(3) Replication Timing for the GC Content Transition Area

Toyoaki TENZEN, Yoshihisa WATANABE, Asako ANDO1, Hidetoshi INOKO1, and Toshimichi IKEMURA (1School of Medicine, Tokai University)

Mammalian genomes are composed of long-range G+C% mosaic structures thought to be related to chromosome bands. We previously reported an example of a boundary of megabase (Mb)-sized GC% mosaic domains at the junction area between major histocompatibility complex (MHC) classes II and III, proposing it as a possible chromosome band boundary. DNA replication timing during S phase is known to be correlated cytogenetically with chromosome band zones, and thus the band boundaries have been predicted to contain a switch point for DNA replication timing. In this study, to identify at the nucleotide sequence level the replication switch point during S phase, we determined the precise DNA replication timing for MHC classes II and III, focusing on the junction area. To do this we used PCR-based quantitation of nascent DNA obtained from synchronized human myeloid leukemia HL60 cells. The replication timing changed precisely in the boundary region with a 2-hour difference between the two sides, supporting the prediction that this region may be a chromosome band boundary. We supposed that replication fork movement terminates (pauses) or significantly slows down in the switch region, which contains dense Alu clusters, polypurine / polypyrimidine tracts (e.g., 209-bp tracts), di-, tri- or tetranucleotide repeats, and medium reiteration frequency sequences (MERs). We found also the replication switch point in the XIST locus in the X chromosome inactivation center (XIC). For details, see Mol. Cell. Biol. 17, 4043-4050.