Microfluidics-Based Chromosome Conformation Capture (3C) Technology for Examining Chromatin Organization with a Low Quantity of Cells [PDF]
Analytical Chemistry, 2018 Detecting three-dimensional (3D) genome organization in the form of physical interactions between various genomic loci is of great importance for understanding transcriptional regulations and cellular fate. Chromosome Conformation Capture (3C) method is the gold standard for examining chromatin organization, but usually requires a large number of cells
Chen Sun, Chang Lu
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Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells [PDF]
Bio-Protocol, 2017 Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells.
A. Marieke Oudelaar +3 more
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Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C) [PDF]
Nature Protocols, 2009 Gene regulation in higher eukaryotes frequently involves physical interactions between genomic sequence elements tens of kilobases apart on the same chromosome but can also entail interactions between different chromosomes. Chromosome Conformation Capture (3C) is a powerful tool to identify such interactions.
Louwers, M. +4 more
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HAT: Hypergraph analysis toolbox. [PDF]
PLoS Computational Biology, 2023 Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions.
Joshua Pickard +7 more
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Analysis of β-globin chromatin micro-environment using a novel 3C variant, 4Cv. [PDF]
PLoS ONE, 2010 Higher order chromatin folding is critical to a number of developmental processes, including the regulation of gene expression. Recently developed biochemical techniques such as RNA TRAP and chromosome conformation capture (3C) have provided us with the ...
Ryan C Pink +4 more
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Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data
Trends in Genetics, 2015 Microbial communities are complex and constitute important parts of our environment. Genomic analysis of these populations is a dynamic research area but remains limited by the difficulty in assembling full genomes of individual species. Recently, a new method for metagenome assembly/analysis based on chromosome conformation capture has emerged (meta3C)
Marbouty, Martial, Koszul, Romain
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Dual native G-quadruplex folding is associated with chromatin looping at the MYC locus. [PDF]
FEBS Open BioBG4‐detectable G‐quadruplex (G4) in HaCaT and NHEK keratinocytes identified folded and unfolded G4s enriched at promoters/TSSs and active enhancers, whereas unfolded G4s also overlapped weak/poised enhancers. At MYC–PVT1, 3C‐qPCR detected enhancer–promoter looping only when G4s were simultaneously folded at both regulatory elements under native ...
de Lima DG +7 more
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Mapping Cis- and Trans- Chromatin Interaction Networks Using Chromosome Conformation Capture (3C) [PDF]
Methods Mol Biol, 2008 Expression of genes can be controlled by regulatory elements that are located at large genomic distances from their target genes (in cis), or even on different chromosomes (in trans). Regulatory elements can act at large genomic distances by engaging in direct physical interactions with their target genes resulting in the formation of chromatin loops ...
Miele, Adriana, Dekker, Job
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Orchestrating chromosome conformation capture analysis with Bioconductor [PDF]
Nature CommunicationsGenome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging.
Jacques Serizay +4 more
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5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design [PDF]
Methods, 2018 Abstract Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations.
Kim, Ji Hun +5 more
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