Two major replicating simian virus 40 chromosome classes. Synchronous replication fork movement is associated with bound large T antigen during elongation.

We have analyzed the asynchronous progression of replication forks through the early (E) and late (L) gene sides in bidirectionally replicating SV40 chromosomes during lytic infection. By cutting purified replicating DNA with an appropriate single-site restriction endonuclease and measuring the contour lengths of replicated and unreplicated segments by electron microscopy, the positions of the two replication forks in each elongating intermediate were determined. Our results indicate that there are at least two major classes of replicating SV40 chromosomes which differ in their relative rate of E and L fork movement, the presence or absence of bound SV40 large T antigen during elongation, and the termination region utilized. These two classes also have altered apparent start sites for initiating bidirectional replication, flanking either side of core ori. The largest group (67%) replicated synchronously was associated with T antigen during elongation, appeared to initiate bidirectional elongation at nucleotide 5203 or 41 base pairs (bp) toward the E side of 0/5243, at the junction of T binding site I and ori, and terminated at the typical region centered at 0.5 map units. A second group (24%) replicated asynchronously with the L fork moving 3 times faster than the E fork, was not associated with T antigen during elongation, and terminated at a broad region centered at 0.73 map units. This group appeared to initiate at nucleotide 29 at the junction of the AT-rich region of ori, T binding site I, and the start of the 21-bp repeated transcriptional control sequences. A third group (9%) appeared to initiate at nucleotide 5148 or 95 bp to the E side of 0/5243 and replicated asynchronously preferentially on the E side at early times. However, this group is related to the synchronous class in that it contains bound T antigen and both forks move synchronously past 30% elongation, terminating at the same region. The association of T antigen with synchronous but not asynchronous DNA molecules indicates that T functions in regulating fork movement during elongation. A synchronization role implies that both forks are closely associated with one another in replicating molecules with bound T. Replicating molecules lacking T not only elongated highly asynchronously but preferential fork progression occurred almost exclusively on the L side. The ori region in asynchronous compared to synchronous intermediates was differentially sensitive to BglI digestion, indicating that nuclease digestion can distinguish between different populations of replicating molecules.(ABSTRACT TRUNCATED AT 400 WORDS)