In eukaryotes transcriptional regulation often involves multiple long-range 
elements and is influenced by the genomic environment. A prime example of this 
concerns the mouse X-inactivation centre (Xic), which orchestrates the 
initiation of X-chromosome inactivation (XCI) by controlling the expression of 
the non-protein-coding Xist transcript. The extent of Xic sequences required for 
the proper regulation of Xist remains unknown. Here we use chromosome 
conformation capture carbon-copy (5C) and super-resolution microscopy to analyse 
the spatial organization of a 4.5-megabases (Mb) region including Xist. We 
discover a series of discrete 200-kilobase to 1 Mb topologically associating 
domains (TADs), present both before and after cell differentiation and on the 
active and inactive X. TADs align with, but do not rely on, several domain-wide 
features of the epigenome, such as H3K27me3 or H3K9me2 blocks and 
lamina-associated domains. TADs also align with coordinately regulated gene 
clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and 
long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit 
illustrates how TADs enable the spatial segregation of oppositely regulated 
chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying 
in adjacent TADs, each containing their known positive regulators. We identify a 
novel distal regulatory region of Tsix within its TAD, which produces a long 
intervening RNA, Linx. In addition to uncovering a new principle of 
cis-regulatory architecture of mammalian chromosomes, our study sets the stage 
for the full genetic dissection of the X-inactivation centre.