The three-dimensional organization of a genome plays a critical role in 
regulating gene expression, yet little is known about the machinery and 
mechanisms that determine higher-order chromosome structure. Here we perform 
genome-wide chromosome conformation capture analysis, fluorescent in situ 
hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) 
maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage 
compensation, which balances gene expression between XX hermaphrodites and XO 
males. The dosage compensation complex (DCC), a condensin complex, binds to both 
hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex 
sites) to reduce chromosome-wide gene expression by half. Most DCC condensin 
subunits also act in other condensin complexes to control the compaction and 
resolution of all mitotic and meiotic chromosomes. By comparing chromosome 
structure in wild-type and DCC-defective embryos, we show that the DCC remodels 
hermaphrodite X chromosomes into a sex-specific spatial conformation distinct 
from autosomes. Dosage-compensated X chromosomes consist of self-interacting 
domains (∼1 Mb) resembling mammalian topologically associating domains (TADs). 
TADs on X chromosomes have stronger boundaries and more regular spacing than on 
autosomes. Many TAD boundaries on X chromosomes coincide with the 
highest-affinity rex sites and become diminished or lost in DCC-defective 
mutants, thereby converting the topology of X to a conformation resembling 
autosomes. rex sites engage in DCC-dependent long-range interactions, with the 
most frequent interactions occurring between rex sites at DCC-dependent TAD 
boundaries. These results imply that the DCC reshapes the topology of X 
chromosomes by forming new TAD boundaries and reinforcing weak boundaries 
through interactions between its highest-affinity binding sites. As this model 
predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary 
using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a 
distinct higher-order structure onto X chromosomes while regulating gene 
expression chromosome-wide.