Capturing Chromosome Conformation

By Job Dekker, K. Rippe, M. Dekker, N. Kleckner. Science, 2002

3,604 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/0dade66448a513114b43319a0dee5a2ebb50869d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Plant Science

Citations in the corpus

The long-range interaction landscape of gene promoters (2012, background): “Spatial proximity and specific long-range interactions between genomic elements can be detected using chromosome conformation capture (3C)-based methods 5 .”
The role of mutations in epigenetic regulators in myeloid malignancies (2012, background): “Gene expression at a particular locus is affected by a number of spatial and temporal complexes, and is highly influenced by the threedimensional nature of chromatin (141).”
CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus (2006, positive): “Previously, we applied chromosome conformation capture (3C) technology (Dekker et al. 2002) to study long-range DNA interactions between these and other sites in the -globin locus.”
Pre-mRNA processing reaches back to transcription and ahead to translation. (2009, neutral): “In this case, a loop structure is predicted to occur in which the promoter and terminator of a gene are in close proximity (Ansari and Hampsey, 2005; O'Sullivan et al., 2004), as detected by the chromatin ligation technique called 3C (Dekker et al., 2002).”
Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops (2004, methodology): “We then validated our observations independently using the chromosome conformation capture (3C) assa”
The physics of epigenetics (2015, background): “In the last two decades, impressive advances in experimental techniques in measurements of 3D chromosomal contacts have been made, starting from the “chromosome conformation capture” approach (Dekker et al., 2002).”
Architectural protein subclasses shape 3D organization of genomes during lineage commitment. (2013, neutral): “…molecular methods based on proximity ligation, such as chromosome conformation capture (3C) or circularized-3C (4C), have been used to detect functional long-range interactions between two specific genomic loci in a population of cells (Dekker et al., 2002; Simonis et al., 2006; Zhao et al., 2006).”
CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. (2007, positive): “Previously, we applied chromosome conformation capture (3C) technology (Dekker et al. 2002) to study long-range DNA interactions between these and other sites in the -globin locus.”
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function (2015, positive): “We developed a CRISPR/Cas9-based DNA-fragment in situ inversion technology (Li et al., 2015)—in conjunction with 3C, as well as related 4C (circularized 3C) and Hi-C methods (Dekker et al., 2002)—to study the chromatin organization in the Pcdh clusters.”
Looping and interaction between hypersensitive sites in the active beta-globin locus. (2002, methodology): “Distant liaisons: long-range enhancer-promoter As shown before (Dekker et al., 2002), formation of ligation prod- interactions in Drosophila.”
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms (2019, background): “, 2014) and high-throughput chromatin conformation capture sequencing (Dekker et al., 2002), more and more species have their genomes sequenced or updated to the chromosome level (Jiao & Schneeberger, 2017; Phillippy, 2017).”
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing (2010, methodology): “Our validations, including 3C [13], ChIP-3C [16], and 4C [17], as well as fluorescent in situ hybridization (FISH) and small interfering RNA experiments, suggest that the majority of the intra-chromosomal chromatin interactions identified in this analysis are bona fide loci bound by ERα as reported ”
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. (2006, background): “Recent evidence indicates that regulatory elements can act over large genomic distances by engaging in direct physical in- teractions with their target genes or with other elements (Dekker 2003; de Laat and Grosveld 2003; Chambeyron and Bickmore 2004; West and Fraser 2005).”