Chromatin globules: a common motif of higher order chromosome structure?

Abstract

Recent technological advances in the field of chromosome conformation capture are facilitating tremendous progress in the ability to map the three-dimensional (3D) organization of chromosomes at a resolution of several Kb and at the scale of complete genomes. Here we review progress in analyzing chromosome organization in human cells by building 3D models of chromatin based on comprehensive chromatin interaction datasets. We describe recent experiments that suggest that long-range interactions between active functional elements are sufficient to drive folding of local chromatin domains into compact globular states. We propose that chromatin globules are commonly formed along chromosomes, in a cell type specific pattern, as a result of frequent long-range interactions among active genes and nearby regulatory elements. Further, we speculate that increasingly longer range interactions can drive aggregation of groups of globular domains. This process would yield a compartmentalized chromosome conformation, consistent with recent observations obtained with genome-wide chromatin interaction mapping.

Figure 1. 3C-based methods

All 3C-based methods use the same principle of chromatin interaction detection (indicated in grey): cross-linking of interacting loci with formaldehyde, followed by DNA fragmentation, DNA ligation, DNA purification and finally ligation product detection. 3C employs restriction enzymes to fragment DNA, and regular PCR to detect ligation products, while 4C employs inverse PCR to detect all fragments ligated to a locus of choice. 5C uses multiplexed ligation mediated amplification (LMA) to detect large numbers of interactions simultaneously using pools of primers for thousands of loci of interest. CHiA-PET employs sonication to fragment cross-linked chromatin followed by an immunoprecipitation step prior to DNA ligation to enrich for loci bound by a protein of interest. Linkers are then ligated (black thick lines) and DNA is analyzed by direct deep sequencing. Finally, Hi-C employs restriction enzymes to fragment chromatin followed by filling in of the staggered ends using biotinylated nucleotides prior to DNA ligation. DNA is sheared and DNA fragments containing ligation junctions are purified using streptavidin-coated beads. DNA is then directly deep sequenced.

Figure 2. 3D model of the α-globin gene domain in lymphoblastoid cells reveals a globular domain

A. Chromatin globule formed by the 500 Kb α-globin gene containing domain in lymphoblastoid cells (From [14]). Long-range interactions between genes and elements such as enhancers and insulators lead to a collapse of the fiber to form a compact chromatin globule. B. 3D model of the α-globin gene containing domain in the absence of looping interactions. A theoretical 5C interaction map was calculated assuming a freely jointed chain, and a 3D model was calculated exactly as in A and as described in [14]. The model accurately reproduces the expected relationship between genomic distance between loci and spatial distance for a freely jointed chain [(spatial distance)² ∼ genomic distance] (inset: Black dots: observed data; Red line: expected relationship) [11]. Deviations from this expected relationship are observed for smaller genomic distances, consistent with the fact that the feely jointed chain model is only valid for long-range interactions between sites separated by several times the persistence length of the fiber.

Figure 3. Chromatin globules as a first building block of chromosome conformation

Hierarchical model of chromosome organization, driven by globule formation, and interactions between globules.