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Volumn 13, Issue 8, 2016, Pages 685-691

UMI-4C for quantitative and targeted chromosomal contact profiling

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; TRANSCRIPTION FACTOR GATA 1; CHROMATIN; HEMOGLOBIN BETA CHAIN;

EID: 84976871478     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3922     Document Type: Article
Times cited : (66)

References (40)
  • 1
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. Capturing chromosome conformation. Science 295, 1306-1311 (2002
    • (2002) Science , vol.295 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 2
    • 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
  • 3
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • Roadmap Epigenomics Consortium., et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015
    • (2015) Nature , vol.518 , pp. 317-330
  • 4
    • 84865708757 scopus 로고    scopus 로고
    • An expansive human regulatory lexicon encoded in transcription factor footprints
    • Neph, S., et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012
    • (2012) Nature , vol.489 , pp. 83-90
    • Neph, S.1
  • 5
    • 84865790047 scopus 로고    scopus 로고
    • An Integrated Encyclopedia of DNA Elements in the Human Genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012
    • (2012) Nature , vol.489 , pp. 57-74
  • 6
    • 79955569948 scopus 로고    scopus 로고
    • Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements
    • Hakim, O., et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21, 697-706 (2011
    • (2011) Genome Res , vol.21 , pp. 697-706
    • Hakim, O.1
  • 7
    • 84887852466 scopus 로고    scopus 로고
    • Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming
    • Apostolou, E., et al. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 12, 699-712 (2013
    • (2013) Cell Stem Cell , vol.12 , pp. 699-712
    • Apostolou, E.1
  • 8
    • 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
  • 9
    • 84861100147 scopus 로고    scopus 로고
    • Spatial partitioning of the regulatory landscape of the X-inactivation centre
    • Nora, E.P., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381-385 (2012
    • (2012) Nature , vol.485 , pp. 381-385
    • Nora, E.P.1
  • 10
    • 79959952919 scopus 로고    scopus 로고
    • The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA
    • Splinter, E., et al. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev. 25, 1371-1383 (2011
    • (2011) Genes Dev , vol.25 , pp. 1371-1383
    • Splinter, E.1
  • 11
    • 84923366733 scopus 로고    scopus 로고
    • Chromatin architecture reorganization during stem cell differentiation
    • Dixon, J.R., et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331-336 (2015
    • (2015) Nature , vol.518 , pp. 331-336
    • Dixon, J.R.1
  • 12
    • 84884134904 scopus 로고    scopus 로고
    • The pluripotent genome in three dimensions is shaped around pluripotency factors
    • De Wit, E., et al. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 501, 227-231 (2013
    • (2013) Nature , vol.501 , pp. 227-231
    • De Wit, E.1
  • 13
    • 84855297335 scopus 로고    scopus 로고
    • A decade of 3C technologies: Insights into nuclear organization
    • De Wit, E., & De Laat, W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11-24 (2012
    • (2012) Genes Dev , vol.26 , pp. 11-24
    • De Wit, E.1    De Laat, W.2
  • 14
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C
    • Simonis, M., et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348-1354 (2006
    • (2006) Nat. Genet , vol.38 , pp. 1348-1354
    • Simonis, M.1
  • 15
    • 84867003195 scopus 로고    scopus 로고
    • Robust 4C-seq data analysis to screen for regulatory DNA interactions
    • Van De Werken, H.J.G., et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods 9, 969-972 (2012
    • (2012) Nat. Methods , vol.9 , pp. 969-972
    • Van De Werken, H.J.G.1
  • 16
    • 84875143934 scopus 로고    scopus 로고
    • Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions
    • Stadhouders, R., et al. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nat. Protoc. 8, 509-524 (2013
    • (2013) Nat. Protoc , vol.8 , pp. 509-524
    • Stadhouders, R.1
  • 17
    • 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.G., Klous, P., & De Laat, W. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods 58, 221-230 (2012
    • (2012) Methods , vol.58 , pp. 221-230
    • Splinter, E.1    De Wit, E.2    Van De Werken, H.J.G.3    Klous, P.4    De Laat, W.5
  • 18
    • 84923378921 scopus 로고    scopus 로고
    • Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
    • Jäger, R., et al. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat. Commun. 6, 6178 (2015
    • (2015) Nat. Commun , vol.6 , pp. 6178
    • Jäger, R.1
  • 19
    • 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
  • 20
    • 84930092058 scopus 로고    scopus 로고
    • Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
    • Mifsud, B., et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598-606 (2015
    • (2015) Nat. Genet , vol.47 , pp. 598-606
    • Mifsud, B.1
  • 21
    • 84904412804 scopus 로고    scopus 로고
    • Targeted Chromatin Capture (T2C): A novel high resolution high throughput method to detect genomic interactions and regulatory elements
    • Kolovos, P., et al. Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin 7, 10 (2014
    • (2014) Epigenetics Chromatin , vol.7 , pp. 10
    • Kolovos, P.1
  • 22
    • 84955668492 scopus 로고    scopus 로고
    • Multiplexed analysis of chromosome conformation at vastly improved sensitivity
    • Davies, J.O.J., et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat. Methods 13, 74-80 (2016
    • (2016) Nat. Methods , vol.13 , pp. 74-80
    • Davies, J.O.J.1
  • 23
    • 84940034154 scopus 로고    scopus 로고
    • Genome-wide mapping of promoter-Anchored interactions with close to single-enhancer resolution
    • Sahlén, P., et al. Genome-wide mapping of promoter-Anchored interactions with close to single-enhancer resolution. Genome Biol. 16, 156 (2015
    • (2015) Genome Biol , vol.16 , pp. 156
    • Sahlén, P.1
  • 24
    • 84948403758 scopus 로고    scopus 로고
    • Chromatin extrusion explains key features of loop and domain formation in wild-Type and engineered genomes
    • Sanborn, A.L., et al. Chromatin extrusion explains key features of loop and domain formation in wild-Type and engineered genomes. Proc. Natl. Acad. Sci. USA 112, E6456-E6465 (2015
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , pp. E6456-E6465
    • Sanborn, A.L.1
  • 25
    • 84905593782 scopus 로고    scopus 로고
    • Enhancer loops appear stable during development and are associated with paused polymerase
    • Ghavi-Helm, Y., et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96-100 (2014
    • (2014) Nature , vol.512 , pp. 96-100
    • Ghavi-Helm, Y.1
  • 26
    • 80054984337 scopus 로고    scopus 로고
    • Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
    • Yaffe, E., & Tanay, A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet. 43, 1059-1065 (2011
    • (2011) Nat. Genet , vol.43 , pp. 1059-1065
    • Yaffe, E.1    Tanay, A.2
  • 27
    • 84901838628 scopus 로고    scopus 로고
    • Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
    • Ay, F., Bailey, T.L., & Noble, W.S. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999-1011 (2014
    • (2014) Genome Res , vol.24 , pp. 999-1011
    • Ay, F.1    Bailey, T.L.2    Noble, W.S.3
  • 28
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R., et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380 (2012
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1
  • 29
    • 84870463249 scopus 로고    scopus 로고
    • HiCNorm: Removing biases in Hi-C data via Poisson regression
    • Hu, M., et al. HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics 28, 3131-3133 (2012
    • (2012) Bioinformatics , vol.28 , pp. 3131-3133
    • Hu, M.1
  • 30
    • 84856484968 scopus 로고    scopus 로고
    • Counting absolute numbers of molecules using unique molecular identifiers
    • Kivioja, T., et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72-74 (2012
    • (2012) Nat. Methods , vol.9 , pp. 72-74
    • Kivioja, T.1
  • 31
    • 78651514974 scopus 로고    scopus 로고
    • Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
    • Bantignies, F., et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214-226 (2011
    • (2011) Cell , vol.144 , pp. 214-226
    • Bantignies, F.1
  • 32
    • 84919949716 scopus 로고    scopus 로고
    • A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
    • Rao, S.S.P., et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014
    • (2014) Cell , vol.159 , pp. 1665-1680
    • Rao, S.S.P.1
  • 33
    • 8644275646 scopus 로고    scopus 로고
    • Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: Implications for cis-element identification
    • Valverde-Garduno, V., et al. Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: implications for cis-element identification. Blood 104, 3106-3116 (2004
    • (2004) Blood , vol.104 , pp. 3106-3116
    • Valverde-Garduno, V.1
  • 34
    • 84867736794 scopus 로고    scopus 로고
    • Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis
    • Xu, J., et al. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev. Cell 23, 796-811 (2012
    • (2012) Dev. Cell , vol.23 , pp. 796-811
    • Xu, J.1
  • 35
    • 84861070995 scopus 로고    scopus 로고
    • Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia
    • Porcu, M., et al. Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia. Blood 119, 4476-4479 (2012
    • (2012) Blood , vol.119 , pp. 4476-4479
    • Porcu, M.1
  • 36
    • 84862245279 scopus 로고    scopus 로고
    • Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
    • Ye, J., et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012
    • (2012) BMC Bioinformatics , vol.13 , pp. 134
    • Ye, J.1
  • 37
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 38
    • 84856747483 scopus 로고    scopus 로고
    • Three-dimensional folding and functional organization principles of the Drosophila genome
    • Sexton, T., et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472 (2012
    • (2012) Cell , vol.148 , pp. 458-472
    • Sexton, T.1
  • 39
    • 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
  • 40
    • 84859169877 scopus 로고    scopus 로고
    • The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
    • Barretina, J., et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012
    • (2012) Nature , vol.483 , pp. 603-607
    • Barretina, J.1


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