Replication timing of the human X-inactivation center (XIC) region: correlation with chromosome bands

The human genome is composed of long-range G+C% mosaic structures, which ar e thought to be related to chromosome bands. Replication timing during S ph ase is associated with chromosomal band zones; thus, band boundaries are th ought to correspond to regions where replication timing switches. The proxi mal limit of the human X-inactivation center (XIC) has been localized cytol ogically to the junction zone between Xq13.1 and Xq13.2. Using PCR-based qu antification of the newly replicated DNA from cell-cycle fractionated THP-I cells, the replication timing in and around the XIC was determined at the genome sequence level. We found two regions where replication timing change s from the early to late period during S phase. One is located near a large inverted duplication proximal to the XIC, and the other is near the XIST l ocus. We propose that the I Mb late-replicated zone (from the large inverte d duplication to XIST) corresponds to a G-band Xq13.2. Several common chara cteristics were observed in the XIST region and the MHC class II-III juncti on which was previously defined as a band boundary. These characteristics i ncluded differential high-density clustering of Alu and LINE repeats, and t he presence of polypurine/polypyrimidine tracts, MER41A, MER57 and MER58B. (C) 2000 Elsevier Science B.V. All rights reserved.