DNA replication origins in the Schizosaccharomyces pombe genome

Abstract

Origins of DNA replication in Schizosaccharomyces pombe lack a specific consensus sequence analogous to the Saccharomyces cerevisiae autonomously replicating sequence (ARS) consensus, raising the question of how they are recognized by the replication machinery. Because all well characterized S. pombe origins are located in intergenic regions, we analyzed the sequence properties and biological activity of such regions. The AT content of intergenes is very high (Ϸ70%), and runs of A's or T's occur with a significantly greater frequency than expected. Additionally, the two DNA strands in intergenes display compositional asymmetry that strongly correlates with the direction of transcription of flanking genes. Importantly, the sequence properties of known S. pombe origins of DNA replication are similar to those of intergenes in general. In functional studies, we assayed the in vivo origin activity of 26 intergenes in a 68-kb region of S. pombe chromosome 2. We also assayed the origin activity of sets of randomly chosen intergenes with the same length or AT content. Our data demonstrate that at least half of intergenes have potential origin activity and that the relative ability of an intergene to function as an origin is governed primarily by AT content and length. We propose a stochastic model for initiation of DNA replication in the fission yeast. In this model, the number of AT tracts in a given sequence is the major determinant of its probability of binding SpORC and serving as a replication origin. A similar model may explain some features of origins of DNA replication in metazoans. T he replicon model postulates that initiation of DNA replication takes place at specific chromosomal sequence elements (replicators) that are recognized by regulatory proteins (initiators) (1). This model was originally proposed to explain features of the replication of prokaryotic cells and viruses and has been validated in such systems by a large body of evidence (2). In eukaryotic cells, DNA replication is initiated from hundreds to thousands of different chromosomal sites in each cell cycle, raising the question of whether the replicon model provides a valid description of the initiation process. Although early genetic studies indicated that DNA replication in the budding yeast Saccharomyces cerevisiae conforms to the main features of the model, it is not yet clear that this is the case for most other eukaryotic species.Origins of DNA replication in S. cerevisiae were identified as sequence elements that conferred the property of autonomous replication on extrachromosomal plasmids (3). Genetic analysis demonstrated that such autonomously replicating sequences (ARS) were Ϸ100 bp in length and contained a common 11-bp consensus sequence essential for origin activity, as well as other sequences that augmented origin activity (3-7). The characterization of S. cerevisiae ARS elements led to the identification of the yeast origin recognition complex (ScORC), the initiator protein that recognizes the ARS-consensus sequence (8). The spe...

Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans

“…For exemplary purposes, we note the following aspects of ultraviolet-induced mutagenesis: (a) UV has been shown to preferentially induce lesions at TT dimers, (b) repair can proceed by either an error-free mechanism (photoreactivation) or an error-prone mechanism (excision and gap repair), and (c) it is conceivable that gap repair would predominate on the outer (exposed) surface of nucleosomes while photoreactivation would predominate on inner (sterically protected) faces. Combining this with other mutagenic processes that might result in formation of A-or T-rich segments in transcriptionally accessible regions of the genome, (Dai et al 2005) one might expect the types of structures that we observe in nematodes.…”

Genome-wide characterization of fission yeast DNA replication origins

“…More than 50% of fission yeast intergenic regions have the propensity to function as origins on extrachromosomal plasmids (Dai et al, 2005), raising the question of how many of them are active in their chromosomal context and how efficiently they are used in S-phases of the mitotic and meiotic cell cycles. Using both intergenic and ORF microarrays, we have globally mapped 401 strong and 503 putative weaker fission yeast origins during the mitotic and premeiotic S-phases, resulting in an average interorigin distance of 14 kb.…”

Cyclin A–Cdk1 regulates the origin firing program in mammalian cells

“…In fission yeast, however, clear late origins have not been characterized (9) and replication origins fire stochastically (10,11). As for mammals, although almost half of origins are activated equally throughout S-phase progression (12), stable subunits of chromosomes equivalent to replication foci maintain their replication timing from S phase to S phase (13).…”