The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae

Abstract

The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5⌬ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.Duplication of eukaryotic chromosomes is a temporally regulated process that involves accurate replication of DNA sequences coupled with assembly of chromatin. In general, transcriptionally active euchromatin replicates before the structurally condensed and transcriptionally silent heterochromatin. The significance of this epigenetic phenomenon remains to be determined; however, the temporal dynamics of chromosomal replication are thought to be mechanistically linked to the establishment and inheritance of gene expression programs encoded in the chromatin structure. Altered replication timing is associated not only with changes in gene expression, but also with chromosome instabilities and human cancers, suggesting that temporal staging of replication may contribute to the fidelity of genome duplication (reviewed in reference 21).DNA replication initiates at specific sites distributed along each chromosome that are termed origins of replication (reviewed in references 4 and 20). Individual origins exhibit characteristic activities defined by their timing of activation in S phase and their likelihood of activation in each S phase (origin efficiency). The activation characteristics of individual origins, their relative chromosomal locations, and normal impediments to replication fork progression determine the overall dynamics of genome replication. Recent genome-wide studies of origin locations and replication timing have revealed much about the replication dynamics and organization of the Saccharomyces cerevisiae genome (36, 54). Nevertheless, differential origin efficiency and activation timing depends upon a largely undefined relationship between chromatin structure and replication initiation mechanisms.In S. cerevisiae, origin relocation...

Conservation of replication timing reveals global and local regulation of replication origin activity

“…These origins offer insight into the mechanisms that regulate origin activity, such as the time during S phase when the origin activates. Long-range global mechanisms that are involved in the regulation of origin activity include chromatin modifications (Friedman et al 1996;Vogelauer et al 2002;Aparicio et al 2004) and proximity to a telomere or a centromere (Raghuraman et al 2001;Pohl et al 2012). Consistent with these findings, we observe that shorter telomeres in a S. cerevisiae/S.…”

mSin3A corepressor regulates diverse transcriptional networks governing normal and neoplastic growth and survival

“…Given that this DNA content anomaly cannot be attributed to chromosomal instability and that there is prominent representation of DNA replication genes in the mSin3A transcriptome, we propose that mSin3A plays a direct role in regulation of DNA replication in mammalian cells. This hypothesis is in line with previous studies in S. cerevisiae, showing a role for Sin3 and Rpd3 (ortholog of HDAC1) in the activation of late origins of replication independent relating to their role in transcriptional repression (Aparicio et al 2004). Additionally, in Drosophila, activation of origin of replication is dependent on Rpd3 as evidenced by the loss of Rpd3 function, resulting in genome-wide hyperacetylation, genomic replication, and redistribution of the origin binding protein ORC2 (Aggarwal and Calvi 2004).…”

“…For example, S. cerevisiae sin3p has been shown to participate in the transcriptional activation (as opposed to repression) of MAPK Hog1 target genes upon osmotic stress (De Nadal et al 2004), and recent links have been forged between S. cerevisiae sin3 and DNA replication (Aparicio et al 2004). S. cerevisiae and Caenorhabditis elegans Sin3 molecules have also been implicated in the DNA damage-repair process in a transcription-independent manner (Pothof et al 2003;Jazayeri et al 2004).…”

Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae

“…Cells were grown in YEPD unless otherwise noted; synchronization methods have been described (34). Myc-tagging, ChIP, ChIP-chip, and BrdU-IP-seq were performed as described (7), except that sonication was performed with a Covaris S2 Instrument.…”