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Nuclear compartments have diverse roles in regulating gene expression, yet the molecular forces and components that drive compartment formation remain largely unclear
1
. The long non-coding RNA
Xist
establishes an intra-chromosomal compartment by localizing at a high concentration in a territory spatially close to its transcription locus
2
and binding diverse proteins
3
–
5
to achieve X-chromosome inactivation (XCI)
6
,
7
. The XCI process therefore serves as a paradigm for understanding how RNA-mediated recruitment of various proteins induces a functional compartment. The properties of the inactive X (Xi)-compartment are known to change over time, because after initial
Xist
spreading and transcriptional shutoff a state is reached in which gene silencing remains stable even if
Xist
is turned off
8
. Here we show that the
Xist
RNA-binding proteins PTBP1
9
, MATR3
10
, TDP-43
11
and CELF1
12
assemble on the multivalent E-repeat element of
Xist
7
and, via self-aggregation and heterotypic protein–protein interactions, form a condensate
1
in the Xi. This condensate is required for gene silencing and for the anchoring of
Xist
to the Xi territory, and can be sustained in the absence of
Xist
. Notably, these E-repeat-binding proteins become essential coincident with transition to the
Xist-
independent XCI phase
8
, indicating that the condensate seeded by the E-repeat underlies the developmental switch from
Xist
-dependence to
Xist
-independence. Taken together, our data show that
Xist
forms the Xi compartment by seeding a heteromeric condensate that consists of ubiquitous RNA-binding proteins, revealing an unanticipated mechanism for heritable gene silencing.
A protein condensate formed by multivalent interactions between the long non-coding RNA Xist and specific RNA-binding proteins drives the compartmentalization required to perpetuate gene silencing on the inactive X chromosome.