SnapShot: Chromosome Conformation Capture

Coverage Commonly < 1Mb Commonly < 1Mb Genome-wide Genome-wide Commonly < 1Mb Genome-wideDetection Locus-specifi c PCR HT-sequencing HT-sequencing HT-sequencing Locus-specifi c qPCR HT-sequencingLimitations Low throughput and coverageLimited coverage Limited to one viewpointRely on one chromatin-associated factor, disregarding other contactsExamples Determine interaction between a known promoter and enhancerDetermine comprehensively higher-order chromosome structure in adefi ned regionAll genes and genomic elements associated with a known LCRAll intra- and interchromosomal associationsDetermine the role of specifi c transcription factors in the interaction between a known promoter and enhancerMap chromatin interaction network of a known transcription factorDerivatives PCR with TaqMan probes

[1]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[2]  Pierre Chartrand,et al.  Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology , 2006, Chromosome Research.

[3]  William Stafford Noble,et al.  A Three-Dimensional Model of the Yeast Genome , 2010, Nature.

[4]  Jennifer A. Mitchell,et al.  Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.

[5]  R. Bremner,et al.  A rapid simple approach to quantify chromosome conformation capture , 2009, Nucleic acids research.

[6]  K. Sandhu,et al.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions , 2006, Nature Genetics.

[7]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[8]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[9]  Marc A. Martí-Renom,et al.  The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation , 2012, RECOMB.

[10]  Benjamin Leblanc,et al.  Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila , 2011, Cell.

[11]  Erik Splinter,et al.  Looping and interaction between hypersensitive sites in the active beta-globin locus. , 2002, Molecular cell.

[12]  Wouter de Laat,et al.  Quantitative analysis of chromosome conformation capture assays (3C-qPCR) , 2007, Nature Protocols.

[13]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[14]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[15]  Marc A Marti-Renom,et al.  The Three-dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation , 2022 .

[16]  Hideki Tanizawa,et al.  Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation , 2010, Nucleic acids research.

[17]  Hui Ling Chen,et al.  CTCF Mediates Interchromosomal Colocalization Between Igf2/H19 and Wsb1/Nf1 , 2006, Science.

[18]  Jan-Fang Cheng,et al.  Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome , 2005, Nature Genetics.

[19]  Richard Axel,et al.  Interchromosomal Interactions and Olfactory Receptor Choice , 2006, Cell.