Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions

By Zhihu Zhao, Gholamreza Tavoosidana, M. Sjölinder, A. Göndör, P. Mariano, Sha Wang, C. Kanduri, M. Lezcano, K. Sandhu, Umashankar Singh and 4 more. Nature Genetics, 2006

990 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e3746c669be7f40d37d36b29efa4d5cd8cf5d08b

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

In Genetics

1. W. de Laat
2. Bing Ren
3. E. de Wit
4. Amos Tanay
5. Ming Hu
6. Anthony D. Schmitt
7. Thomas Cremer
8. Leonid A. Mirny

In Molecular Biology

1. Leonid A. Mirny
2. V. Corces
3. Bing Ren
4. Job Dekker
5. W. de Laat
6. Ming Hu
7. Anthony D. Schmitt
8. E. de Wit

Citations in the corpus

• Hi-C: A comprehensive technique to capture the conformation of genomes (2012, methodology): “In recent years, new approaches such as 4C, 5C, and Hi-C have been developed to utilize Next Generation Sequencing (NGS) technologies in order to interrogate the 3C ligation product library more comprehensively (figure 1D and 1E) [7-10].”
• CTCF: Master Weaver of the Genome (2009, positive): “For example, at the H19/Igf2 ICR all four CTCF-binding sites are regulated by methylation to control allele-specific CTCF occupancy and subsequent loop formation.”
• Beyond the sequence: cellular organization of genome function. (2007, positive): “…of methods to probe the physical association of genome regions in a unbiased and genome-wide scale should lead to rapid progress in our still-rudimentary understanding of the functional significance of chromatin loops (Simonis et al., 2006; Wurtele and Chartrand, 2006; Zhao et al., 2006).”
• Chromosome territories. (2010, methodology): “…of specific genomic loci is the technique of “chromosome conformation capture” (3C) introduced by Dekker et al. (2002) and its recent extension to 4C (chromosome conformation capture-on-chip [Simonis et al. 2006] and “circular chromosome conformation capture” [Zhao et al. 2006]), respectively.”
• 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).”
• Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer (2016, background): “More recent technical developments have focused on higher-throughput analyses and these include circular chromosome conformation capture (4C) [66,67], chromosome conformation capture carbon copy (5C) [68], combined 3C-ChIP-cloning (6C) [69], chromatin interaction analysis with paired-end tag sequenc”
• Genome-wide mapping and analysis of chromosome architecture (2016, methodology): “…using 4C (circular chromosome conformation capture; also known as chromosome conformation capture-on-chip) technology, as 4C interrogates the chromatin looping landscape of only a single restriction fragment with the rest of the genome, rather than all possible pairwise contacts genome-wide 45,46 .”
• CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells (2011, methodology): “Beyond these well-characterized interactions, additional CTCF-dependent inter- and intrachromosomal interactions were identified from these imprinting regions using circular chromosome conformation capture (4C”
• Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data (2013, positive): “4C (also known as ‘circular 3C’ or ‘3C‑on‑chip’) uses inverse PCR to generate genome‑wide interaction profiles for single loci 48,105,106 .”
• Epigenetic modifications and human disease (2010, background): “These physical interactions in trans can regulate transcription, as shown for the H19 imprinting control region and the Osbpl1a/Impact loc”
• Functional and mechanistic diversity of distal transcription enhancers (2011, positive): “This approach has been adapted to produce genome-wide maps of the threedimensional associations that a specific locus makes among all of the other sequences in the genome (‘‘4C’’) (Zhao et al., 2006; Simonis et al., 2006) or even associations among multiple sequences located throughout the genome (‘”
• A decade of 3C technologies: insights into nuclear organization. (2012, background): “In mammals, CTCF sites form chromatin loops by contacting each other in the b-globin locus (Splinter et al. 2006) and H19/Igf2 locus (Zhao et al. 2006).”