Rowlands, H. J.; Peyton-Jones, M.; Robertson, D.; Webb, S.; Spanos, C.; Marston, A. L.

Cohesin organises chromosomes through loop extrusion, yet how cohesin loading is targeted to specific genomic regions to shape chromosome architecture remains poorly understood. Here, we identify a conserved mechanism that directs cohesin loading to specialised chromosomal domains in Schizosaccharomyces pombe. Mutation of a conserved interaction surface in the cohesin loader Scc4/Ssl3 abolishes cohesin enrichment at centromeres and ribosomal DNA while largely preserving cohesin levels along chromosome arms, demonstrating that domain-specific accumulation depends on targeted recruitment rather than global loading capacity. We further identify the nucleolar protein Dnt1 as a receptor for cohesin loading at rDNA and show that it is required for proper organisation of this domain. High-resolution MicroC-XL maps reveal that targeted cohesin loading positions loop-based interactions within pericentromeres and rDNA without disrupting larger-scale domain boundaries. Together, these findings show that domain-specific receptors acting through a conserved loader interface direct cohesin positioning and identify targeted loading as a conserved organising principle for specialised chromosomal domains.