Unraveling how gene regulations are remodeled during evolution is central to understanding how biological processes evolve. We explored this question in the frame of X-chromosome inactivation, a process under strong selective constraint, governed by the
XIST
lncRNA and its cis-regulators. Using functional approaches on closely related primate species, we show that
XIST
regulation has uniquely diverged over a short evolutionary timescale. In human and marmoset embryonic stem cells (ESCs), the
JPX
lncRNA gene is a major regulator of
XIST
expression. In contrast,
JPX
has a minor effect on
XIST
in macaque ESCs, where it acts together with a macaque-specific enhancer. This occurs within a reshuffled 3D organization of the
XIST
neighborhood triggered by the insertion of a HERVK transposon in the macaque lineage. Retrospective sequence comparisons revealed that many
XIST
regulators are not evolutionarily constrained, supporting the hypothesis that neutrally evolving noncoding elements harbor adaptive potential. These results illuminate how evolutionary recent elements are integrated into preexisting regulatory landscapes.
