1.6 Evolution of chromatin organization

While TADs were initially described for mammalian genomes, a similar domain organization was found in the genomes of non-mammalian species such as Drosophila (Sexton et al. 2012), zebrafish (Gómez-Marín et al. 2015) Caenorhabditis elegans (Crane et al. 2015) and yeast (Hsieh et al. 2015; Mizuguchi et al. 2014). However, in C. elegans, TADs were only observed on the X chromosome of XX hermaphrodites and not on autosomes (Crane et al. 2015). The small and compact genome with most of the cis-regulatory information within 10kb from the TSS might not need long-range domains for gene regulation (Long et al. 2016). In contrast, plants have long-range cell-type specific enhancers (Zhu et al. 2015), but TAD like structures could not be observed in Hi-C experiments in A. thaliana. Interestingly, both C.elegans and A.thaliana do not encode a CTCF homolog (Heger et al. 2012), suggesting alternative mechanisms of genome organization and segmentation in these species (Long et al. 2016). TAD-like structures are therefore not required for eukaryotic interphase chromosome folding. Nevertheless, Hi-C experiments in bacteria and yeast suggest that self-interacting domains may be an ancient feature of chromosome organization. Hi-C data in Caulobacter cells revealed so-called chromosomally interacting domains (CIDs) of 30 to 420 kb in size (Le et al. 2013). In fission yeast S. pombe, globule structures at the 40-100 kb scale were identified and depend on cohesin complex (Mizuguchi et al. 2014). Furthermore, in very short CIDs of around 2-10 kb were detected in S.cerevisiae and bounded by highly transcribed genes (Hsieh et al. 2015).

In summary, TAD like structures have been detected in many organisms, including files, worms, fungi, and bacteria, but variations in size and internal structure indicate differences in their formation and biological functions (Dekker and Heard 2015). Further high-resolution experiments in more diverse species are needed to understand the evolutionary origin of genome segregation into TAD-like structures.

The presence of domain-like structures in diverse species across the tree of life leads to the question if not only the genomic sequence but also its folding structure is conserved between species. Interestingly, TADs are not only mostly stable across different cell-types (Dixon et al. 2012; Rao et al. 2014) and during differentiation (Dixon et al. 2015), but also remarkably similar between homologous regions in mouse and human (Dixon et al. 2012). About half of the TAD boundaries identified in human hESC cells occur at homologous genomic positions in mouse ESCs (Dixon et al. 2012). A similar fraction of contact domains was detected at homologous genomic locations in mouse and human lymphoblastoid cells (Rao et al. 2014). Another study could trace back a single TAD boundary at the Six gene loci to the origin of deuterostomes (Gómez-Marín et al. 2015). However, these analyses focused only on the subset of syntenic regions between genomes and therefore, do not allow conclusions about disruptions or the conservation of TADs by chromosomal rearrangements between species.

During evolution, the genome sequence underwent several types of mutations. While single nucleotide mutations only alter a single DNA base at a time, structural variants modify larger chromosomal regions by deletions, duplications, inversions, or translocations. Thereby deletions and duplications can alter the copy number of genes. The breakpoint of such rearrangements can also lead to disruption of genes or gene fusion. However, rearrangement breakpoints can also alter the regulatory environment of genes by disrupting regulatory regions, such as enhancers, or their interactions. Comparative genomic analysis of two species can identify evolutionary rearrangements by altered adjacencies of orthologous genes.

Initial comparative Hi-C studies identified several evolutionary breakpoints at TAD boundaries and highlighted an important role of conserved CTCF binding sites in facilitating conservation of TADs (Vietri Rudan et al. 2015). However, it remains to be investigated systematically if TAD regions as a whole might be stable or disrupted by rearrangements during evolution and how this is associated with conserved or divergent transcriptional regulation between species.