3-C/Capture-C/Hi-C
Chromatin Conformation Capture Sequencing
3C-Seq (Duan et al., 2012), Capture-C, and Hi-C (Lieberman-Aiden et al., 2009) comprise a family of methods for analyzing chromatin interactions. Capture-C adds an additional pull-down of the biotinylated fragments with magnetic beads to the 3C method. A new refinement of the Capture-C method (NG Capture-C) is available (Davies et al., 2016). The Hi-C approach extends 3C-Seq to map chromatin contacts genome-wide, and it has also been applied to studying in situ chromatin interactions(Sati et al., 2016) (Rao et al., 2014).
In this method, DNA-protein complexes are crosslinked with formaldehyde. The sample is fragmented, and the DNA is extracted, ligated, and digested with restriction enzymes. The resulting DNA fragments are PCR-amplified and sequenced. Deep sequencing provides base-pair resolution of the ligated fragments.
Advantages:
- Allows detection of long-range DNA interactions
- High-throughput method
Disadvantages:
- Detection may result from random chromosomal collisions
- Less than 1% of DNA fragments actually yield ligation products (Bourgo et al., 2016)
- Due to multiple steps, the method requires large amounts of starting material
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Sati S. and Cavalli G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma. 2016;
Turaev D. and Rattei T. High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved. Curr Opin Biotechnol. 2016;39:174-181
References:
Criscione S. W., De Cecco M., Siranosian B., et al. Reorganization of chromosome architecture in replicative cellular senescence. Sci Adv. 2016;2:e1500882
Darrow E. M., Huntley M. H., Dudchenko O., et al. Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc Natl Acad Sci U S A. 2016;113:E4504-4512
Krijger P. H., Di Stefano B., de Wit E., et al. Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming. Cell Stem Cell. 2016;18:597-610
Veluchamy A., Jegu T., Ariel F., et al. LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PLoS One. 2016;11:e0158936
Acemel R. D., Tena J. J., Irastorza-Azcarate I., 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
Bigot P., Colli L. M., Machiela M. J., et al. Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41. Nat Commun. 2016;7:12098
Capurso D., Bengtsson H. and Segal M. R. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res. 2016;44:2028-2035
Gunnell A., Webb H. M., Wood C. D., et al. RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth. Nucleic Acids Res. 2016;44:4636-4650
Kim K. D., Tanizawa H., Iwasaki O. and Noma K. Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat Genet. 2016;48:1242-1252
Petryk N., Kahli M., d’Aubenton-Carafa Y., et al. Replication landscape of the human genome. Nat Commun. 2016;7:10208
Pichugina T., Sugawara T., Kaykov A., et al. A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Sci Rep. 2016;6:18757
Putnam N. H., O’Connell B. L., Stites J. C., et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016;26:342-350
Rocha P. P., Raviram R., Fu Y., 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
Tjong H., Li W., Kalhor R., et al. Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A. 2016;113:E1663-1672
Ulianov S. V., Khrameeva E. E., Gavrilov A. A., et al. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res. 2016;26:70-84
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History: 3-C/Capture-C/Hi-C
Revision by sbrumpton on 2017-06-21 09:25:11 - Show/Hide
Chromatin Conformation Capture Sequencing
3C-Seq (Duan et al., 2012), Capture-C, and Hi-C (Lieberman-Aiden et al., 2009) comprise a family of methods for analyzing chromatin interactions. Capture-C adds an additional pull-down of the biotinylated fragments with magnetic beads to the 3C method. A new refinement of the Capture-C method (NG Capture-C) is available (Davies et al., 2016). The Hi-C approach extends 3C-Seq to map chromatin contacts genome-wide, and it has also been applied to studying in situ chromatin interactions(Sati et al., 2016) (Rao et al., 2014).
In this method, DNA-protein complexes are crosslinked with formaldehyde. The sample is fragmented, and the DNA is extracted, ligated, and digested with restriction enzymes. The resulting DNA fragments are PCR-amplified and sequenced. Deep sequencing provides base-pair resolution of the ligated fragments.
Advantages:- Allows detection of long-range DNA interactions
- High-throughput method
Disadvantages:- Detection may result from random chromosomal collisions
- Less than 1% of DNA fragments actually yield ligation products (Bourgo et al., 2016)
- Due to multiple steps, the method requires large amounts of starting material
Reagents:Illumina Library prep and Array Kit SelectorReviews:Sati S. and Cavalli G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma. 2016;Turaev D. and Rattei T. High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved. Curr Opin Biotechnol. 2016;39:174-181References:Criscione S. W., De Cecco M., Siranosian B., et al. Reorganization of chromosome architecture in replicative cellular senescence. Sci Adv. 2016;2:e1500882Darrow E. M., Huntley M. H., Dudchenko O., et al. Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc Natl Acad Sci U S A. 2016;113:E4504-4512Krijger P. H., Di Stefano B., de Wit E., et al. Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming. Cell Stem Cell. 2016;18:597-610Veluchamy A., Jegu T., Ariel F., et al. LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PLoS One. 2016;11:e0158936Acemel R. D., Tena J. J., Irastorza-Azcarate I., et al. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet. 2016;48:336-341Bigot P., Colli L. M., Machiela M. J., et al. Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41. Nat Commun. 2016;7:12098Capurso D., Bengtsson H. and Segal M. R. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res. 2016;44:2028-2035Gunnell A., Webb H. M., Wood C. D., et al. RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth. Nucleic Acids Res. 2016;44:4636-4650Kim K. D., Tanizawa H., Iwasaki O. and Noma K. Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat Genet. 2016;48:1242-1252Petryk N., Kahli M., d'Aubenton-Carafa Y., et al. Replication landscape of the human genome. Nat Commun. 2016;7:10208Pichugina T., Sugawara T., Kaykov A., et al. A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Sci Rep. 2016;6:18757Putnam N. H., O'Connell B. L., Stites J. C., et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016;26:342-350Rocha P. P., Raviram R., Fu Y., et al. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep. 2016;16:48-55Tjong H., Li W., Kalhor R., et al. Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A. 2016;113:E1663-1672Ulianov S. V., Khrameeva E. E., Gavrilov A. A., et al. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res. 2016;26:70-84