Telomeric chromatin modulates replication timing near chromosome ends

TLDR: It is concluded that telomeric chromatin has a Sir3-dependent inhibitory effect on DNA replication.

Abstract: Different regions of the eukaryotic genome are known to replicate at distinct, reproducible times within the period of S phase. This is observed in plants, insects, and vertebrates, as well as in the yeast Saccharomyces cerevisiae (Hand 1978; Fangman and Brewer 1992). In species with large genomes, extensive regions of the chromosomes replicate early in S phase, whereas other domains do not initiate replication until after the early domains have completed synthesis. Frequently, late replication of DNA is associated with its assembly into heterochromatin, which is highly condensed chromatin that often contains repeated DNA sequences such as those found at centromeres and telomeres (John 1988). This condensed chromosome replicates much later in S phase than its transcriptionally active homolog. Telomeric chromatin in S. cerevisiae has several traits typical of heterochromatin (Grunstein 1998). In particular, telomeres confer epigenetic silencing of nearby genes (position effect variegation), and they replicate late in S phase (McCarroll and Fanagman 1988; Gottschling et al. 1990). The special chromatin found near telomeres is composed of hypoacetylated core histones as well as the SIR proteins, which are required for silencing telomeric genes (Grunstein 1998). Of the SIR proteins, Sir3p is probably the key component that defines a telomeric domain of transcriptional repression. It interacts with the tails of histones H3 and H4, spreading from the telomere inward along the chromosome, and its abundance in the cell determines how far a silent domain extends from the telomere (Renauld et al. 1993; Hecht et al. 1996). In yeast, chromosome replication initiates at ARS (autonomous replicating sequences) elements (Fangman and Brewer 1991). ARS elements were originally identified as sequences that permit high-efficiency transformation of plasmids in yeast by serving as origins of DNA replication. However, in their normal chromosomal context, only a subset of the ARS elements initiate DNA replication within the ∼30 min duration of S phase (Fangman and Brewer 1992). Specific chromosomal origins of S. cerevisiae, like ARS1 on chromosome IV, initiate replication relatively early in S phase. Other ARS elements initiate later in S phase, such as ARS501 on chromosome V, which replicates ∼10 min after ARS1 (Ferguson et al. 1991). It appears that telomeres can confer late replication on proximal origins. For instance, telomere-proximal middle repetitive sequences replicate relatively late in S phase (McCarroll and Fangman 1988; Louis 1995). In addition, whereas ARS elements on circular plasmids initiate replication early in S phase, they replicate late in S phase when the plasmid is linearized and telomeric sequences are added to its ends (Ferguson and Fangman 1992). In this study we investigated the role of silent chromatin in imposing late replication on origins near telomeres.