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

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

Nature Methods 9, 969 (2012).
doi:10.1038/nmeth.2173

Authors: Harmen J G van de Werken, Gilad Landan, Sjoerd J B Holwerda, Michael Hoichman, Petra Klous, Ran Chachik, Erik Splinter, Christian Valdes-Quezada, Yuva Öz, Britta A M Bouwman, Marjon J A M Verstegen, Elzo de Wit, Amos Tanay & Wouter de Laat
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.