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

doi:10.1038/nmeth.2173

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 journal › Article › Academic › peer-review

314 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 language	English
Pages (from-to)	969-972
Number of pages	4
Journal	Nature Methods
Volume	9
Issue number	10
DOIs	https://doi.org/10.1038/nmeth.2173
Publication status	Published - Oct 2012

Bibliographical note

Funding Information:
from the Dutch Scientific Organization (NWO) (91204082 and 935170621), a European Research Council Starting Grant (209700, ‘4C’) and InteGeR FP7 Marie Curie Initial Training Networks contract (no. PITN-GA-2007-214902) to W.d.L., and the Israeli Science Foundation integrated technologies grant to A.T.

Funding Information:
We would like to thank R. Palstra, E. Yaffe and other members of our labs for help and input, G. Geeven for testing the 4C-seq pipeline and H.T. Timmers (Netherlands Proteomics Centre and University Medical Center Utrecht) and J.P.P. Meijerink (Erasmus Medical Center-Sophia Children′s Hospital) for providing cells. This work was supported by grants from the Modelling Hepatocellular Carcinoma (MODHEP) Seventh Framework Program (FP7) collaborative project to W.d.L. and A.T., grants

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title = "Robust 4C-seq data analysis to screen for regulatory DNA interactions",

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.",

author = "\{Van De Werken\}, \{Harmen J.G.\} and Gilad Landan and Holwerda, \{Sjoerd J.B.\} and Michael Hoichman and Petra Klous and Ran Chachik and Erik Splinter and Christian Valdes-Quezada and Yuva {\"O}z and Bouwman, \{Britta A.M.\} and Verstegen, \{Marjon J.A.M.\} and \{De Wit\}, Elzo and Amos Tanay and \{De Laat\}, Wouter",

note = "Funding Information: from the Dutch Scientific Organization (NWO) (91204082 and 935170621), a European Research Council Starting Grant (209700, {\textquoteleft}4C{\textquoteright}) and InteGeR FP7 Marie Curie Initial Training Networks contract (no. PITN-GA-2007-214902) to W.d.L., and the Israeli Science Foundation integrated technologies grant to A.T. Funding Information: We would like to thank R. Palstra, E. Yaffe and other members of our labs for help and input, G. Geeven for testing the 4C-seq pipeline and H.T. Timmers (Netherlands Proteomics Centre and University Medical Center Utrecht) and J.P.P. Meijerink (Erasmus Medical Center-Sophia Children′s Hospital) for providing cells. This work was supported by grants from the Modelling Hepatocellular Carcinoma (MODHEP) Seventh Framework Program (FP7) collaborative project to W.d.L. and A.T., grants",

year = "2012",

month = oct,

doi = "10.1038/nmeth.2173",

language = "English",

volume = "9",

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journal = "Nature Methods",

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AU - Van De Werken, Harmen J.G.

AU - Landan, Gilad

AU - Holwerda, Sjoerd J.B.

AU - Hoichman, Michael

AU - Klous, Petra

AU - Chachik, Ran

AU - Splinter, Erik

AU - Valdes-Quezada, Christian

AU - Öz, Yuva

AU - Bouwman, Britta A.M.

AU - Verstegen, Marjon J.A.M.

AU - De Wit, Elzo

AU - Tanay, Amos

AU - De Laat, Wouter

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AB - 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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JF - Nature Methods

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ER -

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

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