The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
Open accessAbstract
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human β-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the β-globin locus. We also identified a new looping interaction in K562 cells between the β-globin Locus Control Region and the γ–β-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure.
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Citations
Cites
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Self-citationLooping and Interaction between Hypersensitive Sites in the Active β-globin Locus
Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344
Long-range chromatin regulatory interactions in vivo
Carter, D., Chakalova, L., Osborne, C. S., Dai, Y.-F., & Fraser, P. (2002) · Nature Genetics · doi:10.1038/ng1051 · Cited by 663
The β-globin nuclear compartment in development and erythroid differentiation
Palstra, R.-J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., & de Laat, W. (2003) · Nature Genetics · doi:10.1038/ng1244 · Cited by 559
Murrell, A., Heeson, S., & Reik, W. (2004) · Nature Genetics · doi:10.1038/ng1402 · Cited by 556
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays
Yuen, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.10.e48 · Cited by 520
Proximity among Distant Regulatory Elements at the β-Globin Locus Requires GATA-1 and FOG-1
Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., & Blobel, G. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.12.028 · Cited by 490
Self-citationControl of globin gene expression during development and erythroid differentiation
Stamatoyannopoulos, G. (2005) · Experimental Hematology · doi:10.1016/j.exphem.2004.11.007 · Cited by 393
The active spatial organization of the β-globin locus requires the transcription factor EKLF
Drissen, R., Palstra, R.-J., Gillemans, N., Splinter, E., Grosveld, F., Philipsen, S., & de Laat, W. (2004) · Genes & Development · doi:10.1101/gad.317004 · Cited by 352
Fraser, P., Pruzina, S., Antoniou, M., & Grosveld, F. (1993) · Genes & Development · doi:10.1101/gad.7.1.106 · Cited by 231
Bender, M. A., Byron, R., Ragoczy, T., Telling, A., Bulger, M., & Groudine, M. (2006) · Blood · doi:10.1182/blood-2006-04-014431 · Cited by 59 · cited 1×
“However, the functional significance of some of these interactions is not well understood as deletion of some of the elements does not directly affect -globin expression (Bender et al. 2006).”
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Cited by
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Self-citationGREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895
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Metadata
- Authors
- 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., & Dekker, J.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-09-05
- Volume
- 16
- Issue
- 10
- Pages
- 1299-1309
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2009576540
- Cited by
- 1,193
- References
- 11
- Type
- posted content
- Language
- en
- Open access
- bronze
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