The NAD⁺-dependent Sir2p histone deacetylase is a negative regulator of chromosomal DNA replication

Abstract

The establishment of DNA synthesis during the S phase is a multistep process that occurs in several stages beginning in late mitosis. The first step is the formation of a large prereplicative complex (pre-RC) at individual replication origins and occurs during exit from mitosis and entry into G1 phase. To better understand the genetic requirements for pre-RC formation, we selected chromosomal suppressors of a temperature-sensitive cdc6-4 mutant defective for pre-RC assembly. Loss-of-function mutations in the chromatin-modifying genes SIR2, and to a lesser extent in SIR3 and SIR4, suppressed the cdc6-4 temperature-sensitive lethality. This suppression was independent of the well-known silencing roles for the SIR proteins at the HM loci, at telomeres, or at the rDNA locus. A deletion of SIR2 uniquely rescued both the DNA synthesis defect of the cdc6-4 mutant and its severe plasmid instability phenotype for many origins. A SIR2 deletion suppressed additional initiation mutants affecting pre-RC assembly but not mutants that act subsequently. These findings suggest that Sir2p negatively regulates the initiation of DNA replication through a novel mechanism and reveal another connection between proteins that initiate DNA synthesis and those that establish silent heterochromatin in budding yeast.[Keywords: DNA replication; SIR2; deacetylase] Supplemental material is available at http://www.genesdev.org.

The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

“…Alternatively, the hyopacetylation of H4K16 in these regions could be due to transient Sir2 association not captured by ChIP-Seq. Previous studies have shown that Sir2, but not Sir3 or Sir4, controls some origins of replication (Pappas et al 2004;Crampton et al 2008;Yoshida et al 2014). However, MACS did not detect any significant enrichment for Sir2 at subtelomeric ARSs outside the core X element.…”

Programming DNA replication origins and chromosome organization

“…Temperature-sensitive mutations in the pre-replication complex components ORC, CDC6, and MCM can be suppressed by inactivation of SIR2, a histone deacetylase (HDAC; Pappas et al 2004). The HDAC Sir2p is also a negative regulator of chromosomal DNA replication (Pappas et al 2004) and controls the frequency of DNA replication origin firing within rDNA (Pasero et al 2002).…”

“…The HDAC Sir2p is also a negative regulator of chromosomal DNA replication (Pappas et al 2004) and controls the frequency of DNA replication origin firing within rDNA (Pasero et al 2002). Some yeast ARS elements contain specific sequences recognized by Sir2p that inhibit DNA replication origin activity, most likely by affecting the local chromatin structure (Crampton et al 2008).…”

Replication Timing: Evolution, Nuclear Organization and Relevance for Human Disease

“…Furthermore chromatin structure, which refers to the chemical characteristics of the chromatin strand, may influence the initiation of replication by affecting the pre-RC assembly. There is evidence to show that histone acetylases and deacetylases play roles in the assembly of pre-RCs by interacting with, or disturbing the loading of, pre-RC elements such as the MCM complex (Burke et al, 2001;Iizuka et al, 2006;Pappas et al, 2004;Pasero et al, 2002). Finally, distal elements, such as locus control regions (LCRs) are known to affect initiation (Hayashida et al, 2006;Kalejta et al, 1998), with the initiation of replication at regions such as the human β-globin locus being controlled by a 5' LCR (Aladjem et al, 1995).…”