2 Eukaryotic DNA Replication Origins

Abstract

Eukaryotic cells replicate their DNA from hundreds to thousands of chromosomal sites termed replication initiation sites or replication origins. Initiation of DNA replication involves interactions between these replication origins and a network of cell cycle regulatory proteins. The replicon model (Fig. 1), which laid the foundation for our understanding of DNA replication control (Jacob et al. 1964), postulated that DNA sequence elements (termed replicators) determine the location of replication initiation. Replicators interact with trans-acting regulatory factors (termed initiators) to initiate replication in response to specific signals that link replication with cell growth.

The replicon model was rapidly validated in prokaryotes, DNA viruses, and single-cell eukaryotes, in which replicators were identified by mediation of extrachromosomal replication. Genetic analyses of replicator sequences and identification of initiators that bind these sequences provided important insights into the regulation of DNA synthesis (Kelly and Brown 2000; Mendez and Stillman 2003). In metazoans, replicators cannot be easily identified by extrachromosomal assays. However, identification of orthologous genes encoding initiators that were identified in unicellular organisms greatly helped elucidate the regulation of DNA replication.

In single-cell eukaryotes, such as budding and fission yeast, each chromosome contains tandemly organized replicons (average size: ~40 kb) and replication initiates from relatively simple replicators that also function as autonomously replicating sequences (ARSs) in plasmids. Replication origins in multicellular eukaryotes seem more complex and require particular chromosomal contexts for initiation. However, even simple replicators exhibit flexible sequence features and are subject to context effects. In this chapter, we discuss the diverse and common...