Protocol

Gene Regulatory Networks

Volume 786 of the series Methods in Molecular Biology pp 211-225

Date:

Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method

  • Nele GheldofAffiliated withCenter for Integrative Genomics, University of Lausanne, Le Génopode, Quartier UNIL-Sorge Email author 
  • , Marion LeleuAffiliated withSchool of Life Sciences and Bioinformatics and Biostatistics Core Facility, Swiss Institute of Bioinformatics, Ecole Polytechnique Fédérale (EPFL)
  • , Daan NoordermeerAffiliated withSchool of Life Sciences, Ecole Polytechnique Fédérale (EPFL)
  • , Jacques RougemontAffiliated withBioinformatics and Biostatistics Core Facility, Swiss Institute of Bioinformatics, Ecole Polytechnique Fédérale (EPFL)
  • , Alexandre ReymondAffiliated withCenter for Integrative Genomics, University of Lausanne, Le Génopode, Quartier UNIL-Sorge

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Abstract

Eukaryotic transcription is tightly regulated by transcriptional regulatory elements, even though these elements may be located far away from their target genes. It is now widely recognized that these regulatory elements can be brought in close proximity through the formation of chromatin loops, and that these loops are crucial for transcriptional regulation of their target genes. The chromosome conformation capture (3C) technique presents a snapshot of long-range interactions, by fixing physically interacting elements with formaldehyde, digestion of the DNA, and ligation to obtain a library of unique ligation products. Recently, several large-scale modifications to the 3C technique have been presented. Here, we describe chromosome conformation capture sequencing (4C-seq), a high-throughput version of the 3C technique that combines the 3C-on-chip (4C) protocol with next-generation Illumina sequencing. The method is presented for use in mammalian cell lines, but can be adapted to use in mammalian tissues and any other eukaryotic genome.

Key words

Chromosome conformation capture Looping interactions Interactome Regulatory elements