Journal
GENOME RESEARCH
Volume 16, Issue 10, Pages 1299-1309Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.5571506
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Funding
- NCI NIH HHS [CA109597, R01 CA109597] Funding Source: Medline
- NHGRI NIH HHS [HG003129, R01 HG003143, HG003143, R01 HG003129] Funding Source: Medline
- NIGMS NIH HHS [R01 GM078986-01, R01 GM078986, R01GM078986] Funding Source: Medline
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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 beta-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the beta-globin locus. We also identified a new looping interaction in K562 cells between the beta-globin Locus Control Region and the beta-delta-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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