Chromatin Domains: The Unit of Chromosome Organization

Abstract

How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the existence of chromatin domains and loops as a pervasive feature of interphase chromosomes, but the biological implications of such organizational features were obscure. Genome-wide analysis of pair-wise chromatin interactions using chromatin conformation capture (3C)-based techniques has shed new light on the organization of chromosomes in interphase nuclei. Particularly, the finding of cell-type invariant, evolutionarily conserved topologically associating domains (TADs) in a broad spectrum of cell types has provided a new molecular framework for the study of animal development and human diseases. Here, we review recent progress in characterization of such chromatin domains and delineation of mechanisms of their formation in animal cells.

Figure 1. Converging evidence of chromatin domains in animal cells

A) BrdU pulse-chase labeling followed by immunofluorescence imaging showed that replicon clusters are stable over many cell divisions. A schematic of replication clusters in the nucleus as visualized immediately or 5 days and 10 days after BrdU labeling are shown. The replication clusters remain together even after multiple cell divisions. Image data from Jackson & Pombo (1998). B) Maps of replication domains and chromatin interactions by Repli-chip and Hi-C, respectively, show one-to-one correspondence between replication domains and TADs. A schematic of TADs is on the right. Figure adopted from Pope et al. (2014).

Figure 2. Hierarchical organization of TADS

A) Interaction heat map of one TAD located near the HoxA locus in GM12878 lymphoblastoid cells from Rao et al. (2014) at 10kb resolution. Also shown below are ChIP-seq tracks from ENCODE and the GC content over the region. Note that the interaction heat map within the TAD has multiple points where the signal is enriched locally, indicative of local “looping” structures. Within the larger TAD there appears to be the presence of multiple smaller sub-TADs and individual loops. B) Diagram of how hierarchical organization within TADs may occur using simulated data. On the top is a heat map of a single TAD with several smaller internal sub-TADs or loops. In the “multimeric association” example, the TAD in each individual cells represents a complex structure consisting of multiple loops or subdomains that would individually largely reflect the population average. In the “probabilistic association of loops example,” individual cells would variable contain single loops or subdomains, and that the population average would reflex a mixture of these single cell structures. In this case, a TAD would represent a region of the genome with increased probability of forming loops or domains within single cells. C) Polymer models of internal TAD structure from Giorgetti et al (2014) indicate that at least in some TADs there is variability in the internal TAD organization from cell to cell.

Figure 3. Function of TADs in genome regulation

A) Example diagram showing the co-regulation of multiple genes by a single regulatory element within a TAD. B) Interaction heat map showing a single TAD encompassing a cluster of olfactory receptor genes (data from Dixon et al. 2015) C) Diagram of the potential for TAD boundaries to serve an enhancer blocking role that restricts enhancers to target genes within the same TAD. D) Diagram of the potential for TAD boundaries to restrict the spread of repressive chromatin into active domains and vice versa. E) Diagram of the role of TADs in forming a barrier to divergent transcriptional “noise” in the genome.

Figure 4. A Strings and Binders Switch model to describe the processes shaping chromatin organization

Chromatin fiber is modeled as a self-avoiding polymer (blue) with binding sites for Brownian binder particles (red) with concentration (c_m) and multiple binding sites on the polymer. Mont Carlo simulation of the polymer and binders leads to three stable states of organization reflecting an open conformation, a fractal conformation and a compact conformation. Figure adopted from Barbieri et al. (2012) and Pombo & Dillon (2015).

Figure 5. Two models for TAD formation

(A) A hand-cuff model describing the formation of TADs by CTCF ad Cohesin complex connecting the two boundary sequences together. (B) The “extrusion” model involves a pair of tethered CTCF proteins bound to chromatin motors that propel the extrusion of chromatin fiber while the two CTCF molecules slide the chromatin fiber in opposite directions before pausing at converging CTCF DNA binding motifs (Red).

Figure 6. Chromatin stiffness may create insulation at TAD boundaries

Diagrammatic representation of a chromatin fiber (blue) spanning two adjacent TADs and the boundary region between them. According to this model, chromatin at the TAD boundary region is less flexible than chromatin in the TAD body, as depicted in the two boxes above the chromatin fiber. The low flexibility of chromatin at the TAD boundary could inhibit interaction between regions on opposite sides of the boundary. Chromatin flexibility may be modulated by nucleosome spacing, as dictated by functional elements including CTCF binding sites and gene promoters. However, chromatin flexibility may be modulated by other properties in addition to or instead of nucleosome spacing. Nucleosomes are represented as orange circles on the chromatin fiber. They are not drawn to scale, as they are intended only to convey that variation in nucleosome spacing occurs along the chromatin fiber. Additional tracks are shown below the chromatin fiber for conceptual representation: “Interaction frequency” shows example Hi-C data from a region with a distinct TAD boundary. The “Insulation” track reflects a defining property of TAD boundaries – there are relatively few interactions that cross TAD boundaries, and thus insulation at TAD boundaries is high. “CTCF” and “Housekeeping gene TSS” tracks depict features typically found at TAD boundaries. The “other sequences?” track is meant to convey the idea that unknown sequence features may also contribute to TAD formation.