X chromosome domain architecture regulates Caenorhabditis elegans lifespan but not dosage compensation [Hi-C]

Mechanisms establishing higher-order chromosome structures and their roles in gene regulation are elusive. We analyzed chromosome architecture during nematode X-chromosome dosage compensation, which represses transcription via a dosage-compensation condensin complex (DCC) that binds hermaphrodite Xs and establishes megabase-size topologically associating domains (TADs). We show that DCC binding at high-occupancy sites (rex sites) defines eight TAD boundary locations. Single rex deletions disrupted boundaries, and single insertions created new boundaries, demonstrating one rex site is necessary and sufficient for DCC-dependent boundary formation. Deleting eight rex sites (8rexΔ) recapitulated TAD structure of DCC mutants, permitting analysis when chromosome-wide domain architecture was disrupted but most DCC binding remained. 8rexΔ animals exhibited no changes in X expression and lacked dosage-compensation mutant phenotypes. Hence, TAD boundaries are neither the cause nor consequence of gene repression during dosage compensation. Abrogating TAD structure did, however, reduce thermotolerance, accelerate aging, and shorten lifespan, implicating chromosome architecture in regulating stress responses and aging. We performed in situ Hi-C on nuclei isolated from mixed stage embryos and processed data as in (Brejc et al., 2017). We performed Hi-C for two biological replicates of wild type, TY5815 rex-47Δ, TY5824 6rexΔ, TY5827 8rexΔ, and TY0810 DCC mutant and a single replicate for TY5818 3rexΔ, TY5868 8rexΔ plus rex-32, TY5872 8rexΔ plus rex-32 & rex-8, TY5854 rex-32 insert, TY5859 3rexΔ plus rex-47 on I, TY5860 3rexΔ plus rex-47 & rex-8 on I, and TY5867 3rexΔ plus rex-14, rex-47 & rex-8 on I.