Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
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DOI：
10.1101/gr.5571506
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发表时间：
2006-10-01
期刊：
影响因子：
7
通讯作者：
Dekker, Job
中科院分区：
文献类型：
--
作者：
Dostie, Josee;Richmond, Todd A.;Dekker, Job
位于整个基因组中的遗传因素之间的物理相互作用在基因调节中起重要作用，并且可以通过染色体构象捕获（3C）方法来识别。 3C将物理染色质相互作用转换为特定的连接产物，这些结扎产物通过PCR单独量化。在这里，我们提出了使用454-TECHNOLOGY作为检测方法采用微阵列或定量DNA测序的高通量3C方法，即3C碳副本（5C）。我们应用5C分析了一个400-kb区域，该区域包含人β-珠蛋白基因座和100 kb保守的基因沙漠区域。我们通过检测β-珠蛋白基因座中的几种先前鉴定的循环相互作用来验证5C。我们还确定了β-珠蛋白基因座控制区域和β-戴尔塔 - 珠蛋白间基因间区域之间K562细胞中的新循环相互作用。有趣的是，该区域与发育环蛋白基因转换的控制有关。 5C应广泛适用于基因组元素的顺式和反相互作用网络的大规模映射以及高阶染色体结构的研究。
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.