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.

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

Related Content

  1. Epigenetics
  2. DNA Protein Interaction Analysis

Related Publications

  1. Sati S. and Cavalli G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma. 2016;
  2. 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
  3. Criscione S. W., De Cecco M., Siranosian B., et al. Reorganization of chromosome architecture in replicative cellular senescence. Sci Adv. 2016;2:e1500882
  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
  5. 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
  6. 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
  7. 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
  8. 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
  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
  10. 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
  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
  15. 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
  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