The three 'C' s of chromosome conformation capture: controls, controls, controls

Dekker, Job

doi:10.1038/nmeth823

Cited by 353 publications

(363 citation statements)

References 17 publications

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“…The 3C method has been described in detail (Dekker et al 2002;Splinter et al 2004;Vakoc et al 2005;Dekker 2006;Miele et al 2006) and is illustrated in Figure 1A. A 3C experiment generates a complex library of ligation products that reflects all chromatin interactions that occur throughout the genome.…”

Section: Resultsmentioning

confidence: 99%

“…As a PCR control, a library is used that contains all ligation products in equimolar amounts. The control library is generated by mixing equimolar amounts of minimally overlapping BAC clones covering the genomic region of interest (Palstra et al 2003;Dekker 2006). This mixture is then digested and randomly ligated.…”

Section: Resultsmentioning

confidence: 99%

“…In both cell lines, we find that HS5 interacts frequently with adjacent DNA fragments. These interactions likely reflect nonfunctional random collisions resulting from the intrinsic close proximity of neighboring restriction fragments (Dekker et al 2002;Dekker 2006). The frequent random interactions between adjacent genomic fragments are likely dependent on local physical properties of the chromatin fiber and limit the ability to detect specific looping interactions between elements separated by small genomic distances (2-5 kb) (Dekker 2006;Gheldof et al 2006).…”

Section: Chromatin Looping In the Human ␤-Globin Locusmentioning

confidence: 99%

“…Recent evidence indicates that regulatory elements can act over large genomic distances by engaging in direct physical interactions with their target genes or with other elements (Dekker 2003;de Laat and Grosveld 2003;Chambeyron and Bickmore 2004;West and Fraser 2005). These observations indicate that the genome may be organized as a complex three-dimensional network that is determined by physical interactions between genes and elements.…”

mentioning

confidence: 99%

“…Physical interactions between elements can be detected with the Chromosome Conformation Capture (3C) method (Dekker et al 2002;Dekker 2003;Splinter et al 2004;Miele et al 2006). 3C uses formaldehyde cross-linking to covalently trap interacting chromatin segments throughout the genome.…”

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confidence: 99%

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Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

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Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human ␤-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the ␤-globin locus. We also identified a new looping interaction in K562 cells between the ␤-globin Locus Control Region and the ␥-␦-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis-and trans-interaction networks of genomic elements and for the study of higher-order chromosome structure.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Chromatin Looping In the Human ␤-Globin Locusmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

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Chromosome Conformation Capture Carbon Copy Technology

Dostie

Dekker

2007

CP Molecular Biology

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Chromosome conformation capture (3C) is used to quantify physical DNA contacts in vivo at high resolution. 3C was first used in yeast to map the spatial chromatin organization of chromosome III, and in higher eukaryotes to demonstrate that genomic DNA elements regulate target genes by physically interacting with them. 3C has been widely adopted for small-scale analysis of functional chromatin interactions along (cis) or between (trans) chromosomes. For larger-scale applications, chromosome conformation capture carbon copy (5C) combines 3C with ligation-mediated amplification (LMA) to simultaneously quantify hundreds of thousands of physical DNA contacts by microarray or ultra-high-throughput DNA sequencing. 5C allows the mapping of extensive networks of physical interactions among large sets of genomic elements throughout the genome. Such networks can provide important biological insights, e.g., by identifying relationships between regulatory elements and their target genes. This unit describes 5C for large-scale analysis of cis- and trans-chromatin interactions in mammalian cells.

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Chromatin Interaction Analysis Using Paired‐End Tag Sequencing

Fullwood

Han

Wei

et al. 2010

CP Molecular Biology

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Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) is a technique developed for large-scale, de novo analysis of higher-order chromatin structures. Cells are treated with formaldehyde to cross-link chromatin interactions, DNA segments bound by protein factors are enriched by chromatin immunoprecipitation, and interacting DNA fragments are then captured by proximity ligation. The Paired-End Tag (PET) strategy is applied to the construction of ChIA-PET libraries, which are sequenced by high-throughput next-generation sequencing technologies. Finally, raw PET sequences are subjected to bioinformatics analysis, resulting in a genome-wide map of binding sites and chromatin interactions mediated by the protein factor under study. This unit describes ChIA-PET for genome-wide analysis of chromatin interactions in mammalian cells, with the application of Roche/454 and Illumina sequencing technologies.

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The three 'C' s of chromosome conformation capture: controls, controls, controls

Cited by 353 publications

References 17 publications

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Chromosome Conformation Capture Carbon Copy Technology

Chromatin Interaction Analysis Using Paired‐End Tag Sequencing

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