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

By J. Dostie, Todd A. Richmond, Ramy Arnaout, R. Selzer, William L Lee, T. Honan, Eric D. Rubio, A. Krumm, J. Lamb, Chad Nusbaum and 2 more. Genome Research, 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 beta-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the beta-globin locus. We also identified a new looping interaction in K562 cells between the beta-globin Locus Control Region and the gamma-beta-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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3b2bba757890bc640c7ec547fff70cb42ccd90c4

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Citations in the corpus

A decade of 3C technologies: insights into nuclear organization. (2012, methodology): “It allows concurrent determination of interactions between multiple sequences (Dostie et al. 2006).”
Functional and mechanistic diversity of distal transcription enhancers (2011, neutral): “, 2006) or even associations among multiple sequences located throughout the genome (‘‘5C’’ and ‘‘Hi-C’’) (Dostie et al., 2006; Lieberman-Aiden et al., 2009).”
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data (2013, background): “5C combines 3C with hybrid capture approaches to identify up to millions of interactions in parallel between two large sets of loci: for example, between a set of promoters and a set of distal regulatory elements 46,107,108 .”
A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping (2014, neutral): “A 3DMap of the Human Genome at Kilobase Resolution Reveals”
A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome (2016, neutral): “…techniques have begun to reveal molecular details of nuclear organization in eukaryotic cells (Dekker et al., 2002; Dixon et al., 2012, 2015; Dostie et al., 2006; Fraser et al., 2015; Jin et al., 2013; Lieberman-Aiden et al., 2009; Rao et al., 2014; Seitan et al., 2013; Simonis et al.,…”
ENCODE whole-genome data in the UCSC Genome Browser: update 2012 (2011, methodology): “New types of data available provided by UCSC this year include chromatin interaction maps by 5C (10) and ChIA-PET (11), nucleosome positioning by Mnase-seq , deep-sequenced DNAseI hypersensitive sites, SNP data for cell lines assayed for copy number variation, and three additional assays of RNA-bind”
Highly Specific Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements (2015, neutral): “The DNase I hypersensitivity profiles of enhancers correlate with associated promoters 22 , and chromatin conformation analyses have shown that the globin LCR physically interacts with HBG1, HBG2, and HBE1 in K562 cells 38 .”
The long-range interaction landscape of gene promoters (2012, background): “We previously found that this TSS located just downstream of the c -globin genes displayed prominent looping interactions with the distal locus control region (LCR) in K562 cells 2 .”