Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

Erik Splinter; Elzo de Wit; Harmen J.G. van de Werken; Petra Klous; Wouter de Laat

doi:10.1016/j.ymeth.2012.04.009

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

Erik Splinter, Elzo de Wit, Harmen J.G. van de Werken, Petra Klous, Wouter de Laat^*

^*Corresponding author for this work

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

175 Citations (Scopus)

Abstract

Chromosome Conformation Capture (3C) and 3C-based technologies are constantly evolving in order to probe nuclear organization with higher depth and resolution. One such method is 4C-technology that allows the investigation of the nuclear environment of a locus of choice. The use of Illumina next generation sequencing as a detection platform for the analysis of 4C data has further improved the sensitivity and resolution of this method. Here we provide a step-by-step protocol for 4C-seq, describing the procedure from the initial template preparation until the final data analysis, interchanged with background information and considerations.

Original language	English
Pages (from-to)	221-230
Number of pages	10
Journal	Methods
Volume	58
Issue number	3
DOIs	https://doi.org/10.1016/j.ymeth.2012.04.009
Publication status	Published - Nov 2012

Bibliographical note

Funding Information:
The authors would like to thank Marieke Simonis and Patrick Wijchers for their contribution to the development of 4C-technology. This work was financially supported by Grants from the Dutch Scientific Organization (NWO) to E.d.W. ( 700.10.402 , ‘Veni’) and to W.d.L. ( 91204082 and 935170621 ), a FP7 Marie Curie ITN ( PITN-GA-2007-214902 ) and a European Research Council Starting Grant ( 209700 , ‘4C’) to W.d.L.

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title = "Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation",

abstract = "Chromosome Conformation Capture (3C) and 3C-based technologies are constantly evolving in order to probe nuclear organization with higher depth and resolution. One such method is 4C-technology that allows the investigation of the nuclear environment of a locus of choice. The use of Illumina next generation sequencing as a detection platform for the analysis of 4C data has further improved the sensitivity and resolution of this method. Here we provide a step-by-step protocol for 4C-seq, describing the procedure from the initial template preparation until the final data analysis, interchanged with background information and considerations.",

author = "Erik Splinter and {de Wit}, Elzo and {van de Werken}, {Harmen J.G.} and Petra Klous and {de Laat}, Wouter",

note = "Funding Information: The authors would like to thank Marieke Simonis and Patrick Wijchers for their contribution to the development of 4C-technology. This work was financially supported by Grants from the Dutch Scientific Organization (NWO) to E.d.W. ( 700.10.402 , {\textquoteleft}Veni{\textquoteright}) and to W.d.L. ( 91204082 and 935170621 ), a FP7 Marie Curie ITN ( PITN-GA-2007-214902 ) and a European Research Council Starting Grant ( 209700 , {\textquoteleft}4C{\textquoteright}) to W.d.L. ",

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doi = "10.1016/j.ymeth.2012.04.009",

language = "English",

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AU - van de Werken, Harmen J.G.

AU - Klous, Petra

AU - de Laat, Wouter

N1 - Funding Information: The authors would like to thank Marieke Simonis and Patrick Wijchers for their contribution to the development of 4C-technology. This work was financially supported by Grants from the Dutch Scientific Organization (NWO) to E.d.W. ( 700.10.402 , ‘Veni’) and to W.d.L. ( 91204082 and 935170621 ), a FP7 Marie Curie ITN ( PITN-GA-2007-214902 ) and a European Research Council Starting Grant ( 209700 , ‘4C’) to W.d.L.

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Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

Abstract

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