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

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 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

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10.1038/nmeth.2173

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Van De Werken, Harmen J.G. ; Landan, Gilad ; Holwerda, Sjoerd J.B. ; Hoichman, Michael ; Klous, Petra ; Chachik, Ran ; Splinter, Erik ; Valdes-Quezada, Christian ; Öz, Yuva ; Bouwman, Britta A.M. ; Verstegen, Marjon J.A.M. ; De Wit, Elzo ; Tanay, Amos ; De Laat, Wouter. / Robust 4C-seq data analysis to screen for regulatory DNA interactions. In: Nature Methods. 2012 ; Vol. 9, No. 10. pp. 969-972.

@article{2097bafa9e324f60a09b1ef9bf392ada,

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",

pages = "969--972",

journal = "Nature Methods",

issn = "1548-7091",

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number = "10",

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Robust 4C-seq data analysis to screen for regulatory DNA interactions. / Van De Werken, Harmen J.G.; Landan, Gilad; Holwerda, Sjoerd J.B.; Hoichman, Michael; Klous, Petra; Chachik, Ran; Splinter, Erik; Valdes-Quezada, Christian; Öz, Yuva; Bouwman, Britta A.M.; Verstegen, Marjon J.A.M.; De Wit, Elzo; Tanay, Amos; De Laat, Wouter.

In: Nature Methods, Vol. 9, No. 10, 10.2012, p. 969-972.

Research output: Contribution to journal › Article › Academic › peer-review

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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

SN - 1548-7091

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

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