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

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

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

254 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)969-972
Number of pages4
JournalNature Methods
Volume9
Issue number10
DOIs
Publication statusPublished - Oct 2012

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