Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Genome Research

Volumn 16, Issue 10, 2006, Pages 1299-1309

  Dostie, Josée ^a   Richmond, Todd A ^b   Arnaout, Ramy A ^c,d,e   Selzer, Rebecca R ^b   Lee, William L ^c   Honan, Tracey A ^c   Rubio, Eric D ^f   Krumm, Anton ^f   Lamb, Justin ^c   Nusbaum, Chad ^c   Green, Roland D ^b   Dekker, Job ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b Roche NimbleGen Inc   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e HARVARD UNIVERSITY   (United States)

^f UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBULIN; DELTA GLOBIN; GAMMA GLOBIN; OLIGONUCLEOTIDE;

ARTICLE; CELL STRAIN K 562; CHROMATIN; CHROMOSOME; CHROMOSOME ANALYSIS; CONFORMATION; CONTROLLED STUDY; DNA SEQUENCE; GENE CONTROL; GENE INTERACTION; GENE LOCUS; GENE MAPPING; GENE SWITCHING; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS;

BASE SEQUENCE; CHROMATIN; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA PRIMERS; EVALUATION STUDIES; EVALUATION STUDIES AS TOPIC; GENE EXPRESSION REGULATION; GENETIC TECHNIQUES; GENOMICS; GLOBINS; HUMANS; MICROARRAY ANALYSIS; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

EID: 33749400168     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5571506     Document Type: Article

References (49)

1. Bender, M.A., Byron, R., Ragoczy, T., Telling, A., Bulger, M., and Groudine, M. 2006. Flanking HS-62.5 and 3′HS1, and regions upstream of the LCR, are not required for β-globin transcription. Blood 108: 1395-1401.
2. Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E.W., Wu, B., Doucet, D., Thomas, N.J., Wang, Y., Vollmer, E., et al. 2005. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16: 383-393.
3. Bulger, M., Bender, M.A., van Doorninck, J.H., Wertman, B., Farrell, C.M., Felsenfeld, G., Groudine, M., and Hardison, R. 2000. Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse β-globin gene clusters. Proc. Natl. Acad. Sci. 97: 14560-14565.
4. Bulger, M., Schubeler, D., Bender, M.A., Hamilton, J., Farrell, C.M., Hardison, R.C., and Groudine, M. 2003. A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse β-globin locus. Mol. Cell. Biol. 23: 5234-5244.
5. Calzolari, R., McMorrow, T., Yannoutsos, N., Langeveld, A. and Grosveld, F. 1999. Deletion of a region that is a candidate for the difference between the deletion forms of hereditary persistence of fetal hemoglobin and δβ-thalassemia affects β- but not γ-globin gene expression. EMBO J. 18: 949-958.
6. Carter, D., Chakalova, L., Osborne, C.S., Dai, Y.-F., and Fraser, P. 2002. Long-range chromatin regulatory interactions in vivo. Nat. Genet. 32: 623-626.
7. Chakalova, L., Osborne, C.S., Dai, Y.F., Goyenechea, B., Metaxotou-Mavromati, A., Kattamis, A., Kattamis, C., and Fraser, P. 2005. The Corfu δβ thalassemia deletion disrupts γ-globin gene silencing and reveals post-transcriptional regulation of HbF expression. Blood 105: 2154-2160.
8. Chambeyron, S. and Bickmore, W.A. 2004. Does looping and clustering in the nucleus regulate gene expression? Curr. Opin. Cell Biol. 16: 256-262.
9. Dekker, J. 2003. A closer look at long-range chromosomal interactions. Trends Biochem. Sci. 28: 277-280.
10. _. 2006. The 3 C's of chromosome conformation capture: Controls, controls, controls. Nat. Methods 3: 17-21.
11. Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. 2002. Capturing chromosome conformation. Science 295: 1306-1311.
12. de Laat, W. and Grosveld, F. 2003. Spatial organization of gene expression: The active chromatin hub. Chromosome Res. 11: 447-459.
13. Drissen, R., Palstra, R.J., Gillemans, N., Splinter, E., Grosveld, F., Philipsen, S., and de Laat, W. 2004. The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes & Dev. 18: 2485-2490.
14. ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306: 636-640.
15. Fan, J.B., Yeakley, J.M., Bibikova, M., Chudin, E., Wickham, E., Chen, J., Doucet, D., Rigault, P., Zhang, B., Shen, R., et al. 2004. A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 14: 878-885.
16. Farrell, C.M., West, A.G., and Felsenfeld, G. 2002. Conserved CTCF insulator elements flank the mouse and human β-globin loci. Mol. Cell. Biol. 22: 3820-3831.
17. Fraser, P., Pruzina, S., Antoniou, M., and Grosveld, F. 1993. Each hypersensitive site of the human β-globin locus control region confers a different developmental pattern of expression on the globin genes. Genes & Dev. 7: 106-113.
18. Gheldof, N., Tabuchi, T.M., and Dekker, J. 2006. The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc. Natl. Acad. Sci. 103: 12463-12468.
19. Gribnau, J., Diderich, K., Pruzina, S., Calzolari, R., and Fraser, P. 2000. Intergenic transcription and developmental remodeling of chromatin subdomains in the human β-globin locus. Mol. Cell 5: 377-386.
20. Hardenbol, P., Yu, F., Belmont, J., Mackenzie, J., Bruckner, C., Brundage, T., Boudreau, A., Chow, S., Eberle, J., Erbilgin, A., et al. 2005. Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 15: 269-275.
21. Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., and Ren, B. 2005. A high-resolution map of active promoters in the human genome. Nature 436: 876-880.
22. Landegren, U., Kaiser, R., Sanders, J., and Hood, L. 1988. A ligase-mediated gene detection technique. Science 241: 1077-1080.
23. Li, Q., Peterson, K.R., Fang, X., and Stamatoyannopoulos, G. 2002. Locus control regions. Blood 100: 3077-3086.
24. Li, J., Chu, X., Liu, Y., Jiang, J.H., He, Z., Zhang, Z., Shen, G., and Yu, R.Q. 2005. A colorimetric method for point mutation detection using high-fidelity DNA ligase. Nucleic Acids Res. 33: e168.
25. Ling, J.Q., Li, T., Hu, J.F., Vu, T.H., Chen, H.L., Qiu, X.W., Cherry, A.M., and Hoffman, A.R. 2006. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312: 269-272.
26. Liu, Z. and Garrard, W.T. 2005. Long-range interactions between three transcriptional enhancers, active Vκ gene promoters, and a 3′ boundary sequence spanning 46 kilobases. Mol. Cell. Biol. 25: 3220-3231.
27. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
28. Miele, A., Gheldof, N., Tabuchi, T.M., Dostie, J., and Dekker, J. 2006. Mapping chromatin interactions by chromosome conformation capture (3C). In Current protocols in molecular biology (eds. F.M. Ausubel et al.), pp. 21.11.21-21.11-20. John Wiley & Sons, New York.
29. 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.
30. Ning, Z., Cox, A.J., and Mullikin, J.C. 2001. SSAHA: A fast search method for large DNA databases. Genome Res. 11: 1725-1729.
31. Nuwaysir, E.F., Huang, W., Albert, T.J., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J.P., Ballin, J., et al. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12: 1749-1755.
32. O'Neill, D., Yang, J., Erdjument-Bromage, H., Bornschlegel, K., Tempst, P., and Bank, A. 1999. Tissue-specific and developmental stage-specific DNA binding by a mammalian SWI/SNF complex associated with human fetal-to-adult globin gene switching. Proc. Natl. Acad. Sci. 96: 349-354.
33. Palstra, R.J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., and de Laat, W. 2003. The β-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 35: 190-194.
34. Patrinos, G.P., de Krom, M., de Boer, E., Langeveld, A., Imam, A.M., Strouboulis, J., de Laat, W., and Grosveld, F.G. 2004. Multiple interactions between regulatory regions are required to stabilize an active chromatin hub. Genes & Dev. 18: 1495-1509.
35. Peck, D., Crawford, E.D., Ross, K.N., Stegmaier, K., Golub, T.R., and Lamb, J. 2006. A method for high-throughput gene expression signature analysis. Genome Biol. 7: R61.
36. Peterson, K.R., Clegg, C.H., Navas, P.A., Norton, E.J., Kimbrough, T.G., and Stamatoyannopoulos, G. 1996. Effect of deletion of 5′HS3 or 5′HS2 of the human β-globin locus control region on the developmental regulation of globin gene expression in β-globin locus yeast artificial chromosome transgenic mice. Proc. Natl. Acad. Sci. 93: 6605-6609.
37. Rippe, K. 2001. Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26: 733-740.
38. Selzer, R.R., Richmond, T.A., Pofahl, N.J., Green, R.D., Eis, P.S., Nair, P., Brothman, A.R., and Stallings, R.L. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
39. Singh-Gasson, S., Green, R.D., Yue, Y., Nelson, C., Blattner, F., Sussman, M.R., and Cerrina, F. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17: 974-978.
40. 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.
41. Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R., and Flavell, R.A. 2005. Interchromosomal associations between alternatively expressed loci. Nature 435: 637-645.
42. Splinter, E., Grosveld, F., and de Laat, W. 2004. 3C technology: Analyzing the spatial organization of genomic loci in vivo. Methods Enzymol. 375: 493-507.
43. Stamatoyannopoulos, G. 2005. Control of globin gene expression during development and erythroid differentiation. Exp. Hematol. 33: 256-271.
44. Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., and de Laat, W. 2002. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell 10: 1453-1465.
45. Vakoc, C., Letting, D.L., Gheldof, N., Sawado, T., Bender, M.A., Groudine, M., Weiss, M.J., Dekker, J., and Blobel, G.A. 2005. Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Mol. Cell 17: 453-462.
46. Wang, Y., Moorhead, M., Karlin-Neumann, G., Falkowski, M., Chen, C., Siddiqui, F., Davis, R.W., Willis, T.D., and Faham, M. 2005. Allele quantification using molecular inversion probes (MIP). Nucleic Acids Res. 33: e183.
47. West, A.G. and Fraser, P. 2005. Remote control of gene transcription. Hum. Mol. Genet. 14: R101-R111.
48. Xu, N., Tsai, C.L., and Lee, J.T. 2006. Transient homologous chromosome pairing marks the onset of X inactivation. Science 311: 1149-1152.
49. Yuen, T., Wurmbach, E., Pfeffer, R.L., Ebersole, B.J., and Sealfon, S.C. 2002. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res. 30: e48.