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

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

doi:10.1038/nmeth.2173

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

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

Department of Computer Science and Applied Mathematics

Weizmann Institute of Science

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

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
State	Published - Oct 2012

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.2173

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van de Werken, D. W. H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes-Quezada, C., Oz, Y., Bouwman, B. A. M., Verstegen, M. J. A. M., de Wit, W. E., Tanay, A., & de Laat, L. W. (2012). Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods, 9(10), 969-972. https://doi.org/10.1038/nmeth.2173

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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}, {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 Oz and Bouwman, {Britta A. M.} and Verstegen, {Marjon J. A. M.} and {de Wit}, {Wit, Elzo} and Amos Tanay and {de Laat}, {Laat, Wouter}",

note = "Modelling Hepatocellular Carcinoma (MODHEP) Seventh Framework Program (FP7) collaborative project; Dutch Scientific Organization (NWO) [91204082, 935170621]; European Research Council [209700]; InteGeR FP7 Marie Curie Initial Training Networks [PITN-GA-2007-214902]; Israeli Science FoundationWe 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 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.",

year = "2012",

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doi = "10.1038/nmeth.2173",

language = "الإنجليزيّة",

volume = "9",

pages = "969--972",

journal = "Nature Methods",

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AU - van de Werken, 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 - Oz, Yuva

AU - Bouwman, Britta A. M.

AU - Verstegen, Marjon J. A. M.

AU - de Wit, Wit, Elzo

AU - Tanay, Amos

AU - de Laat, 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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U2 - 10.1038/nmeth.2173

DO - 10.1038/nmeth.2173

M3 - مقالة

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EP - 972

JO - Nature Methods

JF - Nature Methods

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ER -

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

Abstract

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