (Pubitemid 40129787)
    • (2005) Developmental Dynamics , vol.232 , Issue.2 , pp. 345-348
    • Maas, S.A.1    Fallon, J.F.2
  • 11
    • 84877807425 scopus 로고    scopus 로고
    • Nuclear location and the control of developmental progression
    • 10.1016/j.gde.2012.11.010 23266214
    • Nuclear location and the control of developmental progression. Lin YC, Murre C, Curr Opin Genet Dev 2013 23 104 108 10.1016/j.gde.2012.11.010 23266214
    • (2013) Curr Opin Genet Dev , vol.23 , pp. 104-108
    • Lin, Y.C.1    Murre, C.2
  • 13
    • 33748259774 scopus 로고    scopus 로고
    • CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus
    • DOI 10.1101/gad.399506
    • CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Splinter E, Heath H, Kooren J, Palstra RJ, Klous P, Grosveld F, Galjart N, de Laat W, Genes Dev 2006 20 2349 2354 10.1101/gad.399506 16951251 (Pubitemid 44320383)
    • (2006) Genes and Development , vol.20 , Issue.17 , 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
  • 15
    • 84861964135 scopus 로고    scopus 로고
    • Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor
    • 10.1016/j.cell.2012.03.051 22682246
    • 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, Cell 2012 149 1233 1244 10.1016/j.cell.2012.03.051 22682246
    • (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
  • 16
    • 5444255213 scopus 로고    scopus 로고
    • The active spatial organization of the β-globin locus requires the transcription factor EKLF
    • DOI 10.1101/gad.317004
    • The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Drissen R, Palstra RJ, Gillemans N, Splinter E, Grosveld F, Philipsen S, de Laat W, Genes Dev 2004 18 2485 2490 10.1101/gad.317004 15489291 (Pubitemid 39362891)
    • (2004) Genes and Development , vol.18 , Issue.20 , pp. 2485-2490
    • Drissen, R.1    Palstra, R.-J.2    Gillemans, N.3    Splinter, E.4    Grosveld, F.5    Philipsen, S.6    De Laat, W.7
  • 17
    • 77649261872 scopus 로고    scopus 로고
    • Cell type specificity of chromatin organization mediated by CTCF and cohesin
    • 10.1073/pnas.0912087107 20133600
    • Cell type specificity of chromatin organization mediated by CTCF and cohesin. Hou C, Dale R, Dean A, Proc Natl Acad Sci U S A 2010 107 3651 3656 10.1073/pnas.0912087107 20133600
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 3651-3656
    • Hou, C.1    Dale, R.2    Dean, A.3
  • 18
    • 84869502375 scopus 로고    scopus 로고
    • Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate
    • 10.1038/ni.2432 23064439
    • Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Lin YC, Benner C, Mansson R, Heinz S, Miyazaki K, Miyazaki M, Chandra V, Bossen C, Glass CK, Murre C, Nat Immunol 2012 13 1196 1204 10.1038/ni.2432 23064439
    • (2012) Nat Immunol , vol.13 , pp. 1196-1204
    • Lin, Y.C.1    Benner, C.2    Mansson, R.3    Heinz, S.4    Miyazaki, K.5    Miyazaki, M.6    Chandra, V.7    Bossen, C.8    Glass, C.K.9    Murre, C.10
  • 19
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • DOI 10.1126/science.1067799
    • Capturing chromosome conformation. Dekker J, Rippe K, Dekker M, Kleckner N, Science 2002 295 1306 1311 10.1126/science.1067799 11847345 (Pubitemid 34157624)
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 20
    • 0036923833 scopus 로고    scopus 로고
    • Looping and interaction between hypersensitive sites in the active β-globin locus
    • DOI 10.1016/S1097-2765(02)00781-5
    • Looping and interaction between hypersensitive sites in the active beta-globin locus. Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W, Mol Cell 2002 10 1453 1465 10.1016/S1097-2765(02)00781-5 12504019 (Pubitemid 36050885)
    • (2002) Molecular Cell , vol.10 , Issue.6 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.-J.2    Splinter, E.3    Grosveld, F.4    De Laat, W.5
  • 21
    • 34548565667 scopus 로고    scopus 로고
    • Quantitative analysis of chromosome conformation capture assays (3C-qPCR)
    • 10.1038/nprot.2007.243 17641637
    • Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Hagege H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forne T, Nat Protoc 2007 2 1722 1733 10.1038/nprot.2007.243 17641637
    • (2007) Nat Protoc , vol.2 , pp. 1722-1733
    • Hagege, H.1    Klous, P.2    Braem, C.3    Splinter, E.4    Dekker, J.5    Cathala, G.6    De Laat, W.7    Forne, T.8
  • 22
    • 84870344301 scopus 로고    scopus 로고
    • Analysis of long-range chromatin interactions using Chromosome Conformation Capture
    • 10.1016/j.ymeth.2012.07.022 22903059
    • Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Naumova N, Smith EM, Zhan Y, Dekker J, Methods 2012 58 192 203 10.1016/j.ymeth.2012.07.022 22903059
    • (2012) Methods , vol.58 , pp. 192-203
    • Naumova, N.1    Smith, E.M.2    Zhan, Y.3    Dekker, J.4
  • 25
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    • DOI 10.1038/ng1896, PII NG1896
    • 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, Nat Genet 2006 38 1348 1354 10.1038/ng1896 17033623 (Pubitemid 44646300)
    • (2006) Nature Genetics , vol.38 , Issue.11 , 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
  • 26
    • 84866786102 scopus 로고    scopus 로고
    • Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip
    • 10.1038/nprot.2012.071 22722369
    • Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip. Sexton T, Kurukuti S, Mitchell JA, Umlauf D, Nagano T, Fraser P, Nat Protoc 2012 7 1335 1350 10.1038/nprot.2012.071 22722369
    • (2012) Nat Protoc , vol.7 , pp. 1335-1350
    • Sexton, T.1    Kurukuti, S.2    Mitchell, J.A.3    Umlauf, D.4    Nagano, T.5    Fraser, P.6
  • 27
    • 39449139894 scopus 로고    scopus 로고
    • High-resolution circular chromosome conformation capture assay
    • DOI 10.1038/nprot.2007.540, PII NPROT.2007.540
    • High-resolution circular chromosome conformation capture assay. Gondor A, Rougier C, Ohlsson R, Nat Protoc 2008 3 303 313 10.1038/nprot.2007.540 18274532 (Pubitemid 351266514)
    • (2008) Nature Protocols , vol.3 , Issue.2 , pp. 303-313
    • Gondor, A.1    Rougier, C.2    Ohlsson, R.3
  • 29
    • 34248524473 scopus 로고    scopus 로고
    • Mapping networks of physical interactions between genomic elements using 5C technology
    • DOI 10.1038/nprot.2007.116, PII NPROT.2007.116
    • Mapping networks of physical interactions between genomic elements using 5C technology. Dostie J, Dekker J, Nat Protoc 2007 2 988 1002 10.1038/nprot.2007.116 17446898 (Pubitemid 46745595)
    • (2007) Nature Protocols , vol.2 , Issue.4 , pp. 988-1002
    • Dostie, J.1    Dekker, J.2
  • 34
    • 84870806502 scopus 로고    scopus 로고
    • Super-resolution imaging reveals three-dimensional folding dynamics of the beta-globin locus upon gene activation
    • 10.1242/jcs.108522 22767512
    • Super-resolution imaging reveals three-dimensional folding dynamics of the beta-globin locus upon gene activation. van de Corput MP, de Boer E, Knoch TA, van Cappellen WA, Quintanilla A, Ferrand L, Grosveld FG, J Cell Sci 2012 125 4630 4639 10.1242/jcs.108522 22767512
    • (2012) J Cell Sci , vol.125 , pp. 4630-4639
    • Van De Corput, M.P.1    De Boer, E.2    Knoch, T.A.3    Van Cappellen, W.A.4    Quintanilla, A.5    Ferrand, L.6    Grosveld, F.G.7
  • 35
    • 0141730403 scopus 로고    scopus 로고
    • The β-globin nuclear compartment in development and erythroid differentiation
    • DOI 10.1038/ng1244
    • The beta-globin nuclear compartment in development and erythroid differentiation. Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W, Nat Genet 2003 35 190 194 10.1038/ng1244 14517543 (Pubitemid 37187640)
    • (2003) Nature Genetics , vol.35 , Issue.2 , pp. 190-194
    • Palstra, R.-J.1    Tolhuis, B.2    Splinter, E.3    Nijmeijer, R.4    Grosveld, F.5    De Laat, W.6
  • 36
    • 36749056884 scopus 로고    scopus 로고
    • A Positive Role for NLI/Ldb1 in Long-Range β-Globin Locus Control Region Function
    • DOI 10.1016/j.molcel.2007.09.025, PII S1097276507006375
    • A positive role for NLI/Ldb1 in long-range beta-globin locus control region function. Song SH, Hou C, Dean A, Mol Cell 2007 28 810 822 10.1016/j.molcel.2007.09.025 18082606 (Pubitemid 350217055)
    • (2007) Molecular Cell , vol.28 , Issue.5 , pp. 810-822
    • Song, S.-H.1    Hou, C.2    Dean, A.3
  • 37
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • 10.1038/nature11247 22955616
    • An integrated encyclopedia of DNA elements in the human genome. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, ENCODE Project Consortium, Nature 2012 489 57 74 10.1038/nature11247 22955616
    • (2012) Nature , vol.489 , pp. 57-74
  • 39
    • 34249307315 scopus 로고    scopus 로고
    • Nuclear organization of the genome and the potential for gene regulation
    • DOI 10.1038/nature05916, PII NATURE05916
    • Nuclear organization of the genome and the potential for gene regulation. Fraser P, Bickmore W, Nature 2007 447 413 417 10.1038/nature05916 17522674 (Pubitemid 46816747)
    • (2007) Nature , vol.447 , Issue.7143 , pp. 413-417
    • Fraser, P.1    Bickmore, W.2
  • 40
    • 33847077659 scopus 로고    scopus 로고
    • Beyond the Sequence: Cellular Organization of Genome Function
    • DOI 10.1016/j.cell.2007.01.028, PII S0092867407001262
    • Beyond the sequence: cellular organization of genome function. Misteli T, Cell 2007 128 787 800 10.1016/j.cell.2007.01.028 17320514 (Pubitemid 46273571)
    • (2007) Cell , vol.128 , Issue.4 , pp. 787-800
    • Misteli, T.1
  • 43
    • 78649441087 scopus 로고    scopus 로고
    • A requirement for Lim domain binding protein 1 in erythropoiesis
    • 10.1084/jem.20100504 21041453
    • A requirement for Lim domain binding protein 1 in erythropoiesis. Li L, Lee JY, Gross J, Song SH, Dean A, Love PE, J Exp Med 2010 207 2543 2550 10.1084/jem.20100504 21041453
    • (2010) J Exp Med , vol.207 , pp. 2543-2550
    • Li, L.1    Lee, J.Y.2    Gross, J.3    Song, S.H.4    Dean, A.5    Love, P.E.6
  • 45
    • 84879447932 scopus 로고    scopus 로고
    • Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis
    • 10.1182/blood-2012-11-467654 23390196
    • Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis. Mylona A, Andrieu-Soler C, Thongjuea S, Martella A, Soler E, Jorna R, Hou J, Kockx C, van Ijcken W, Lenhard B, Grosveld F, Blood 2013 121 2902 2913 10.1182/blood-2012-11-467654 23390196
    • (2013) Blood , vol.121 , pp. 2902-2913
    • Mylona, A.1    Andrieu-Soler, C.2    Thongjuea, S.3    Martella, A.4    Soler, E.5    Jorna, R.6    Hou, J.7    Kockx, C.8    Van Ijcken, W.9    Lenhard, B.10    Grosveld, F.11
  • 47
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • [Epub ahead of print]
    • Trimmomatic: a flexible trimmer for Illumina sequence data. Bolger AM, Lohse M, Usadel B, Bioinformatics 2014 [Epub ahead of print]
    • (2014) Bioinformatics
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 48
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • 10.1093/bioinformatics/btp324 19451168
    • Fast and accurate short read alignment with Burrows-Wheeler transform. Li H, Durbin R, Bioinformatics 2009 25 1754 1760 10.1093/bioinformatics/btp324 19451168
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 49
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033 20110278
    • BEDTools: a flexible suite of utilities for comparing genomic features. Quinlan AR, Hall IM, Bioinformatics 2010 26 841 842 10.1093/bioinformatics/ btq033 20110278
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 52
    • 84863304598 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for Statistical Computing
    • R-Core-Team, R: A language and environment for statistical computing Vienna, Austria: R Foundation for Statistical Computing 2013 [ http://www.r-project.org/ ]
    • (2013) R: A Language and Environment for Statistical Computing


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