The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

Abstract

SummaryGene expression often requires interaction between promoters and distant enhancers, which occur within the context of highly organized topologically associating domains (TADs). Using a series of engineered chromosomal rearrangements at the Shh locus, we carried out an extensive fine-scale characterization of the factors that govern the long-range regulatory interactions controlling Shh expression. We show that Shh enhancers act pervasively, yet not uniformly, throughout the TAD. Importantly, changing intra-TAD distances had no impact on Shh expression. In contrast, inversions disrupting the TAD altered global folding of the region and prevented regulatory contacts in a distance-dependent manner. Our data indicate that the Shh TAD promotes distance-independent contacts between distant regions that would otherwise interact only sporadically, enabling functional communication between them. In large genomes where genomic distances per se can limit regulatory interactions, this function of TADs could be as essential for gene expression as the formation of insulated neighborhoods.

The Three-Dimensional Organization of Mammalian Genomes

“…Similarly, deletion of the centromeric or telomeric boundary of the EPHA4 TAD causes activation of IHH or PAX , leading to brachydactyly or polydactyly, respectively (Lupiáñez et al 2015). By contrast, deletions that do not perturb the TAD boundary had no effect on the expression level of neighboring genes (Lupiáñez et al 2015, Symmons et al 2016). Besides deletions, inversions encompassing a TAD boundary can also bring enhancers and promoters from two different TADs into close proximity and trigger ectopic gene expression (Figure 5 b ).…”

“…Because the TAD plays a critical role in securing promoter-enhancer interactions and limiting interdomain interactions (Symmons et al 2016, Zhan et al 2017), its alteration may also induce ectopic interactions between regulatory elements, leading to gene dysregulation. A number of studies have demonstrated that genetic manipulation of specific TAD boundaries can change the surrounding interaction patterns and can thus affect the expression of nearby genes.…”

Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation

“…Interestingly, it has been recently shown that the position of an enhancer relative to its target within a TAD has no effect on its regulatory potential 66 . These results are consistent with our finding that the relative position of an enhancer relative to its target gene is effectively neutral.…”

Two independent modes of chromatin organization revealed by cohesin removal

“…TADs appear as squares of enriched contact frequency with s harp boundaries; they usually span hundreds of kilobases and do not necessarily exhibit any checkering 7,8 . TADs are thought to contribute to gene expression, notably by promoting or preventing interactions between promoters and distant regulatory elements 9–11 . Finally, peaks (often termed loops 12 ) are visible as focal enrichments in contact frequency between pairs of loci, often at the corner of TAD squares.…”