A practical metaphase marker of the inactive X chromosome

It is paradoxical that the inactivated X is the only chromosome that can be identified in the interphase nucleus, yet in metaphase, it is indistinguishable from its genetically active homolog unless special culture and staining procedures are employed. A specific inactivation-associated fold in proximal Xq resolves that paradox. We describe here how the fold in the proximal long arm can be used as a simple and reliable marker to identify the inactivated X in G-, Q-, or R-banded preparations. Several examples are given, including localization of the inactivation center to band Xq13 or q21.1, identification of nonrandom inactivation in X-chromosome rearrangements, identification of multiple active X chromosomes in tumor cell lines, analysis of X-inactivation patterns in female carriers of the fragile site at Xq27, and comparison of X-inactivation patterns among primate species.