Atypical genome folding and gene regulation by SMC complexes in the nematode C. elegans
In the majority of species studied thus far, chromosomes are organized into topologically associated domains (TADs). TAD formation depends on between cohesin, a member of the structural maintenance of chromosome (SMC) complexes family, and boundary sequence elements recognized by transcription factors. TADs are highly conserved across different cell types or species in syntenic regions and are crucial for regulating transcription by restricting the search space of enhancers for target promoters. However, in nematodes, TADs have not been detected in chromosome conformation studies, except on the dosage compensated X chromosomes.
To understand how the nematode genome is folded and how this folding regulates gene expression, we systematically assessed the function of each SMC complex using an inducible cleavage system – cohesin, condensin I and condensin II. Surprisingly, we found that in nematodes, cohesin is functionally replaced by condensin I for long-range chromatin looping. Additionally, we discovered an X-specific looping compartment that aggregates X-specific TAD boundaries, which resembles phase-separated superenhancers described in mammalian cells. This raised the question of the function of cohesins in C. elegans.
The pentameric cohesin complex plays two roles in mammals: sister chromatid cohesion during mitosis and chromatin looping during interphase. In nematodes, these two functions are split between two cohesin isoforms that differ by a single subunit. Our study found that the interphasic cohesin complex is crucial for the formation of 3D hairpin structures that extend from previously characterized enhancer sequences by 10-50 kb, structures which were previously named fountains or jets. Fountains are specific to active enhancers, accumulate the major interphasic cohesin, and disappear when the latter is cleaved in vivo. Additionally, fountains accumulate topological constraints, bind topoisomerases and the negatively supercoiled DNA binder psoralen. Functionally, the disappearance of fountains correlates with active enhancer-proximal gene activation and changes in splicing isoforms for more than 120 genes. Together, this suggests that fountains play a similar role to TADs in directing enhancer-promoter interactions, highlighting an alternative role for cohesin in the regulation of gene expression.
Institute of Cell Biology - University of Bern