Condensin I folds the Caenorhabditis elegans genome

The structural maintenance of chromosome (SMC) complexes—cohesin and condensins—are crucial for chromosome separation and compaction during cell division. During the interphase, mammalian cohesins additionally fold the genome into loops and domains. Here we show that, in Caenorhabditis elegans , a species with holocentric chromosomes, condensin I is the primary, long-range loop extruder. The loss of condensin I and its X-specific variant, condensin I DC , leads to genome-wide decompaction, chromosome mixing and disappearance of X-specific topologically associating domains, while reinforcing fine-scale epigenomic compartments. In addition, condensin I/I DC inactivation led to the upregulation of X-linked genes and unveiled nuclear bodies grouping together binding sites for the X-targeting loading complex of condensin I DC . C. elegans condensin I/I DC thus uniquely organizes holocentric interphase chromosomes, akin to cohesin in mammals, as well as regulates X-chromosome gene expression. Inactivation of somatic SMC complexes in Caenorhabditis elegans shows that condensin I is the major long-range genome loop extruder, while cohesin forms small loops. Inactivation of cohesin, condensin II and condensin I/I DC causes minor transcriptional changes in autosomes.