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Study reveals why women are at greater risk of autoimmune disease
(med.stanford.edu)
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It's an interesting article, and well exposed.
It basically goes to say that the inactivation mechanism (Xist noncoding RNA strand) which gets triggered when there are two X chromosomes present in a cell, almost completely coats one of the X chromosomes, disabling it... but the result is not completely inert, still allowing the attachment of other partial strands, in weird combinations that can lead to an (auto)immune response.