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

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

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

Translated title of the contribution: Robust 4C-seq data analysis to screen for regulatory DNA interactions.

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

Cancer

Research output: Contribution to journal › Article › Academic › 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.

Translated title of the contribution	Robust 4C-seq data analysis to screen for regulatory DNA interactions.
Original language	Undefined/Unknown
Pages (from-to)	969-72
Number of pages	4
Journal	Nature Methods
Volume	9
Issue number	10
Publication status	Published - 2012

Cite this

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

year = "2012",

language = "Undefined/Unknown",

volume = "9",

pages = "969--72",

journal = "Nature Methods",

issn = "1548-7091",

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number = "10",

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TY - JOUR

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.B.

AU - Hoichman, M.

AU - Klous, P.

AU - Chachik, R.

AU - Splinter, E.

AU - Valdes-Quezada, C.

AU - Oz, Y.

AU - Bouwman, B.A.M.

AU - Verstegen, M.J.

AU - de Wit, E.

AU - Tanay, A.

AU - de Laat, W.

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.

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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