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J Vis Exp. 2011 Apr 23;(50). pii: 2621. doi: 10.3791/2621.

Associated chromosome trap for identifying long-range DNA interactions.

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1
Medical Service, VA Palo Alto Health Care System, USA.

Abstract

Genetic information encoded by DNA is organized in a complex and highly regulated chromatin structure. Each chromosome occupies a specific territory, that may change according to stage of development or cell cycle. Gene expression can occur in specialized transcriptional factories where chromatin segments may loop out from various chromosome territories, leading to co-localization of DNA segments which may exist on different chromosomes or far apart on the same chromosome. The Associated Chromosome Trap (ACT) assay provides an effective methodology to identify these long-range DNA associations in an unbiased fashion by extending and modifying the chromosome conformation capture technique. The ACT assay makes it possible for us to investigate mechanisms of transcriptional regulation in trans, and can help explain the relationship of nuclear architecture to gene expression in normal physiology and during disease states.

PMID:
21540824
PMCID:
PMC3169263
DOI:
10.3791/2621
[Indexed for MEDLINE]
Free PMC Article
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