6.3 TADs are stable across large evolutionary time-scales

In light of the regulatory functions of TADs, such as enhancer sharing and co-expression, we hypothesized that TADs provide essential regulatory environments for genes and are therefore conserved during evolution. More specifically, we asked whether genomic rearrangement between distantly related species would more frequently occur at TAD boundaries or within TAD regions. Furthermore, we hypothesized that disruption of TADs during evolution might be associated with changes in gene expression programs between the species.

We find evolutionary rearrangements between distant vertebrate species highly enriched at TAD boundaries and depleted within TADs (Chapter 3). This is consistent with the enrichment of non-coding sequence conservation in TADs (Harmston et al. 2017; Polychronopoulos et al. 2017). Interestingly, another study investigated the requirement of the ultra-conserved non-coding regions containing enhancers by knock-out experiments in mice (Dickel et al. 2018). Knock-out mice that lack individual or combination of enhancers were viable but showed strong neurological phenotypes. These effects indicate that the remarkably strong sequence conservation, which is also found in TADs, likely results from fitness deficit upon mutations although they appear subtle in a laboratory setting (Dickel et al. 2018). Targeted deletions of strongly conserved TAD boundaries could result in similar effects, but this has to be demonstrated.

Interestingly, genetic variation data across human populations revealed that loci in the same TAD have a reduced recombination rate (Liu et al. 2017). Consistent with this finding, the linkage disequilibrium, which measures co-transmission of genetic variants in populations, correlates with Hi-C interaction frequencies (Gerber et al. 2018). This association indicates functional interactions between alleles in regulatory domains (Liu et al. 2017).

We observed enrichment for expression conservation for genes in TADs and even stronger for genes in conserved TADs. This is somewhat consistent with a recent study, analyzing promoter and enhancer activity in liver samples from 15 species (Berthelot et al. 2017). In this study gene expression conservation could be best explained by the number and conservation of surrounding enhancers and promoters.

In summary, our analysis of genomic rearrangements between human and other species during evolution leads to the conclusion that TADs are essential regulatory building blocks of genomes. This is supported by strong enrichment for non-coding conservation in TADs (Harmston et al. 2017). Furthermore, changes of expression profiles are associated with the disruption of TADs during evolution. This altered regulation upon TAD disruption might be beneficial for an organism and allow evolutionary leaps (as discussed above). However, in most cases, these gene miss-expressions might be detrimental to an organism, as was observed in genetic diseases and cancers (as discussed below). Therefore, we interpret the depletion of evolutionary rearrangements in TADs and the expression change associated with TAD disruption to be a consequence of selective pressure on TAD structures.