Chromosome conformation capture technologies and their impact in understanding genome function

Abstract

It has been more than a decade since the first chromosome conformation capture (3C) assay was described. The assay was originally devised to measure the frequency with which two genomic loci interact within the three-dimensional (3D) nuclear space. Over time, this method has evolved both qualitatively and quantitatively, from detection of pairwise interaction of two unique loci to generating maps for the global chromatin interactome. Combined with the analysis of the epigenetic chromatin context, these advances led to the unmasking of general genome folding principles. The evolution of 3C-based methods has been supported first by the revolution in ChIP and then by sequencingbased approaches, methods that were primarily tools to study the unidimensional genome. The gradual improvement of 3C-based methods illustrates how the field adapted to the need to gradually address more subtle questions, beginning with enquiries of reductionist nature to reach more holistic perspectives, as the technology advanced, in a process that is greatly improving our knowledge on genome behavior and regulation. Here, we describe the evolution of 3C and other 3C-based methods for the analysis of chromatin interactions, along with a brief summary of their contribution in uncovering the significance of the threedimensional world within the nucleus. We also discuss their inherent limitations and caveats in order to provide a critical view of the power and the limits of this technology.

Recent advances in high-throughput approaches to dissect enhancer function

“…One main limitation of these approaches remains the fact that they do not provide direct information towards uncovering enhancer target genes. Therefore, the combination of enhancer assays with recently developed 3C-related methodologies, such as 4C-seq, Hi-C or Capture Hi-C 49 , should greatly facilitate the assignment of discovered enhancers to their putative target genes. Finally, with the expected decrease in the cost of sequencing and oligo synthesis, it will be possible to systematically test the impact of regulatory variants in different diseases and developmental contexts.…”

On TADs and LADs: Spatial Control Over Gene Expression

“…Large multicomponent complexes [ 5 9 _ T D $ D I F F ] facilitate long-range interactions, [ 6 0 _ T D $ D I F F ] forming [ 6 1 _ T D $ D I F F ] both intrachromosomal loops [ 6 2 _ T D $ D I F F ] and interchromosomal contacts. A decade ago, a method was developed that monitors the likelihood of sequencesequence [ 6 3 _ T D $ D I F F ] proximity in nuclei, namely chromosome conformation capture (3C) [1], from which several related techniques such as genome-wide 3C (Hi-C) were elaborated (reviewed in [2,3]). These techniques have improved both the resolution and sensitivity of the assay for [ 6 4 _ T D $ D I F F ] contact between sequences at very long range, allowing one to identify chromatin subdomains that share[ 3 _ T D $ D I F F ] 3D space.…”

Three-Dimensional Genome Organization and Function in Drosophila

“…Recently, different variants of the Hi-C method have been applied in different species, both in the eukaryote and the prokaryote domains. Each of these variants has advantages and limitations, which should be carefully considered when designing experiments and interpreting their results, as reviewed and discussed elsewhere (Sati and Cavalli 2016). However, the existing work shows that Hi-C is a powerful and robust method, which enables reliably detecting chromatin interactions even when present in only a few percent of the cells in the sample, as in the case of very long-distance interactions in the same (Sexton et al 2012) or in different chromosomes (Schoenfelder et al 2015).…”