Autonomously replicating sequences (ARSs) function as chromosomal replication origins in Saccharomyces cerevisiae, and play an essential role in chromosome maintenance (5, 6). During S phase, chromosomes are duplicated so that each mother cell retains, and each daughter cell receives, a full complement as a result of mitotic cell division. Each chromosome initiates replication at multiple sites at intervals of 40-100 kb, with each origin regulated to fire only once per cell cycle, mostly around mid-S phase, although different origins are activated continuously throughout S phase (7, 8, 9). Most origins are intergenic in nature, and only a subset operate during any given cell cycle, giving rise to highly-efficient origins that function in most cell cycles and extremely inefficient origins that are used in only a small percentage of cell cycles, as well as a range of efficiencies in between (8). Origins also fire in a characteristic order, which appears to be independent of the origin itself, but often correlates with the transcriptional activity of surrounding genes, with early-firing origins associated with active genes, and late-firing origins associated with silent genes (7).

ARSs have proven difficult to identify because they vary greatly in sequence and functional element composition, although they do share an elevated A-T content, interpreted to promote localized ease of DNA unwinding, which increases efficiency of replication initiation (10). ARSs are modular in structure, generally ~100-200 bp long, and depend on an exact match, or very near match, of an essential copy of an 11-base pair (bp) ARS consensus sequence (ACS), 5'-WTTTAYRTTTW-3', mutations in which abolish ARS function (11, 12). Some ARSs also contain additional near-match ACSs that are dispensable for function (11). Substantial sequence conservation has been observed in the 3 bp on either side of the essential match ACS, allowing for the identification of a 17-bp extended ACS (EACS), 5'-WWWWTTTAYRTTTWGTT-3' (11). The core ACS is part of "domain A", and is bound by the Origin Recognition Complex (ORC), a six-subunit DNA-dependent ATPase that functions as the replication initiator protein and launching pad for the assembly of the prereplication complex (pre-RC) (11). Immediately downstream of domain A (3' to the T-rich strand of the ACS) is "domain B", which exhibits little sequence conservation among ARSs and is composed of several nonredundant sequence elements (B1, B2, B3, B4), which vary from one ARS to another (11). Some, but not all, mutations in the B1 subelement can reduce the efficiency of ORC binding, suggesting that B1 functions with domain A as part of the ORC binding site (11). The B2 subelement, or DUE (DNA Unwinding Element), is AT-rich and serves as the site for the initial DNA unwinding, allowing the replication machinery to enter the DNA duplex in this area and assemble the first new nucleotides (13, 14). The B3 subelement is a 12-bp degenerate sequence that acts as a binding site for the transcriptional activator/repressor ARS binding factor 1 (ABF1) (11, 14). The function of the B4 subelement is as yet unknown (13). Some ARSs also have stimulatory sequences upstream of domain A (on the opposite side of the ACS) known as "domain C", as well as binding sites for the Rap1p transcription factor (13).

Last updated: 2006-05-09