Figure 1. Specificity of initiating DNA replication from bacteria to metazoans. The bacterial chromosome exemplifies the prototypic replicon. It contains a single, genetically defined, specific sequence (oriC), to which the replication initiator dnaA binds. SV40 represents a prototype of a eukaryotic viral DNA replicon. It contains a single, genetically defined specific sequence, to which the viral-encoded replication initiator T-antigen binds. All S. cerevisiae origins (ARS) share an 11-bp consensus sequence and are genetically defined; however, many ARS elements that are functional in plasmids are not functional in a chromosomal context. Multicellular eukaryotes have mainly site-specific origins. These sites usually contain one or several potential origins. The ORC complex recognize the sequence-specific yeast origin. In human and other multicellular eukaryotes the ORC complex is also involved in origin recognition by a mechanism that may not involve strict consensus sequence specificity.

Figure 2. Organization of a DNA replication origin in various organisms from E. coli to human. (a) E. coli oriC contains a single, genetically defined sequence of 245 bp. Binding of dnaA to the 9-bp repeats, followed by melting of the 13-bp sequences, facilitates entry of the helicase (dnaB). (b) SV40 origin contains an element of 64 bp that constitutes the main ORE element necessary for binding the T-antigen – the virally encoded initiation protein. It is flanked by an AT-rich element (A/T) and an early DUE element. Two auxiliary elements are present: an auxiliary T-antigen binding site (Aux 1) and a transcription factor (Sp1) binding site (Aux 2). (Figure reproduced with permission from DePamphilis (2000).) (c) S. cerevisiae origin ARS1 contains a consensus sequence of 11 bp (domain A). The ORC complex binds to domains A and B1. B2 contains a DUE element, whereas B3 is a binding site for a transcription factor (Abf1). (d) Mammalian DHFR origin has been characterized extensively by different methods. It contains an initiation zone of 55 kbp located between the dihydrofolate reductase (DHFR) and BE2121 genes, where three origins – ori, ori¢ and ori – are used preferentially (De Pamphilis, 1999; Dijkwel et al., 2002). (e) Human -globin origin is located in a region of 2 kbp that lies upstream and encompasses the hemoglobin, beta (HBB) gene, and may contain a core component and two auxiliary sequence elements. (f) Human lamin B2 origin is located in a region of 500 kbp between the lamin B2 (LMNB2) and PPV1 genes. Important regions for origin activity are indicated by dark shading. Filled arrows indicate the precise sites where DNA synthesis initiates.

Figure 3. Replication foci provide a clear example of the formation of specific chromatin territories that organize the genome for replication. The foci shown here were detected on a single nucleus after a short period of labeling with biotin-conjugated dUTP followed by visualization of the replication sites by wide-field microscopy using streptavidin-conjugated Texas Red dye.