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Mol. Cell. Biol., Jul 1997, 4043-4050, Vol 17, No. 7
Copyright © 1997, American Society for Microbiology

Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex

T Tenzen, T Yamagata, T Fukagawa, K Sugaya, A Ando, H Inoko, T Gojobori, A Fujiyama, K Okumura and T Ikemura
Department of Evolutionary Genetics, National Institute of Genetics, and The Graduate University for Advanced Studies, Shizuoka-ken, Japan. ttenzen@ddbj.nig.ac.jp

The human genome is composed of long-range G+C% (GC%) mosaic structures thought to be related to chromosome bands. We previously reported a boundary of megabase-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 the 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 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 synchronized 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 dense Alu clusters; polypurine/polypyrimidine tracts; di-, tri-, or tetranucleotide repeats; and medium-reiteration- frequency sequences. Because the nascent DNA in the switch region was recovered at low efficiency, we investigated whether this region is associated with the nuclear scaffold and found three scaffold- associated regions in and around the switch region.


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