PubMed ID

16954542

UMMS Affiliation

Program in Gene Function and Expression; Department of Biochemistry and Molecular Pharmacology

Date

10-2006

Document Type

Article

Subjects

Base Sequence; Chromatin; Chromosomes, Artificial, Bacterial; DNA Primers; Evaluation Studies as Topic; *Gene Expression Regulation; *Genetic Techniques; Genomics; Globins; Humans; Microarray Analysis; Molecular Sequence Data; Sequence Analysis, DNA

Disciplines

Genetics and Genomics | Life Sciences | Medicine and Health Sciences

Abstract

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 gamma-beta-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.

Comments

Citation: Genome Res. 2006 Oct;16(10):1299-309. Epub 2006 Sep 5. Link to article on publisher's site

©2006 by Cold Spring Harbor Laboratory Press.

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons license(Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

Related Resources

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