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

doi:10.1038/NMETH.2173

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

Hubrecht Institute

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

301 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
Journal	Nature Methods
Volume	9
Issue number	10
DOIs	https://doi.org/10.1038/NMETH.2173
Publication status	Published - 2012

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

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doi = "10.1038/NMETH.2173",

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T1 - Robust 4C-seq data analysis to screen for regulatory DNA interactions

AU - van de Werken, H.J.

AU - Landan, G.

AU - Holwerda, S.J.

AU - Hoichman, M.

AU - Klous, P.

AU - Chachik, R.

AU - Splinter, E.

AU - Valdes-Quezada, C.

AU - Oz, Y.

AU - Bouwman, B.A.

AU - Verstegen, M.J.

AU - de Wit, E.

AU - Tanay, A.

AU - de Laat, W.

N1 - Reporting year: 2012

PY - 2012

Y1 - 2012

N2 - 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.

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.

U2 - 10.1038/NMETH.2173

DO - 10.1038/NMETH.2173

M3 - Article

SN - 1548-7091

VL - 9

SP - 969

EP - 972

JO - Nature Methods

JF - Nature Methods

IS - 10

ER -

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

Abstract

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