Meister, Peter, Statzer, Cyril, Campos, Julie, Ewald, Collin, Semple, Jennifer, Das, Moushumi, Gitchev, Todor
[
International Worm Meeting,
2021]
Recent data in mammalian cells have shown the role of cohesin, a Structural Maintenance of chromosomes (SMC) complex, in interphase genome organization into loops and domains. Since these complexes are involved in cell division, it is difficult to evaluate the functional consequences of their absence in animals. Here we use Caenorhabditis elegans, an animal, 90% of whose cells are post-mitotic at birth. Similarly to mammals, nematodes have three SMC complexes: cohesin, condensin I and condensin II. Additionally, condensin IDC, a variant of condensin I, is involved in dosage compensation (DC). To uncover which SMC complex(es) organize the C. elegans interphase genome and evaluate functional consequences of genome unfolding, we constructed strains in which individual SMC complexes - cohesin, condensin I/IDC and II - are acutely inactivated in vivo in fully differentiated animals. We then assessed their phenotype and carried out chromatin conformation capture (Hi-C) and RNA-seq. Our data shows that in contrast to mammalian cells, the major determinant of genome folding in C. elegans is condensin I/IDC and not cohesin. Its cleavage reduces short-range contact probabilities and causes genome-wide de-compaction on all chromosomes. In contrast, cohesin cleavage has marginal impact while condensin II cleavage has no consequence on genome folding. RNA-seq data show that about a third of expressed genes are significantly differently expressed upon cohesin and condensin II inactivation, however the effect sizes were very small, and a similar number of genes were up and down regulated. In contrast, cleavage of condensin I/IDC leads to up-regulation of 93% of all expressed X-linked genes versus only 1% down regulated, indicating the necessity of the constant presence of condensin IDC for maintenance of DC. Cleavage of cohesin and condensin II has little effect on animal post-embryonic survival, as their lifespan are similar to control animals. In contrast, inactivation of condensin I/IDC causes drastic reduction in life expectancy; yet additional experiments show that lifespan reduction is due to lack of DC rather than genome unfolding. Taken together, we discovered that condensin I is the main SMC complex folding the nematode interphase genome, yet genome unfolding has no major effect in C. elegans in standard laboratory conditions, apart from X-linked gene up-regulation and its consequences.