Telomeric chromatin modulates replication timing near chromosome ends

Abstract

Saccharomyces cerevisiae telomeric DNA replicates late in S phase, and telomeric genes are transcriptionally silent. Transcriptional repression of telomere-proximal genes results from silent chromatin initiating at the chromosome end, but the relationship between telomeric chromatin and DNA replication is unknown. Mutations in SIR3, a silent chromatin component, cause telomeric DNA on chromosome V to replicate much earlier because of earlier initiation of a nearby replication origin, the Y ARS. A second telomere-proximal ARS, from an X element, does not act as an origin in a wildtype strain, whereas in a sir3 cell it does. We conclude that telomeric chromatin has a Sir3-dependent inhibitory effect on DNA replication.Received October 6, 1998; revised version accepted December 1, 1998. 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 . 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 re...

Behavior of replication origins in Eukaryota – spatio-temporal dynamics of licensing and firing

“…25,67,68 The thesis of origins being controlled by chromosome structure or subnuclear localization appears to be validated by experiments that analyze the effects of deletion of chromatin modifiers such as SIR3 (required for subtelomeric chromatin assembly) which results in earlier replication of normally late telomeric parts. 69 Deletions of other corresponding factors such as YKU70, RPD3 or GCN5 result in a similar hastened initiation of late ROs. [70][71][72][73] However, increased histone acetylation due to GCN5 tethering or RPD3 deletion, does not cause late ROs to initiate as early as the earliest origins.…”

Sir3-dependent assembly of supramolecular chromatin structuresin vitro

“…The relevance to chromatin fiber structure-function relationships is discussed above. In terms of silencing, we have started with yeast Sir3p in part because several in vivo studies indicate that Sir3p alone can modulate both silencing (34) and chromatin-mediated effects on replication (35), in a manner that is at least somewhat independent of the other Sir proteins (6). Although the following hypotheses remain to be tested directly, our results are consistent with the idea that Sir3-mediated assembly of specialized higher order chromatin structures at specific loci in yeast is a key component of achieving a transcriptionally silenced state.…”

The promoter of the Chinese hamster ovary dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries

“…Indeed, the yeast transcriptional silencer, Sir3p, which is abundant at telomeres, is also responsible for the latereplicating pattern of sub-telomeric sequences, apparently establishing a heterochromatin-like architecture in the region (Stevenson and Gottschling 1999;Wyrick et al 1999). However, an analysis of heterochromatic centromeres and silent mating-type cassettes in Schizosaccharomyces pombe shows clearly that both of these elements are early-replicating (Kim et al 2003).…”