DOI QR코드

DOI QR Code

3C (Chromatin Conformation Capture): A Technique to Study Chromatin Organization

3C (chromatin conformation capture): 크로마틴 입체 구조 연구를 위한 기법

  • Kim, Yea Woon (Department of Molecular Biology, College of Natural Sciences, Pusan National University) ;
  • Kim, AeRi (Department of Molecular Biology, College of Natural Sciences, Pusan National University)
  • 김예운 (부산대학교 자연과학대학 분자생물학과) ;
  • 김애리 (부산대학교 자연과학대학 분자생물학과)
  • Received : 2012.09.03
  • Accepted : 2012.11.11
  • Published : 2012.11.30

Abstract

3C (chromatin conformation capture) is a technique to analyze chromatin organization in nuclei of eukaryotic cells. The procedure of 3C includes the formaldehyde treatment of cells to fix interactions between proteins and between proteins and DNA in chromatin, the digestion of fixed chromatin with restriction enzyme, and the ligation of fragmented DNA. The efficiency of DNA ligation represents proximity between DNA fragments in chromatin organization. Studies in the ${\beta}$-globin locus using 3C showed that the locus control region is in close proximity to the transcriptionally-active globin genes, indicating that chromatin organization has a role in transcriptional regulation of the genes. 3C has been advanced by combining with ChIP and genome-wide sequencing. This review presents the principle and procedure of the 3C technique, the chromatin organization of the ${\beta}$-globin locus explained by 3C, and advanced techniques based on 3C.

Acknowledgement

Supported by : 부산대학교

References

  1. de Wit, E. and de Laat, W. 2012. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11-24. https://doi.org/10.1101/gad.179804.111
  2. Dean, A. 2011. In the loop: long range chromatin interactions and gene regulation. Brief Funct. Genomics 10, 3-10. https://doi.org/10.1093/bfgp/elq033
  3. Dekker, J. 2006. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat. Methods 3, 17-21. https://doi.org/10.1038/nmeth823
  4. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. 2002. Capturing chromosome conformation. Science 295, 1306-1311. https://doi.org/10.1126/science.1067799
  5. Dostie, J., Richmond, T. A., Arnaout, R. A., Selzer, R. R., Lee, W. L., Honan, T. A., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., Green, R. D. and Dekker, J. 2006. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299-1309. https://doi.org/10.1101/gr.5571506
  6. Ethier, S. D., Miura, H. and Dostie, J. 2012. Discovering genome regulation with 3C and 3C-related technologies. Biochim. Biophys. Acta. 1819, 401-410. https://doi.org/10.1016/j.bbagrm.2011.12.004
  7. Fang, X., Xiang, P., Yin, W., Stamatoyannopoulos, G. and Li, Q. 2007. Cooperativeness of the higher chromatin structure of the $\beta$-globin locus revealed by the deletion mutations of DNase I hypersensitive site 3 of the LCR. J. Mol. Biol. 365, 31-37. https://doi.org/10.1016/j.jmb.2006.09.072
  8. Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Xu, H., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Mei, P. H., Chew, E. G., Huang, P. Y., Welboren, W. J., Han, Y., Ooi, H. S., Ariyaratne, P. N., Vega, V. B., Luo, Y., Tan, P. Y., Choy, P. Y., Wansa, K. D., Zhao, B., Lim, K. S., Leow, S. C., Yow, J. S., Joseph, R., Li, H., Desai, K. V., Thomsen, J. S., Lee, Y. K., Karuturi, R. K., Herve, T., Bourque, G., Stunnenberg, H. G., Ruan, X., Cacheux-Rataboul, V., Sung, W. K., Liu, E. T., Wei, C. L., Cheung, E. and Ruan., Y. 2009. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58-64. https://doi.org/10.1038/nature08497
  9. Gheldof, N., Smith, E. M., Tabuchi, T. M., Koch, C. M., Dunham, I., Stamatoyannopoulos, J. A. and Dekker, J. 2010. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res. 38, 4325-4336. https://doi.org/10.1093/nar/gkq175
  10. Hagege, H., Klous, P., Braem, C., Splinter, E., Dekker, J., Cathala, G., de Laat, W. and Forne, T. 2007. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722-1733. https://doi.org/10.1038/nprot.2007.243
  11. Horike, S., Cai, S., Miyano, M., Cheng, J. F. and Kohwi-Shigematsu, T. 2005. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat. Genet. 37, 31-40. https://doi.org/10.1038/ng1570
  12. Jing, H., Vakoc, C. R., Ying, L., Mandat, S., Wang, H., Zheng, X. and Blobel, G. A. 2008. Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. Mol. Cell 29, 232-242. https://doi.org/10.1016/j.molcel.2007.11.020
  13. Kadauke, S. and Blobel, G. A. 2009. Chromatin loops in gene regulation. Biochim. Biophys. Acta. 1789, 17-25. https://doi.org/10.1016/j.bbagrm.2008.07.002
  14. Kim, S., Kim, Y. W., Shim, S. H., Kim, C. G. and Kim, A. 2012. Chromatin structure of the LCR in the human $\beta$-globin locus transcribing the adult $\delta$- and $\beta$-globin genes. Int. J. Biochem. Cell Biol. 44, 505-513. https://doi.org/10.1016/j.biocel.2011.12.001
  15. Kim, Y. W., Kim, S., Kim, C. G. and Kim, A. 2011. The distinctive roles of erythroid specific activator GATA-1 and NF-E2 in transcription of the human fetal γ-globin genes. Nucleic Acids Res. 39, 6944-6955. https://doi.org/10.1093/nar/gkr253
  16. Krivega, I. and Dean, A. 2012. Enhancer and promoter interactions- long distance calls. Curr. Opin. Genet. Dev. 22, 79-85. https://doi.org/10.1016/j.gde.2011.11.001
  17. Kurukuti, S., Tiwari, V. K., Tavoosidana, G., Pugacheva, E., Murrell, A., Zhao, Z., Lobanenkov, V., Reik, W. and Ohlsson, R. 2006. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc. Natl. Acad. Sci. USA 103, 10684-10689. https://doi.org/10.1073/pnas.0600326103
  18. Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., Sandstrom, R., Bernstein, B., Bender, M. A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L. A., Lander, E. S. and Dekker, J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293. https://doi.org/10.1126/science.1181369
  19. Majumder, P., Gomez, J. A., Chadwick, B. P. and Boss, J. M. 2008. The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J. Exp. Med. 205, 785-798. https://doi.org/10.1084/jem.20071843
  20. Murrell, A., Heeson, S. and Reik, W. 2004. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36, 889-893. https://doi.org/10.1038/ng1402
  21. Orlando, V., Strutt, H. and Paro, R. 1997. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11, 205-214. https://doi.org/10.1006/meth.1996.0407
  22. Ott, C. J., Blackledge, N. P., Kerschner, J. L., Leir, S. H., Crawford, G. E., Cotton, C. U. and Harris, A. 2009. Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc. Natl. Acad. Sci. USA 106, 19934-19939. https://doi.org/10.1073/pnas.0900946106
  23. Palstra, R. J. 2009. Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation. Brief Funct. Genomic. Proteomic. 8, 297-309. https://doi.org/10.1093/bfgp/elp016
  24. Palstra, R. J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F. and de Laat, W. 2003. The $\beta$-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 35, 190-194. https://doi.org/10.1038/ng1244
  25. Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B. and de Laat, W. 2006. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348-1354. https://doi.org/10.1038/ng1896
  26. Spilianakis, C. G. and Flavell, R. A. 2004. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat. Immunol. 5, 1017-1027. https://doi.org/10.1038/ni1115
  27. Splinter, E., Heath, H., Kooren, J., Palstra, R. J., Klous, P., Grosveld, F., Galjart, N. and de Laat, W. 2006. CTCF mediates long-range chromatin looping and local histone modification in the $\beta$-globin locus. Genes Dev. 20, 2349-2354. https://doi.org/10.1101/gad.399506
  28. Tiwari, V. K., McGarvey, K. M., Licchesi, J. D., Ohm, J. E., Herman, J. G., Schübeler, D. and Baylin, S. B. 2008. PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol. 6, 2911-2927.
  29. Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F. and de Laat, W. 2002. Looping and interaction between hypersensitive sites in the active $\beta$-globin locus. Mol. Cell 10, 1453-1465. https://doi.org/10.1016/S1097-2765(02)00781-5
  30. Tsytsykova, A. V., Rajsbaum, R., Falvo, J. V., Ligeiro, F., Neely, S. R. and Goldfeld, A. E. 2007. Activation-dependent intrachromosomal interactions formed by the TNF gene promoter and two distal enhancers. Proc. Natl. Acad. Sci. USA 104, 16850-16855. https://doi.org/10.1073/pnas.0708210104
  31. Zhao, Z., Tavoosidana, G., Sjölinder, M., Göndör, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K. S., Singh, U., Pant, V., Tiwari, V., Kurukuti, S. and Ohlsson, R. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341-1347. https://doi.org/10.1038/ng1891