Activation of a mammalian origin of replication by chromosomal rearrangement

Replication of minichromosomes in Saccharomyces cerevisiae is sensitive to histone gene copy number and strain ploidy

We have characterized a defect in the mitotic transmission of plasmid minichromosomes in yeast strains deleted for the more highly expressed pair of histone H3 and H4 genes. Several observations indicate that an impairment in DNA replication contributes to the decrease in minichromosome stability. First, the maintenance of ARS plasmids that lack centromeres was also defective. Second, the addition of multiple ARS elements suppressed the defect in plasmid maintenance. Third, a synergistic increase in plasmid loss rate was seen when a plasmid containing an inefficient mutated ARS was tested in a strain deleted for histone genes, implying an interaction between ARS activity and the histone gene deletion. These results support the existence of a histone-dependent step in the initiation of DNA replication. We find that the stability of native chromosomes is not affected in strains deleted for histone genes. We propose that reduced histone H3 and H4 protein decreases the efficiency of initiation at ARS elements on plasmids and chromosomes, but that the presence of multiple origins on chromosomes compensates for the reduced efficiency. We find that decreased minichromosome stability is suppressed by increases in strain ploidy. The greater stability due to ploidy increases is not due to a relative increase in the expression of histone genes. We discuss models for the effect of strain ploidy on minichromosome maintenance.

Distal sequences, but not ori-beta/OBR-1, are essential for initiation of DNA replication in the Chinese hamster DHFR origin

In the Chinese hamster dihydrofolate reductase replication initiation zone, the ori-beta locus is preferred over other start sites. To test the hypothesis that ori-beta contains a genetic replicator, we restored a deletion in the 3' end of the DHFR gene with a cosmid that provides the missing sequence and simultaneously knocks out the downstream ori-beta locus. Replication initiates normally in ori-beta knockout cell lines, and the DHFR domain is still synthesized in early S phase. However, initiation is completely suppressed in the starting deletion variant lacking the 3' end of the gene. We conclude that ori-beta does not contain an essential replicator, but that distant sequence elements have profound effects on origin activity in this locus.

Fine structure mapping of DNA repair within a 100 kb genomic region in Chinese hamster ovary cells

We have investigated at a high level of resolution the repair of cyclobutane pyrimidine dimers (CPD) in a large amplified genomic region in Chinese hamster ovary B11 cells. We found strand selective repair in DNA fragments within two active genes, DHFR and an unknown gene adjacent to DHFR. These genes generate divergent transcripts from the same promoter region; their transcribed strands were virtually free of CPD within 24 h after irradiation with 10 j/m2 of ultraviolet light (254nm), while their non-transcribed strands were poorly repaired. We also examined the repair of CPD in three DNA fragments within a 50 kb region downstream of DHFR, in which two origins of replication flanking a matrix attachment site have been characterized from independently derived cell lines with amplified DHFR domains; repair of CPD in this non-transcribed region was similarly poor in both DNA strands. Transcription-coupled repair of CPD in the DHFR gene exhibited the same proficiency throughout the transcription unit: analysis of the efficiency of removal of CPD over time revealed no differences between repair in the 5' and the 3' ends of the DHFR gene. Implications for mechanisms of transcription-coupled repair are discussed.

Origins of replication and the nuclear matrix: the DHFR domain as a paradigm

The eukaryotic genome appears to be organized in a loopwise fashion by periodic attachment to the nuclear matrix. The proposal that a chromatin loop corresponds to a functional domain has stirred interest in the properties of the DNA sequences at the bases of these loops, the matrix-attached regions (MARs). Evidence has been presented suggesting that certain MARs act as boundary elements isolating domains from their chromosomal context. MARs have also been found in the vicinity of promoters and enhancers and they could act by displacing these cis-regulatory elements into the proper nuclear subcompartment. Attachment to the matrix might also play a role in DNA replication. A large body of evidence indicates that replication occurs on the nuclear matrix. This implies that any DNA sequence will be attached to the matrix at a certain time during the cell cycle. This transient mode of attachment contrasts with the proposed permanent attachment of origins of DNA replication with the nuclear matrix. While some data exist that support this suggestion, the current lack of understanding of the mammalian replication origin precludes definitive conclusions regarding the role of MARs in the initiation process.