The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication

The origin recognition complex (ORC) marks chromosomal sites as replication origins and is essential for replication initiation. In yeast, ORC also binds to DNA elements called silencers, where its primary function is to recruit silent information regulator (SIR) proteins to establish transcriptional silencing. Indeed, silencers function poorly as chromosomal origins. Several genetic, molecular, and biochemical studies of HMR-E have led to a model proposing that when ORC becomes limiting in the cell (such as in the orc2-1 mutant) only sites that bind ORC tightly (such as HMR-E) remain fully occupied by ORC, while lower affinity sites, including many origins, lose ORC occupancy. Since HMR-E possessed a unique non-replication function, we reasoned that other tight sites might reveal novel functions for ORC on chromosomes. Therefore, we comprehensively determined ORC “affinity” genome-wide by performing an ORC ChIP–on–chip in ORC2 and orc2-1 strains. Here we describe a novel group of orc2-1–resistant ORC–interacting chromosomal sites (ORF–ORC sites) that did not function as replication origins or silencers. Instead, ORF–ORC sites were comprised of protein-coding regions of highly transcribed metabolic genes. In contrast to the ORC–silencer paradigm, transcriptional activation promoted ORC association with these genes. Remarkably, ORF–ORC genes were enriched in proximity to origins of replication and, in several instances, were transcriptionally regulated by these origins. Taken together, these results suggest a surprising connection among ORC, replication origins, and cellular metabolism.

Chromosomes must be replicated prior to cell division. The process of duplication of each eukaryotic chromosome starts at discrete sites called origins of replication. An evolutionarily conserved Origin Recognition Complex (ORC) binds origins and helps make them replication-competent. ORC also binds another class of chromosomal sites that primarily function not as origins but as “silencers.” Silencers serve as starting points for the formation of silent chromatin, a special structure that represses local gene transcription in a promoter-independent fashion. One yeast silencer studied in great detail was found to bind ORC in vitro and in vivo with high affinity (“tightly”). On the other hand, several replication origins were found to bind ORC with lower affinity (“loosely”). We performed a genome-wide comparison of ORC affinity and found a novel class of high-affinity ORC–binding sites. Surprisingly, this class consisted neither of origins nor of silencers but of highly expressed genes involved in various metabolic processes. Transcriptional activation helped target ORC to these sites. These genes were frequently found near origins of replication, and in several instances their transcription was affected by deletion of the nearby origin. These results may shed light on a new molecular mechanism connecting nutrient status and cell division.