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Nat Methods. 2012 Oct;9(10):969-72. doi: 10.1038/nmeth.2173. Epub 2012 Sep 9.

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

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  • 1Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands.


Regulatory DNA elements can control the expression of distant genes via physical interactions. Here we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq). Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.

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