Circular Chromatin Conformation Capture 4C (Zhao et al., 2006), (Simonis et al., 2006), also called 4C-seq, is a method similar to 3C and is sometimes called circular 3C. It allows the unbiased detection of all genomic regions that interact with a particular region of interest (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented, and the DNA is ligated and digested. The resulting DNA fragments self-circularize, followed by reverse PCR and sequencing. Deep sequencing provides base-pair resolution of the ligated fragments. Advantages:

• Preferred strategy to assess the DNA contact profile of individual genomic sites
• Highly reproducible data

Disadvantages:

• Will miss local interactions (< 50 kb) from the region of interest
• Large circles do not amplify efficiently

Reagents: Illumina Library prep and Array Kit Selector Reviews: None available yet References: Cai M., Kim S., Wang K., Farnham P. J., Coetzee G. A. and Lu W. 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Sci Rep. 2016;6:22462 Loviglio M. N., Leleu M., Mannik K., et al. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry. 2016; Yang R., Kerschner J. L., Gosalia N., Neems D., Gorsic L. K., et al. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res. 2016;44:3082-3094 Acemel R. D., Tena J. J., Irastorza-Azcarate I., Marletaz F., Gomez-Marin C., et al. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet. 2016;48:336-341 De S., Mitra A., Cheng Y., Pfeifer K. and Kassis J. A. Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet. 2016;12:e1006200 Eckart N., Song Q., Yang R., et al. Functional Characterization of Schizophrenia-Associated Variation in CACNA1C. PLoS One. 2016;11:e0157086 Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146 Kandaswamy R., Sava G. P., Speedy H. E., et al. Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism. Cell Rep. 2016;16:2061-2067 Lin C. Y., Erkek S., Tong Y., et al. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature. 2016;530:57-62 Proudhon C., Snetkova V., Raviram R., Lobry C., Badri S., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169 Rocha P. P., Raviram R., Fu Y., Kim J., Luo V. M., et al. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep. 2016;16:48-55 Vermunt M. W., Tan S. C., Castelijns B., et al. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016;19:494-503 Wang Q., Sawyer I. A., Sung M. H., et al. Cajal bodies are linked to genome conformation. Nat Commun. 2016;7:10966 Wani A. H., Boettiger A. N., Schorderet P., et al. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun. 2016;7:10291 Smemo S., Tena J.J., Kim, K.H., et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 2014;507:371 Andrey G., Montavon T., Mascrez B., et al. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science. 2013;340:1195 De Wit E., Bouwman B.A., Zhu Y., et al. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature. 2013;501:227 Van de Werken H.J., Landan G., Holwerda S.J., et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods. 2012;9:969 Noordermeer D., Leleu M., Splinter E., et al. The dynamic architecture of Hox gene clusters. Science. 2011;334:222  

Circular Chromatin Conformation Capture

4C (Zhao et al., 2006) , also called 4C-seq, is a method similar to 3C and is sometimes called circular 3C. It allows the unbiased detection of all genomic regions that interact with a particular region of interest (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented, and the DNA is ligated and digested. The resulting DNA fragments self-circularize, followed by reverse PCR and sequencing. Deep sequencing provides base-pair resolution of the ligated fragments.

Advantages:

• Preferred strategy to assess the DNA contact profile of individual genomic sites
• Highly reproducible data

Disadvantages:

• Will miss local interactions (< 50 kb) from the region of interest
• Large circles do not amplify efficiently

Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

None available yet

References:

Cai M., Kim S., Wang K., Farnham P. J., Coetzee G. A. and Lu W. 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Sci Rep. 2016;6:22462

Loviglio M. N., Leleu M., Mannik K., et al. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry. 2016;

Yang R., Kerschner J. L., Gosalia N., Neems D., Gorsic L. K., et al. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res. 2016;44:3082-3094

Acemel R. D., Tena J. J., Irastorza-Azcarate I., Marletaz F., Gomez-Marin C., et al. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet. 2016;48:336-341

De S., Mitra A., Cheng Y., Pfeifer K. and Kassis J. A. Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet. 2016;12:e1006200

Eckart N., Song Q., Yang R., et al. Functional Characterization of Schizophrenia-Associated Variation in CACNA1C. PLoS One. 2016;11:e0157086

Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146

Kandaswamy R., Sava G. P., Speedy H. E., et al. Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism. Cell Rep. 2016;16:2061-2067

Lin C. Y., Erkek S., Tong Y., et al. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature. 2016;530:57-62

Proudhon C., Snetkova V., Raviram R., Lobry C., Badri S., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169

Rocha P. P., Raviram R., Fu Y., Kim J., Luo V. M., et al. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep. 2016;16:48-55

Vermunt M. W., Tan S. C., Castelijns B., et al. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016;19:494-503

Wang Q., Sawyer I. A., Sung M. H., et al. Cajal bodies are linked to genome conformation. Nat Commun. 2016;7:10966

Wani A. H., Boettiger A. N., Schorderet P., et al. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun. 2016;7:10291

Circular Chromatin Conformation Capture

4C (Zhao et al., 2006) , also called 4C-seq, is a method similar to 3C and is sometimes called circular 3C. It allows the unbiased detection of all genomic regions that interact with a particular region of interest (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented, and the DNA is ligated and digested. The resulting DNA fragments self-circularize, followed by reverse PCR and sequencing. Deep sequencing provides base-pair resolution of the ligated fragments.

Advantages:

• Preferred strategy to assess the DNA contact profile of individual genomic sites
• Highly reproducible data

Disadvantages:

• Will miss local interactions (< 50 kb) from the region of interest
• Large circles do not amplify efficiently

Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

None available yet

References:

Cai M., Kim S., Wang K., Farnham P. J., Coetzee G. A. and Lu W. 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. Sci Rep. 2016;6:22462

Loviglio M. N., Leleu M., Mannik K., et al. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry. 2016;

Yang R., Kerschner J. L., Gosalia N., Neems D., Gorsic L. K., et al. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res. 2016;44:3082-3094

Acemel R. D., Tena J. J., Irastorza-Azcarate I., Marletaz F., Gomez-Marin C., et al. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet. 2016;48:336-341

De S., Mitra A., Cheng Y., Pfeifer K. and Kassis J. A. Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet. 2016;12:e1006200

Eckart N., Song Q., Yang R., et al. Functional Characterization of Schizophrenia-Associated Variation in CACNA1C. PLoS One. 2016;11:e0157086

Kaaij L. J., Mokry M., Zhou M., Musheev M., Geeven G., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146

Kandaswamy R., Sava G. P., Speedy H. E., et al. Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism. Cell Rep. 2016;16:2061-2067

Lin C. Y., Erkek S., Tong Y., et al. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature. 2016;530:57-62

Proudhon C., Snetkova V., Raviram R., Lobry C., Badri S., et al. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep. 2016;15:2159-2169

Rocha P. P., Raviram R., Fu Y., Kim J., Luo V. M., et al. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep. 2016;16:48-55

Vermunt M. W., Tan S. C., Castelijns B., et al. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016;19:494-503

Wang Q., Sawyer I. A., Sung M. H., et al. Cajal bodies are linked to genome conformation. Nat Commun. 2016;7:10966

Wani A. H., Boettiger A. N., Schorderet P., et al. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun. 2016;7:10291