4C-seq
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
Related
History: 4C-seq
Revision by DaanNoordermeer on 2018-01-05 07:57:02 - Show/Hide
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
Revision by sbrumpton on 2017-06-21 09:25:28 - Show/Hide
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 SelectorReviews: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;6:22462Loviglio 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;44:3082-3094Acemel 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;48:336-341De 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:e1006200Eckart N., Song Q., Yang R., et al. Functional Characterization of Schizophrenia-Associated Variation in CACNA1C. PLoS One. 2016;11:e0157086Kaaij 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;17:146Kandaswamy 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;16:2061-2067Lin C. Y., Erkek S., Tong Y., et al. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature. 2016;530:57-62Proudhon 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;15:2159-2169Rocha 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;16:48-55Vermunt M. W., Tan S. C., Castelijns B., et al. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016;19:494-503Wang Q., Sawyer I. A., Sung M. H., et al. Cajal bodies are linked to genome conformation. Nat Commun. 2016;7:10966Wani A. H., Boettiger A. N., Schorderet P., et al. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun. 2016;7:10291Revision by sbrumpton on 2017-06-21 09:25:13 - Show/Hide
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 SelectorReviews: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;6:22462Loviglio 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;44:3082-3094Acemel 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;48:336-341De 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:e1006200Eckart N., Song Q., Yang R., et al. Functional Characterization of Schizophrenia-Associated Variation in CACNA1C. PLoS One. 2016;11:e0157086Kaaij 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;17:146Kandaswamy 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;16:2061-2067Lin C. Y., Erkek S., Tong Y., et al. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature. 2016;530:57-62Proudhon 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;15:2159-2169Rocha 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;16:48-55Vermunt M. W., Tan S. C., Castelijns B., et al. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016;19:494-503Wang Q., Sawyer I. A., Sung M. H., et al. Cajal bodies are linked to genome conformation. Nat Commun. 2016;7:10966Wani A. H., Boettiger A. N., Schorderet P., et al. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun. 2016;7:10291