Reverse replication timing for the XIST gene in human fibroblasts.

The timing of DNA replication appears to be an important epigenetic regulator of gene expression during development. Replication of active genes in expressing tissues occurs earlier than does replication of their inactive counterparts in nonexpressing tissues. This pattern is also observed for active and inactive alleles present in the same cell, as exemplified by genes subject to X chromosome inactivation in females. We find that the replication timing of the X-linked XIST gene in normal human fibroblasts provides a striking exception to this well-established pattern. Within the same cell, the expressed allele of XIST replicates late in S phase and the silent allele replicates early. This 'reverse' replication timing may have functional significance with respect to XIST or could be a passive consequence of the replication timing requirements of neighboring genes that are subject to X chromosome inactivation. Our finding of early replication for XIST in male fibroblasts contrasts with a report of late replication in such cells as determined by an in situ hybridization method [Torchia et al., (1994) Am. J. Hum. Genet. 55, 96-104]. We propose that our data and those obtained by the in situ method can be accommodated by the existence of structural features that differ between the silent and expressed alleles of XIST. Similar features may be important determinants of the replication asynchrony found by the in situ method for other genes subject to monoallelic expression.