Hi-C/3C-Seq/Capture-C

Hi-C/3C-Seq/Capture-C

Method Category: Epigenome > DNA-Protein Interactions

Description: Hi-C, 3C-Seq, and Capture-C 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. 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.

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.

Pros:

• Allows detection of long-range DNA interactions
• High-throughput method

Cons:

• Detection may result from random chromosomal collisions
• Less than 1% of DNA fragments actually yield ligation products¹
• Due to multiple steps, the method requires large amounts of starting material

• Hi-C: Lieberman-Aiden E., van Berkum N. L., Williams L., Imakaev M., Ragoczy T., et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293
• 3-C: Duan Z., Andronescu M., Schutz K., Lee C., Shendure J., et al. (2012) A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods 58: 277-288
• Capture-C:Hughes J. R., Roberts N., McGowan S., Hay D., Giannoulatou E., et al. (2014) Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 46: 205-212
• 1. Bourgo R. J., Singhal H. and Greene G. L. Capture of associated targets on chromatin links long-distance chromatin looping to transcriptional coordination. Nat Commun. 2016;7:12893

Related Content

1. Epigenetics
2. DNA Protein Interaction Analysis

Related Publications

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4. 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
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9. 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
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11. 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
12. Petryk N., Kahli M., d'Aubenton-Carafa Y., et al. Replication landscape of the human genome. Nat Commun. 2016;7:10208
13. 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
14. 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
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16. 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
17. 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