Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?

Abstract

We discuss here a series of testable hypotheses concerning the role of chromosome folding into topologically associating domains (TADs). Several lines of evidence suggest that segmental packaging of chromosomal neighborhoods may underlie features of chromatin that span large domains, such as heterochromatin blocks, association with the nuclear lamina and replication timing. By defining which DNA elements preferentially contact each other, the segmentation of chromosomes into TADs may also underlie many properties of long-range transcriptional regulation. Several observations suggest that TADs can indeed provide a structural basis to regulatory landscapes, by controlling enhancer sharing and allocation. We also discuss how TADs may shape the evolution of chromosomes, by causing maintenance of synteny over large chromosomal segments. Finally we suggest a series of experiments to challenge these ideas and provide concrete examples illustrating how they could be practically applied.

Keywords: chromatin domains; chromatin folding; chromosome conformation capture (3C); long-range transcriptional regulation; regulatory landscapes; topologically associating chromosome domains.

Figure 1

Scales of genome architecture. The folding rules of the genome are hierarchical, with different principles applying at each scale. Local DNA contacts, by means of looping or other configurations, play a central role in controlling the communication between enhancers and promoters. These contacts most often take place within TADs, which define what groups of sequences cluster together. Relative arrangement of TADs then shapes the chromosome territory, within which transcriptionally competent regions are typically segregated away from the transcriptionally inert ones. Within the nucleus each chromosome tends to occupy a preferential radial position, sometimes depending on the cell type.

Figure 2

The Link between TADs and domain-wide chromatin features. The positions of TADs along chromosomes align with several types of domain structures that suggest a possible mechanistic link between the two. We hypothesize that these mechanisms can rely on local three-dimensional diffusion sites A: histone methyl-transferases (HMT) or B: histone kinases (HK) from primary recruitment sites. C: Mechanistic cross-talk, such as for example between the polycomb and DNA methyl-transferase machineries (DNMTs), could explain the indirect correspondence with other types of domains such as partially DNA methylated domains. TADs may therefore represent modular units of chromosomes that can assume different structural fates. For example D: LADs are found to correspond to TADs, and their developmental dynamics could be explained by the repositioning of TADs to or away from the nuclear envelope. E: Similarly, even though most replication domains overlap multiple TADs, changes in timing during cell differentiation typically involve TAD-sized regions. Data are from published sources for H3K27me3 , γH2AX , Bisulfite (Bi)-seq , LaminB1 and replication timing , and TADs –.

Figure 3

The link between TADs and domain-wide transcriptional regulation. Folding into TADs fosters long-range transcriptional regulation by allowing distal sequences to frequently contact each other. Folding into TADs allows A: multiple regulatory sequences to target the same promoter and conversely, B: multiple promoters to be targeted by a given regulatory element. C: Spatial partitioning segregates neighboring regulatory domains, allowing juxtaposed clusters to assume opposite transcriptional fates upon response to a stimulus. D: Activation of a regulatory element within a TAD can have minor yet measurable effects on secondary promoter targets, possibly explaining ripple effects of transcriptional activation. E: Elements controlling chromatin architecture or transcriptional activity can be distinct. When separate, architectural elements will control access of the transcription-controlling element to its target promoter, thereby playing an indirect but nonetheless integral role in the regulation of transcriptional activity.

Figure 4

TAD-driven Mb-wide synteny. Synteny breaks within TADs would be expected to be counter-selected in general because they would disrupt underlying cis-regulatory connections. Such a phenomenon would lead to synteny of large chromosomal regions corresponding to groups of TADs, or even single TADs, with macrosynteny breaks occurring close to their boundaries. Expansion or retraction of these macrosyntenic regions can be observed, so that syntenic TADs or groups of TADs do not necessarily have the same genomic size in different species. The example shown here is illustrative.

Figure 5

Experimental strategies to disrupt folding into TAD. Chromosome engineering could be used in various ways to alter TAD architecture and study the effects on domain-wide chromatin features and long-range regulation. For example, disrupting a TAD boundary separating two chromatin domains or inserting a boundary within a chromatin domain could be used to address the role of spatial organization in defining segmental chromatin blocks. Inversion around a TAD boundary or ectopic insertion within a TAD could be used to test to what extent DNA sequences are autonomous in setting up their chromatin state and to what extent they are influenced by the chromatin state of their TAD. The same experiments could be used to address the role that folding into TADs plays at the level of long-range transcriptional regulation.