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Capturing Chromosome Conformation
2020The genome is organized in 3D topology-associated domains to ensure proper gene transcriptional processes. The chromosome conformation capture (3C) is an affordable method to investigate local chromatin structure and dynamics in cells and tissue. Herein I describe an easy to design and a cost-effective protocol.
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Quantitative Chromosome Conformation Capture
2012It is becoming increasingly apparent that chromatin is not randomly folded into the nucleus, but instead is highly organized into specific conformations within the nucleus. One consequence of such higher order structure is that chromatin looping can bring together genomic elements which are separated by several hundreds of kilobases, such as enhancers ...
Raffaella, Nativio +2 more
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Chromosome Conformation Capture Carbon Copy Technology
Current Protocols in Molecular Biology, 2007AbstractChromosome 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
Dostie, Josee, Zhan, Ye, Dekker, Job
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Randomized Ligation Control for Chromosome Conformation Capture
Cold Spring Harbor Protocols, 2015In experiments using chromosome conformation capture followed by PCR (3C-PCR) or chromosome conformation capture carbon copy (5C), it is critical to control for intrinsic biases in the restriction fragments of interest and the probes or primers used for detection. Characteristics such as GC%, annealing temperature, efficiency of 3C primers or 5C probes,
Belton, Jon-Matthew, Dekker, Job
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Chromosome Conformation Capture in Drosophila
2016Linear chromatin fiber is packed inside the nuclei as a complex three-dimensional structure, and the organization of the chromatin has important roles in the appropriate spatial and temporal regulation of gene expression. To understand how chromatin organizes inside nuclei, and how regulatory proteins physically interact with genes, chromosome ...
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Mapping Chromatin Interactions by Chromosome Conformation Capture
Current Protocols in Molecular Biology, 2006AbstractChromosome conformation capture (3C) is one of the only techniques that allows for analysis of an intermediate level of chromosome structure ranging from a few to hundreds of kilobases, a level most relevant for gene regulation. The 3C technique is used to detect physical interactions between sequence elements that are located on the same or on
Miele, Adriana +4 more
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Chromosome conformation capture assays in bacteria
Methods, 2012Bacterial chromosomes must be compacted by three-orders of magnitude to fit within the cell. While such compaction could in theory yield disordered structures, it is becoming increasingly clear that bacterial chromosomes are in fact arranged in regular and reproducible fashions and that their configurations are tightly connected to fundamental ...
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Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
Nature, 2016Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-
Pedro Olivares-Chauvet +8 more
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High-resolution circular chromosome conformation capture assay
Nature Protocols, 2008The pioneering chromosome conformation capture (3C) method provides the opportunity to study chromosomal folding in the nucleus. It is based on formaldehyde cross-linking of living cells followed by enzyme digestion, intramolecular ligation and quantitative (Q)-PCR analysis.
Anita, Göndör +2 more
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Circular Chromosome Conformation Capture in Plants
2017The study of nuclear architecture promises novel insights into genome function and regulation. Hereby, quantitative methods based on chromosome conformation capture (3C) revolutionized the field, as they allow accurate and unbiased characterization of 3D genome organization of genomic regions of interest.
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