PRECISE SWITCHING OF DNA-REPLICATION TIMING IN THE GC CONTENT TRANSITION AREA IN THE HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX

The human genome is composed of long-range G+C% (GC%) mosaic structure s thought to be related to chromosome bands, We previously reported a boundary of megabase-sized GC% mosaic domains at the junction area bet ween major histocompatibility complex (MHC) classes II and III, propos ing it as a possible chromosome band boundary, DNA replication timing during the S phase is known to be correlated cytogenetically with chro mosome band zones, and thus the band boundaries have been predicted to contain a switch point for DNA replication timing, In this study, to identify to the nucleotide sequence level the replication switch point during the 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 synchroni zed human myeloid leukemia HL60 cells. The replication timing changed precisely in the boundary region with a 2-h 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 in the switch region, which contains d ense Alu clusters; polypurine/polypyrimidine tracts; di-, tri-, or tet ranucleotide repeats; and medium-reiteration-frequency sequences. Beca use the nascent DNA in the switch region was recovered at low efficien cy, we investigated whether this region is associated with the nuclear scaffold and found three scaffold-associated regions in and around th e switch region.