Abstract
Chromosome conformation capture (3C) technology and its derivatives are currently the primary methodologies measuring contacts among genomic elements. In fact, the lion share of what is currently known about chromosome folding is based on 3C-related approaches. For example, distal enhancers are commonly in physically proximity with their target genes, forming chromatin loops. Additional layers of chromatin organization have been described using 3C-based techniques, including topological domains (TADs) and sub-TADs. Finally, inter-chromosomal interactions have been reported although they are much less frequent. 3C is becoming increasingly widespread in its use for understanding genome organization. Here we provide a protocol for quantitative 3C using real-time PCR analysis, along with essential quality controls and normalization methods.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Dekker J (2002) Capturing chromosome conformation. Science 295:1306–1311
Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293
Li G, Fullwood MJ, Xu H et al (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11:R22
van de Werken HJG, Landan G, Holwerda SJB et al (2012) Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Meth 9:969–972
Hughes JR, Roberts N, McGowan S et al (2014) Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 46:205–212
Nagano T, Lubling Y, Stevens TJ et al (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–64
Rao SSP, Huntley MH, Durand NC et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Deng, W., Blobel, G.A. (2017). Detecting Long-Range Enhancer–Promoter Interactions by Quantitative Chromosome Conformation Capture. In: Ørom, U. (eds) Enhancer RNAs. Methods in Molecular Biology, vol 1468. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-4035-6_6
Download citation
DOI: https://doi.org/10.1007/978-1-4939-4035-6_6
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-4033-2
Online ISBN: 978-1-4939-4035-6
eBook Packages: Springer Protocols