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

H.J. van de Werken, G. Landan, S.J. Holwerda, M. Hoichman, P. Klous, R. Chachik, E. Splinter, C. Valdes-Quezada, Y. Oz, B.A. Bouwman, M.J. Verstegen, E. de Wit, A. Tanay, W. de Laat

Research output: Contribution to journal/periodicalArticleScientificpeer-review

293 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
JournalNature Methods
Volume9
Issue number10
DOIs
Publication statusPublished - 2012

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