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. 2009 Feb;181(2):379–391. doi: 10.1534/genetics.108.099101

Mcm10 Mediates the Interaction Between DNA Replication and Silencing Machineries

Ivan Liachko 1, Bik K Tye 1,1
PMCID: PMC2644934  PMID: 19064704

Abstract

The connection between DNA replication and heterochromatic silencing in yeast has been a topic of investigation for >20 years. While early studies showed that silencing requires passage through S phase and implicated several DNA replication factors in silencing, later works showed that silent chromatin could form without DNA replication. In this study we show that members of the replicative helicase (Mcm3 and Mcm7) play a role in silencing and physically interact with the essential silencing factor, Sir2, even in the absence of DNA replication. Another replication factor, Mcm10, mediates the interaction between these replication and silencing proteins via a short C-terminal domain. Mutations in this region of Mcm10 disrupt the interaction between Sir2 and several of the Mcm2–7 proteins. While such mutations caused silencing defects, they did not cause DNA replication defects or affect the association of Sir2 with chromatin. Our findings suggest that Mcm10 is required for the coupling of the replication and silencing machineries to silence chromatin in a context outside of DNA replication beyond the recruitment and spreading of Sir2 on chromatin.

LARGE regions of eukaryotic genomes are packaged into transcriptionally silent heterochromatin. Yeast heterochromatic silencing is established and maintained by the action of a group of factors called silent information regulators (SIRs) (Rusche et al. 2003). Sir2, Sir3, and Sir4 are recruited to chromatin and spread bidirectionally in a stepwise fashion until encountering a boundary element (Hoppe et al. 2002; Rusche et al. 2002; Thon et al. 2002). The silencing activity of these proteins is attributed to the histone deacetylase function of Sir2, although Sir3 and Sir4 are also required for silencing (Imai et al. 2000). Silencing in the budding yeast Saccharomyces cerevisiae is largely limited to telomeres, the silent mating type loci, and rDNA. In telomeres the SIRs are recruited to chromatin by Rap1 (Kyrion et al. 1993; Moretti et al. 1994). In the silent mating type loci (HML and HMR) the binding and spreading of SIRs is initiated by the combined action of the origin recognition complex (ORC), Rap1, and Abf1 binding to DNA elements termed silencers (Rusche et al. 2003). Once formed, this transcriptionally silent epigenetic structure can be stably inherited for up to 40 generations (Pillus and Rine 1989).

An early study in the cell-cycle regulation of silent chromatin showed that passage through S phase was required for the establishment of silencing (Miller and Nasmyth 1984), suggesting that DNA replication is involved in silencing. Indeed, several members of the replication machinery, such as ORC, Mcm10, Mcm5, Cdc7, Abf1, and PCNA have since been implicated in silencing and chromatin structure (Axelrod and Rine 1991; McNally and Rine 1991; Bell et al. 1993; Ehrenhofer-Murray et al. 1999; Zhang et al. 2000; Burke et al. 2001; Christensen and Tye 2003; Dziak et al. 2003; Liachko and Tye 2005). However, several studies have shown that DNA replication is not required for the establishment of silencing (Kirchmaier and Rine 2001; Li et al. 2001; Lau et al. 2002; Martins-Taylor et al. 2004). A more recent study showed that recruitment of Sir proteins to chromatin is a necessary but not the final step for the establishment of silencing, which may be completed as late as M phase (Kirchmaier and Rine 2006).

One key component of DNA replication machinery is the prereplication complex (pre-RC), which assembles on replication origins in late M/early G1 phases of the cell cycle prior to the initiation of DNA replication at the beginning of S phase. The pre-RC consists of a large number of proteins such as Orc1–6, Cdc6, Cdt1, and the replicative helicase Mcm2–7 complex (Forsburg 2004). The Mcm2–7 complex consists of six minichromosome maintenance (MCM) proteins (Tye 1999; Forsburg 2004). One distinct characteristic of the MCM2–7 family is a conserved domain known as the MCM box, which spans ∼200 residues near the center of the protein (Tye and Sawyer 2000). The MCM box includes two ATPase motifs, the Walker A motif and the Walker B motif, as well as an arginine-finger motif. In addition to these features, all six of the MCM2–7 proteins, with the exception of Mcm3, have zinc binding motifs near the N-terminal regions, and some have nuclear localization signal (NLS) sequences and sites of phosphorylation by cyclin dependent kinases (CDKs) (Ishimi 1997; Lee and Hurwitz 2000). The MCM2–7 proteins are highly abundant proteins (estimated at >30,000 copies per cell in S. cerevisiae) whose levels are stable during the cell cycle (Lei et al. 1996; Forsburg 2004). In S. cerevisiae, MCM complexes outnumber the ∼400 DNA replication origins by a factor of 75. The reason for this vast overabundance is unclear and only a small subset of the MCM2–7 proteins is associated with chromatin even during the G1–S transition, when their chromatin association is at its peak. Interestingly, reducing the levels of the MCM2–7 proteins causes defects in genetic stability, suggesting that the extra protein molecules are necessary for a function that is yet unknown (Lei et al. 1996; Liang et al. 1999).

Mcm10 is an essential factor (Merchant et al. 1997) that is closely associated with the Mcm2–7 complex, although it is not part of the same protein family. Much like the MCM2–7 proteins, it is highly abundant in the cell (Kawasaki et al. 2000). Mcm10 stabilizes the Polα–primase complex (Ricke and Bielinsky 2004; Yang et al. 2005; Ricke and Bielinsky 2006) and is important for mediating interactions between other replication proteins (Lee et al. 2003; Das-Bradoo et al. 2006). Temperature sensitive mutations in MCM10, mcm10-1 (P269L), and mcm10-43 (C320Y), cause multiple defects, including loss of interactions with other proteins, defects in plasmid replication, and pausing of replication forks at semi-permissive temperature (Merchant et al. 1997; Homesley et al. 2000). At restrictive temperature, mcm10 cells arrest at the end of S phase with aberrant DNA structures (Merchant et al. 1997; Kawasaki et al. 2000). Recently, Mcm10 has been implicated to function in chromatin structure in yeast as well as Drosophila melanogaster (Christensen and Tye 2003; Douglas et al. 2005; Liachko and Tye 2005). In Drosophila, Mcm10 interacts with HP-1, an important heterochromatin protein (Christensen and Tye 2003), while in yeast Mcm10 interacts with Sir2 (Douglas et al. 2005; Liachko and Tye 2005). In addition, genetic experiments suggest that the silencing function of Mcm10 is separate from its replication function (Douglas et al. 2005; Liachko and Tye 2005).

In this study we show that several members of the MCM2–7 complex play a role in heterochromatic silencing. In addition, they physically interact with Sir2, even in the absence of DNA replication. Mcm10 is required for the interactions between Sir2 and MCM2–7. We have localized the Mcm10 domain responsible for the interaction with Sir2 to a 53-amino-acid domain in the C terminus of Mcm10. Mutations in this region inhibit Mcm10–Sir2 interactions as well as the interaction of Sir2 with members of the MCM2–7 family. These mutants also exhibit defects in silencing, but not in DNA replication. Interestingly, mcm2–7 and mcm10 mutations that have a significant effect on both DNA replication and silencing do not affect the association of Sir2 with chromatin. Our findings show that MCM2–7 proteins have a silencing function which requires a coupling of the replication and silencing machineries via Mcm10.

MATERIALS AND METHODS

Strains and plasmids:

Strains used in this study are listed in Table 1. All strains are isogenic derivatives of W303-1A, unless otherwise indicated. All procedures were performed according to standard yeast methodology (Sherman 1991). Strains carrying silencing reporters were made by crossing strain YB541 or YB697 to the appropriate mutant strain and selecting desired segregants by their conditional phenotypes and/or auxotrophy. Genotypes were confirmed by PCR or by plasmid complementation where applicable.

TABLE 1.

Strains used in this study

Strains Source
Isogenic to W303
    W303-1A MATaade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1 R. Rothstein
    W303-1B MATα ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1 R. Rothstein
    BTY100 W303 MATamcm10-1 This lab
    BTY101 W303 MATα mcm10-1 This lab
    BTY103 W303 MATamcm10-43 This lab
    BTY102 W303 MATα mcm10-43 This lab
    ILY115 W303 MATamcm7-1(cdc47-1) This lab
    ILY360 W303 MATα mcm3-10 This lab
    ILY171 W303 MATahmr∷ADE2 adh4∷URA3 Tel (VII-L) This lab
    ILY180 ILY171 mcm10-1 This lab
    ILY270 ILY171 mcm10-43 This lab
    ILY248 ILY171 MATα 13myc-MCM10 TRP1 This study
    ILY288 ILY248 MATamcm10-T515V This study
    ILY295 ILY248 MATamcm10-I517T This study
    ILY298 ILY248 MATamcm10-D519N This study
    ILY332 ILY248 MATamcm10-43 This study
    ILY330 ILY273 mcm10(503-571)∷HIS3 This study
    ILY331 ILY275 mcm10-43(503-571)∷HIS3 This study
    ILY336 ILY330 MATα hmr∷ADE2 adh4∷URA3 Tel (VII-L) This study
    ILY334 ILY331 hmr∷ADE2 adh4∷URA3 Tel (VII-L) This study
    ILY178 ILY171 mcm2-1 This study
    ILY253 ILY171 mcm3-10 This study
    ILY255 ILY171 cdc54-1 This study
    ILY254 ILY171 MATα mcm7-1 This study
    ILY264 ILY171 cdc6-3 This study
    ILY230 MATa13myc-MCM10 TRP1 This study
    ILY232 MATa13myc-mcm10-43 TRP1 This study
    ROY1515 W303 MATa9xMyc-NET∷LEU2 pep∷4Δ∷TRP1 ade2 LYS2 6xHis-3xHA-SIR2 R. Kamakaka
    ILY273 ILY230 6xHis-3xHA-SIR2 This study
    ILY274 ILY230 MATα 6xHis-3xHA-SIR2 This study
    ILY275 ILY232 6xHis-3xHA-SIR2 This study
    ILY276 ILY232 MATα 6xHis-3xHA-SIR2 This study
    ILY185 W303 MATasir2∷HIS3 This lab
    ILY338 ILY273 mcm3-10 This study
    ILY346 ILY273 mcm7-1 This study
    ILY348 ILY273 sir4∷HIS3 This study
    ILY349 ILY171 6xHis-3xHA-SIR2 This study
    ILY351 ILY180 6xHis-3xHA-SIR2 This study
    ILY353 ILY332 6xHis-3xHA-SIR2 This study
    ILY355 ILY253 MATα 6xHis-3xHA-SIR2 This study
    ILY357 ILY254 6xHis-3xHA-SIR2 This study
    ILY328 ILY273 sir3:HIS3 This study
Other backgrounds
    EGY40[pSH18-34] MATaura3-52 trp1-1 leu2-3,112 [pSH18-34] E. Golemis
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Plasmids used in this study are listed in Table 2. Plasmids used for the expression of two-hybrid fusions were constructed by the Gateway system (Invitrogen). Gateway cassettes were ligated into plasmids pBTM116 and pGAD2F, creating pBTMgw and pGADgw, respectively. pDONR201 entry clones containing MCM10 and SIRs ready for N-terminal fusions were constructed according to Invitrogen instructions and sequenced. LR recombination reactions (Invitrogen) were set up between pGBT9gw, pGADgw, pBTMgw, and each of the aforementioned entry clones. These are recombination reactions that replace the Gateway cassette in the relevant vector with the gene from the entry clone. The full-length pBTM–MCM10 was described in (Merchant et al. 1997). All yeast transformations were carried out using standard lithium acetate protocols (Orr-Weaver et al. 1981; Sherman 1991).

TABLE 2.

Plasmids used in this study

Plasmid Description Source
pRS315 YCP LEU2 New England Biolabs
pRS315MCM10 YCP LEU2 MCM10 This lab
pGAD2F 2μ LEU2 GAD4-AD S. Fields
pBTM116 2μ TRP1 LEXA-DBD S. Fields
pSH18-34 URA3 LacZ with LEXA binding sites S. Fields
pGADgw pGAD2F with Gateway cassette This study
pBTMgw pBTM116 with Gateway cassette This study
pBTMMCM10 pBTMgw MCM10 This study
pBTMmcm10-1 pBTMgw mcm10-1 This study
pBTMmcm10-43 pBTMgw mcm10-43 This study
pBTMMCM10(386–end) pBTMgw MCM10 (386–571) This study
pBTMMCM10(480–end) pBTMgw MCM10 (480–571) This study
pBTMMCM10(503–end) pBTMgw MCM10 (503–571) This study
pBTMMCM10(143–555) pBTMgw MCM10 (143–555) This study
pBTMMCM10(386–555) pBTMgw MCM10 (386–555) This study
pBTMMCM10(386–512) pBTMgw MCM10 (386–512) This study
pBTMMCM10(386–480) pBTMgw MCM10 (386–480) This study
pBTMMCM10(503–555) pBTMgw MCM10 (503–555) This study
pBTMMCM10(503–555)-T515V pBTMgw MCM10 (503–555)-T515V This study
pBTMMCM10(503–555)-I517T pBTMgw MCM10 (503–555)-I517T This study
pBTMMCM10(503–555)-D519N pBTMgw MCM10 (503–555)-D519N This study
pBTMMCM10-T515V pBTMgw MCM10-T515V This study
pBTMMCM10-I517T pBTMgw MCM10-I517T This study
pBTMMCM10-D519N pBTMgw MCM10-D519N This study
pBTMMCM2 pBTMgw MCM2 This lab
pBTMMCM3 pBTMgw MCM3 This lab
pBTMMCM4 pBTMgw MCM4 This lab
pBTMMCM5 pBTMgw MCM5 This lab
pBTMMCM6 pBTMgw MCM6 This lab
pBTMMCM7 pBTMgw MCM7 This lab
pBTMCDC6 pBTMgw CDC6 This lab
pBTMCDC45 pBTMgw CDC45 This lab
pGADSIR2 pGADgw SIR2 This study
pGADMCM7 pGADgw MCM7 This lab
YCp1 LEU2 CENV ARS1 This lab
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Point mutations were introduced using a fusion-PCR (Horton et al. 1989) mutagenesis method. The DNA region to be mutagenized was PCR amplified in two separate fragments that overlap by 50–60 bp. The overlap primers contained the desired mutation. After the initial PCR, the two fragments were purified separately and used together in another PCR reaction without any template DNA or primers. The overlapping regions in the two DNA fragments acted as primers for each other and PCR produced a final molecule that contained the entire gene fragment including the mutation of interest. This fragment was then cloned into the relevant vector.

To create the strains with tagged proteins, the SIR2-3HA and MCM10-13MYC alleles were crossed out of strains WCY15, WCY39 (this lab), and ROY1515 (R. Kamakaka). These were then crossed to make strains that have both alleles. C-terminal mutations were introduced into these strains by standard homologous gene replacement methodology (Orr-Weaver et al. 1981). The last 68 amino acids from the C terminus of MCM10 were deleted and replaced with HIS3 through one-step gene replacement with a PCR product containing the HIS3 gene flanked by appropriate MCM10 homology regions.

Silencing assays:

Yeast strains bearing the URA3 reporter were grown overnight in appropriate dropout media. Tenfold serial dilutions were setup in sterile 96-well plates and a constant volume of each dilution was spotted onto the appropriate plate using a multichannel pipettor. 5-FOA was used at a concentration of 1 mg/ml. For experiments using the hmr∷ADE2 color reporter, strains were streaked out on rich media (YPD) plates, grown at 30° for 2–3 days, then placed at 4° for 3 days for further color development.

Yeast two-hybrid:

pGAD2F and pBTM116 constructs were transformed into the two-hybrid strain EGY40 carrying the pSH18-34 reporter plasmid (Fields and Song 1989). Interactions were assessed by the appearance of blue colonies on plates containing X-gal (Sigma). Ten microliters of a relevant saturated culture were spotted onto X-gal plates and photographed after 2–4 days of growth at 30°.

Minichromosome maintenance assays:

Minichromosome maintenance (MCM) assays were performed exactly as described in (Donato et al. 2006) using the plasmid YCp1.

Chromatin immunoprecipitation:

Chromatin immunoprecipitation (ChIP) experiments were performed as previously described (Goldfarb and Alani 2004) using exponentially growing cultures at 30°. Cultures of appropriate cells were grown to log phase and then the cells were lysed in buffer containing 50 mm HEPES, 1 mm EDTA, 140 mm NaCl, 1% Triton X-100, 0.1% NaDOC, and a mix of protease inhibitors as described. Five micrograms of commercially available anti-HA antibody were used for each immunoprecipitation (Roche 12CA5 no. 11583816001). Protein G agarose beads (Roche no. 1719416) were used. The immunoprecipitated DNA was analyzed with real-time PCR using SYBR Green PCR master mix from Applied Biosciences (4309155) on the DNA Engine cycler (PTC-200) with Opticon Detector (CFD-3200) from MJ Research, according to the manufacturer's instructions.

Co-immunoprecipitation:

Co-immunoprecipitation (Co-IP) experiments were performed using the same protocol as ChIP with the following differences. For experiments using DNAseI, the lysis buffer was changed to contain no EDTA, which was replaced with 5 mm MgCl2. Cells were arrested in G2/M phase using 15 μg/ml of nocodazole. The DNAseI used was from Invitrogen (no. 18068-015), and the samples were digested for 20 min at 37° with 20 units/ml of the enzyme. After the lysates were incubated with the beads and the beads were washed (same as ChIP protocol), the beads were boiled in SDS buffer containing DTT (New England Biolabs no. B7703S) for at least 1 hr and the samples were analyzed by Western blot according to standard protocols. Input lanes contained 1 μl of cell extract. Antibodies used to probe Western blots were commercial [anti-myc from Santa Cruz (9E10), anti-HA from Roche (12CA5)], from this lab (anti-LexA and anti-Mcm3), or were generously provided by other labs (anti-actin from A. Bretscher, anti-Stu2 from T. Huffaker).

Fluorescence-activated cell sorting:

For fluorescence-activated cell sorting (FACS) analysis, 1-ml aliquots of growing yeast cells were spun down and fixed using cold 70% EtOH. The cells were then rinsed twice with 1 ml of 50 mm NaCitrate. The cells were then sonicated briefly (3 times for 5 sec) at setting 4 on the VirSonic Ultrasonic Cell Disrupter 100 (SP Industries). Twelve microliters of 10 mg/ml RNAse A (QIAGEN no. 1007885) were added and the cells were incubated at 42° for 1 hr. Proteinase K (0.5 mg) was added and the sample was incubated for 1 hr at 42°. One microliter of 1 mm SYTOX Green (Invitrogen Molecular Probes no. S7020) was added for each 1 ml of cell suspension before processing the samples. The analysis was performed at The Biomedical Sciences Flow Cytometry Core Laboratory at Cornell University.

RESULTS

Pre-RC components play a role in heterochromatic silencing:

Several previously identified pre-RC mutants were tested for silencing defects. Interestingly, almost all replication mutants tested exhibited some level of silencing defect both at the telomere (Figure 1A) as well as at the HMR (Figure 1B). This observation raised the possibility that some pre-RC proteins may interact with silencing factors. Indeed, when tested in a two-hybrid system using LexA binding domain (BTM) and Gal4 activation domain (GAD) fusion proteins, several bait BTM–MCM protein constructs showed an interaction with the prey GAD–SIR2 (Figure 1C), but not with the empty GAD vector. The most obvious SIR2-interactor in this experiment was MCM7, whereas MCM3, MCM5, and MCM6 constructs showed weaker interaction signals. In addition, Mcm10 has been previously shown to interact with Sir2 (Douglas et al. 2005; Liachko and Tye 2005). Plasmids expressing mutant versions of Mcm10 (mcm10-43), Mcm3 (mcm3-10), and Mcm7 (mcm7-1) failed to activate the LacZ reporter indicating that their interaction with GAD–SIR2 was abolished (Figure 1D). These findings are interesting because they suggest a greater interaction between silencing and replication than previously described.

Figure 1.—

Figure 1.—

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Pre-RC proteins play a role in silencing. (A) Silencing reporter strains bearing conditional alleles of pre-RC proteins were plated at 30° on media containing or lacking 5-FOA, a chemical that kills cells expressing URA3. Strains used were ILY171 [wild type (WT)], ILY270 (mcm10-43), ILY178 (mcm2-1), ILY253 (mcm3-10), ILY255 (mcm4-1, or cdc54-1), ILY254 (mcm7-1), and ILY264 (cdc6-3). Silencing defects are indicated by lack of growth on 5-FOA media. Several of the mutant strains show telomeric silencing defects. (B) The effect of mcm mutants on HMR silencing was assayed using strains bearing an hmr∷ADE2 reporter (ILY171, ILY270, ILY253, and ILY254). When the HMR locus is silenced, hmr∷ADE2 cells form pink colonies, the white color of the mutant strain indicates a derepression of the HMR locus (left). No effect was observed on the color of control mutant strains BTY103, ILY115, and ILY360 (right). (C) Yeast two-hybrid experiments were conducted using BTM bait constructs containing pre-RC genes and prey constructs expressing either GAD–SIR2 or GAD (empty vector). MCM3 and MCM7 constructs showed strong activation of the LacZ reporter (indicated in blue) with GAD–SIR2 while MCM5 and MCM6 showed weaker activation. (D) Bait plasmids expressing pre-RC mutants fail to interact with GAD–SIR2 as well as the wild-type fusion proteins.

Mcm10 and Mcm3 interact with Sir2 in G2 phase in a DNA-independent manner:

Mcm10, Mcm3, and Mcm7 are all DNA replication proteins. Therefore, it is important to examine whether their interaction with Sir2 is restricted within the context of DNA replication. Since the process of DNA replication is limited to S phase, this question can be addressed by performing Co-IP experiments on cells arrested in the G2/M phase of the cell cycle. Yeast cells expressing 3HA-tagged Sir2, and 13myc-tagged Mcm10, or Mcm10-43 proteins were arrested at the beginning of M phase using nocodazole, a microtubule inhibitor. Their FACS profiles showed strong arrest phenotypes (Figure 2A). These arrested cultures were subsequently used for Co-IPs. Immunoprecipitation either without anti-HA antibody or using an untagged Sir2 strain (data not shown) did not precipitate any assayed proteins. However, both Mcm3 and 13myc–Mcm10 were precipitated by the anti-HA antibody in a SIR2–3HA cell extract. In all cases, Sir2–3HA failed to pull down either actin or a microtubule associated protein Stu2. There was no detectable change in the Mcm3/Sir2 interaction or in the Mcm10/Sir2 interaction between asynchronous and G2/M arrested cells (Figure 2A). In both cases, Mcm10-43 mutant protein failed to interact with Sir2 and inhibited the ability of Mcm3 to interact with Sir2 as well. To test whether the Sir2/Mcm interaction is DNA dependent, we performed Co-IPs using extracts that were treated with DNAseI (Figure 2B). Our results showed no difference in interaction between DNAseI treated and untreated samples. To exclude the possibility that the Sir2–MCM interaction is protected by silent chromatin, we performed a similar experiment in a sir3Δ background strain and observed no effect of DNAse on the interaction between Mcm10 and Sir2 (Figure 2C). These findings correlate with the two-hybrid results and support the hypothesis that DNA replication proteins, in this case Mcm10 and Mcm3, play a role in silencing that may not be restricted to S phase.

Figure 2.—

Figure 2.—

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Sir2's interaction with Mcm3 and Mcm10 is not dependent on DNA and can occur in G2/M phase. (A) Strains ILY273 (SIR2-HA) and ILY275 (SIR2-HA mcm10-43) were arrested using nocodazole. FACS analysis shows the arrest profiles of cells used for Co-IP experiments. Both arrested and asynchronous cultures were used for Co-IPs either with no antibody added or using anti-HA antibody (anti-HA IP). Precipitated samples were analyzed by Western blots probed for myc-Mcm10, Mcm3, actin, and Stu2. One microliter of cell extract was used as input control (IN) for each immunoprecipitated sample (IP). (B) Co-IPs were performed using strain ILY273. Before the addition of antibody, cell extracts were either treated with DNAseI (two rightmost lanes) or not (four leftmost lanes). (C) The same as in B, only using strains ILY230 (two leftmost lanes) and ILY328 (four rightmost lanes).

A 53-amino-acid domain in the C terminus of Mcm10 is necessary and sufficient for the interaction of Mcm10 with Sir2, Mcm3, and Mcm7:

The Mcm10-43 and Mcm10-1 mutant proteins are temperature labile proteins (Ricke and Bielinsky 2004; Sawyer et al. 2004) each containing a single-amino-acid change that affects the overall structure of Mcm10 and destroys its interaction with Sir2. Previous work showed that Mcm10 interacts with Sir2 and that this interaction depends on the C terminus of Mcm10 (Douglas et al. 2005; Liachko and Tye 2005). To isolate the domain that is responsible for the Mcm10/Sir2 interaction, bait plasmids expressing fragments of the C terminus of MCM10 were coexpressed with a SIR2 prey construct in a yeast two-hybrid system. The BTM–MCM10 truncation constructs were designed by using a comparative genomic approach to identify conserved regions within the C terminus (data not shown). All BTM constructs expressed robustly in vivo as shown by Western blots (Figure 3B). Several BTM–MCM10 truncation constructs interacted with GAD–SIR2, but some did not (Figure 3A). The pattern of interactions indicated that a region between amino acids Ser503 and Lys555 of Mcm10 was necessary for the interaction with Sir2. The expression of the bait plasmid bearing this 53-amino-acid fragment resulted in an interaction with GAD–SIR2 in the two-hybrid system (Figure 3A). None of the truncation constructs activated the two-hybrid reporter when coexpressed with an empty GAD plasmid, suggesting that amino acids 503–555 of Mcm10 are necessary and sufficient for the interaction with Sir2.

Figure 3.—

Figure 3.—

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Amino acids Ser503–Lys555 of Mcm10 are necessary and sufficient for interaction with Sir2. (A) Yeast two-hybrid experiments were performed using the EGY40 strain and BTM bait constructs expressing truncations of MCM10 as indicated. The blue color indicates the activation of the LacZ reporter signaling a positive interaction. (B) Western blots were used to confirm the expression of the truncation constructs used in A. (C) Constructs expressing mutant versions of MCM10 were used in two-hybrid experiments. (D) The expression of bait constructs from C assayed by Western blots.

To further characterize the Sir2-interaction domain of Mcm10 we used a computational approach to identify potential secondary structures within this region. Secondary structure prediction (http://www.compbio.dundee.ac.uk/∼www-jpred/) suggested that there was an amphipathic helical region between amino acids Thr515 and Tyr523 of Mcm10 (data not shown). To test whether this region was necessary for the Sir2/Mcm10 interaction, site-directed mutagenesis was used to introduce one of three mutations (T515V, I517T, and D519N) into this helical domain. Two of these mutations (I517T and D519N) abolished the interaction between Mcm10 and Sir2 in two-hybrid assays (Figure 3C). In addition, deletion of the last 68 amino acids of Mcm10 [mcm10(1–502)] also disrupted the Mcm10/Sir2 interaction. These mutations did not cause the destabilization of the bait proteins (Figure 3D), suggesting that the loss of interaction was due to the effect of the mutations on the structure of Mcm10. In addition, The D519N mutant, as well as the truncation removing the interacting domain (1–502) abolished the interaction of BTM–MCM10 with GAD–MCM3 and GAD–MCM7 (Figure 3C).

Mcm10 mediates the interaction between MCM2-7 and SIR2:

The disruption of Mcm10's interaction with Sir2 as well as with Mcm3 and Mcm7 by the mcm10-D519N mutation (Figure 3C) suggests that Mcm10 may mediate the interactions between the MCM2–7 complex and Sir2. This possibility is further supported by our Co-IP results, which showed that the Sir2/Mcm3 interaction is disrupted in mcm10-43 background (Figure 2A). To test this hypothesis, interaction studies were performed using strains bearing different mcm mutant alleles. In a strain bearing the mcm10-43 allele or the mcm10(1–502) allele, Sir2 was not able to efficiently coprecipitate Mcm10 or Mcm3 (Figure 4A). However, some Sir2/Mcm3 interaction remained in mcm10(1–502) background, suggesting that mcm10-43 has a greater effect on the Sir/MCM2–7 interactions than mcm10(1–502). These Co-IP results support the two-hybrid data showing that mutant Mcm10 proteins are not able to interact with Sir2 (Douglas et al. 2005; Liachko and Tye 2005). To test whether Mcm10 is also required for the Sir2/Mcm7 interaction, yeast two-hybrid experiments were performed in a mcm10-1 strain background. While BTM–MCM7 is able to interact with GAD–SIR2 in a wild-type strain background, this interaction disappears in a mcm10 mutant strain (Figure 4B). This finding supports the hypothesis that Mcm10 mediates the interaction between MCMs and Sir2.

Figure 4.—

Figure 4.—

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Mcm10 mediates Sir2's interaction with Mcm3 and Mcm7. (A) Co-IP experiments were performed on strains ILY273 (first four lanes), ILY275 (fifth and sixth lanes), and ILY330 (the two rightmost lanes). The Western blot was probed with anti-myc and anti-Mcm3 antibodies. (B) The two-hybrid reporter plasmid pSH18-34 was transformed into strains W303-1A (WT), BTY100 (mcm10-1), and ILY185 (sir2Δ). Two-hybrid bait and prey constructs bearing SIR2, MCM3, and MCM7 were used to assay interactions. (C) Co-IP experiments were performed in strains ILY273 (first four lanes), ILY338 (mcm3-10), and ILY346 (mcm7-1) as in A and B.

While Mcm10 is required for the interaction of Mcm3 and Mcm7 with Sir2, it is also possible that Mcm3 and Mcm7 are required for the interaction of Mcm10 with Sir2. To test this possibility, Co-IPs were performed in strains bearing mutant mcm3 or mcm7 alleles (Figure 4C). Both mcm3-10 and mcm7-1 mutations abolished the interaction between Mcm3 and Sir2, suggesting that Mcm3 and Mcm7 may interact with Sir2 as a complex. However, these mutations had no effect on the Mcm10/Sir2 interaction supporting the hypothesis that Mcm10 acts as a bridge between the MCMs and the SIRs.

Mutations in the Sir2 interacting domain of Mcm10 cause defects in silencing, but not replication:

To test what effect the mcm10 C-terminal mutations have on silencing and replication, these mutations were introduced into the genome of a strain bearing a telomeric silencing reporter. Both T515V and I517T mutations did not confer a measurable silencing defect, while D519N conferred a slight defect that could be complemented by a wild-type copy of MCM10 (Figure 5A). This defect was relatively weak compared to the defect conferred by the temperature-sensitive mcm10-1 or mcm10-43 alleles. In addition, an mcm10(1–502) mutant strain bearing a deletion of the C-terminal 68 amino acids of MCM10 was viable, which is consistent with previous results showing that this region is not essential for growth (Douglas et al. 2005). This truncation allele conferred a slight silencing defect (Figure 5A). This defect was very similar to that caused by the mcm10-D519N allele, suggesting that the D519N mutation has a significant effect on the structure of the C terminus of Mcm10 since its phenotype resembles a deletion of the C terminus. Deletion of the C-terminal fragment in a mcm10-43 background increased the silencing defect indicating that mcm10-43 retains some silencing function that is mediated by the C-terminal domain.

Figure 5.—

Figure 5.—

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C-terminal mutants of MCM10 exhibit silencing, but not replication defects. (A) Serial dilutions of mcm10 mutant strains bearing a telomeric URA3 reporter gene were plated on media with or without 5-FOA to assay telomeric silencing. The strains used were ILY248 (WT), ILY180 (mcm10-1), ILY288 (mcm10-T515V), ILY295 (mcm10-I517T), ILY298 (mcm10-D519N), ILY336 [mcm10(1–502)], ILY332 (mcm10-43), and ILY334 [mcm10-43(1–502)]. The mcm10-D519N mutant strain displays a silencing defect, but the same strain with a YCp plasmid bearing a copy of MCM10 (pRS315-MCM10) does not. (B) mcm10-1 mutant strain ILY180 was transformed with two-hybrid bait plasmids expressing MCM10 alleles as indicated. The cells were assayed for silencing activity on 5-FOA media and for temperature sensitivity on complete media at 37°. (C) Minichromosome maintenance assays performed on strains from A to measure the rate of loss of ARS1-bearing plasmid YCp1.

Expression plasmids bearing different MCM10 alleles were transformed into a silencing reporter strain bearing the temperature-sensitive mcm10-1 mutation (Figure 5B). Plasmids expressing MCM10, mcm10-T515V, and mcm10-I517T fully complemented both the temperature sensitivity of mcm10-1 as well as its silencing defect. Plasmids expressing mcm10-D519N and mcm10(1–502) complemented the temperature sensitivity, but did not fully complement the silencing defect. These results further corroborate the silencing phenotypes observed in Figure 5A. Expression of the mcm10(503–555) domain did not complement the silencing defect nor the temperature sensitivity of the mcm10-1 strain. This suggests that although this short domain of Mcm10 is necessary and sufficient for the interaction of Mcm10 with Sir2, it is not sufficient to restore silencing or replication functions of Mcm10.

We have previously shown that second site suppressors of the conditional lethality of mcm10-1 do not suppress the silencing defect caused by this mutation (Liachko and Tye 2005). This phenotype-specific suppression suggests that the replication function of Mcm10 can be modulated independently of its silencing function. Since the C-terminal mutations in Mcm10 cause silencing defects, we assayed them for replication defects as well. To test the effect of C-terminal Mcm10 mutations on DNA replication, minichromosome maintenance assays were performed. These assays are used to measure the loss of an ARS-bearing plasmid, indicative of a defect in replication (Maine et al. 1984; Donato et al. 2006). Despite the fact that the mutation in mcm10-D519N caused a silencing defect, it did not cause a measurable minichromosome maintenance defect (Figure 5C). Furthermore, deletion of the last 68 amino acids from the C terminus of Mcm10 in either wild-type or mcm10-43 backgrounds did not increase minichromosome loss (Figure 5C). These findings suggest that the replication function of MCM10 is separate from its silencing function.

Mcm10 does not regulate the association of Sirs with silent chromatin:

Previous work has shown that Mcm10 plays a role in the maintenance of silent heterochromatin; however, very little is known about the mechanism through which this occurs (Liachko and Tye 2005). One possibility is that Mcm10 may have an effect on the association of Sir proteins with chromatin. A defect in such a function could lead to a gradual dissociation of the Sirs from the silent regions without necessarily affecting the initial establishment of silencing. To test this possibility, ChIP experiments were conducted to measure the association of Sir2 with silenced regions of the genome in mcm mutant strains (Figure 6). ChIP experiments were performed on SIR2 (untagged) and SIR2–3HA strains using the anti-HA antibody and the precipitated DNA was analyzed by real-time PCR.

Figure 6.—

Figure 6.—

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Mcm10 does not regulate the association of Sir2 with chromatin. (A) DNA obtained by anti-HA ChIP from strains ILY230 (untagged), ILY273 (WT), ILY275 (mcm10-43), ILY253 (mcm3-10), and ILY348 (sir4Δ) was analyzed by quantitative real-time PCR. The bars show relative enrichment of IP samples over 10% input controls. The sites probed were the silencers HMR-E, HML-E, the nearby genes a1 and α2, and the GPX1 gene region as a negative control. (B) A similar ChIP experiment using strains bearing telVII∷URA3 and hmr∷ADE2 silencing reporters. The mcm mutants did not significantly reduce the amount of DNA precipitated with an anti-HA antibody. This holds true for both the telomeric and HMR loci. The strains used were ILY171 (untagged), ILY351 (mcm10-1), ILY353 (mcm10-43), ILY355 (mcm3-10), and ILY357 (mcm7-1). All ChIP experiments were performed at 30°.

Our results show that Sir2–3HA readily associates with silent regions HMR-E and HML-E, but not with a control gene region GPX1. No DNA was precipitated from a strain bearing an untagged SIR2 allele. A control strain bearing the deletion of SIR4 abolished the interaction of Sir2–3HA with chromatin as previously shown (Figure 6A) (Rusche et al. 2002). We have observed previously that mcm10-1 and mcm10-43 mutations cause the derepression of the HMR and HML loci (Liachko and Tye 2005). Strains bearing mcm3-10 and mcm7-1 alleles also show similar defects in silencing (Figure 1). However, neither mcm10-43 nor mcm3-10 strains had a measurable effect on the association of Sir2 with these regions. We have also tested the effect of mcm alleles on the association of Sir2 with silencing reporters used in Figure 1. We did not detect a significant difference in Sir2's association with the telomeric URA3 reporter nor the hmr∷ADE2 reporter (Figure 6B). These results suggest that Mcm10 does not regulate the association of Sir2 with silent chromatin.

In addition, neither mcm10 nor mcm3 mutations affected the association of Sir2 with a1 or α2 genes (Figure 6). These genes reside within the HM loci and are silenced by the spreading of the Sir2–4 proteins from the HMR and HML silencers (Rusche et al. 2002, 2003). Our finding suggests that mcm mutations do not affect the spreading of Sir proteins after the initial binding to the HMR and HML silencers.

DISCUSSION

We have used several assays to demonstrate that novel protein–protein interactions between components of the replication fork complex (Mcm3 and Mcm7) and the Sir2 histone deacetylase are essential for silencing (Figure 1C). This study is the first direct evidence that members of the replicative helicase physically interact with the chromatin silencing machinery. This interaction is not affected by DNAse treatment and persists in the G2/M phases of the cell cycle (Figure 2), suggesting the possibility that it takes place outside of the context of DNA replication. The mutant allele mcm7-1 disrupts the interaction between Sir2 and Mcm3 (Figure 4C), but not between Sir2 and Mcm10. This finding suggests that Mcm3 and Mcm7 act in a complex, possibly in a fashion similar to their action in DNA replication. In addition, silencing assays performed on mutants of these genes showed defects in telomeric as well as HMR silencing (Figure 1, A and B). Together these results implicate members of the pre-RC in transcriptional silencing. It is not yet known by what mechanism these proteins influence the formation of silent chromatin, but it has become clear that Mcm10 mediates these interactions. The net outcome of a failure to mediate these interactions is that the silencing machinery that is recruited to chromatin no longer efficiently silences chromatin.

Previously, Mcm10, an essential protein involved in both the initiation and elongation of DNA replication (Merchant et al. 1997; Kawasaki et al. 2000; Ricke and Bielinsky 2004) has been implicated in the maintenance of silencing (Douglas et al. 2005; Liachko and Tye 2005). Here we show that this protein interacts with several members of the silencing machinery and is required for the interaction between Sir2 and Mcm3 and Mcm7 (Figures 2A and 4). Careful dissection of this interaction has isolated a short region at the C terminus of the Mcm10 protein that is both necessary and sufficient for the interaction with Sir2 (Figure 3A). Mutations in this region abolish not only the interaction of Mcm10 with Sir2, but also with several previously characterized interacting partners of Mcm10 involved in DNA replication (Figure 3C). However, only the mutants that abolish interactions between Mcm10 as well as the other replication factors are able to confer a silencing defect (Figures 3C and 5). This observation suggests that the function of Mcm10 in silencing may be as a mediator between these other factors.

It is also notable that C-terminal mcm10 mutations confer much weaker silencing defects than mcm10-1 and mcm10-43 mutations despite the fact that both types of mutations disrupt interactions with Sir2. In addition, mutating the C terminus of mcm10-43 increases its already significant silencing defect (Figure 5A). One explanation is that the C terminus is only partially responsible for mediating these interactions and other parts of Mcm10 also contribute. This idea is supported by the observation that in Co-IP experiments C-terminal mutants disrupt the Sir2/Mcm10 interaction, but retain some of the Sir2/Mcm3 interaction (Figure 4A). It is unlikely that an overall conformational change of Mcm10-43p is the whole explanation for the disruption of Mcm10's interactions with Sir2 and Mcm3 (Figure 1) because a mutation in the C terminus exacerbated this phenotype (Figure 5A). A more plausible explanation for these observations is that Mcm10's function in silencing is more complex, possibly involving numerous interactions with yet unidentified proteins. The C-terminal domain could regulate some aspects of this function, whereas other aspects could be regulated by another part of the protein, so mutating both regions of Mcm10 has a cumulative effect on silencing. Recent studies suggest that Mcm10 may function as a ring complex of six subunits (Cook et al. 2003; Okorokov et al. 2007). It is conceivable that individual subunits of the Mcm10 complex may interact with a different set of interactors.

Several models have been proposed for the mechanism of Mcm10 function in silent chromatin structure on the basis of previous findings (Liachko and Tye 2005). One model suggested that Mcm10 may be part of silent chromatin itself. However, a recent study showed that Mcm10 is only associated with chromatin during S phase (Ricke and Bielinsky 2004), making this model unlikely since silent chromatin must persist throughout most of the cell cycle. Another model suggested that Mcm10 may regulate the association of Sir2 with chromatin. However, results of this study have shown that this is not the case (Figure 6). Another hypothesis suggested that Mcm10 regulates the transition from initial binding of Sir proteins to their spreading along the chromatin. We have shown that mcm mutations did not have an effect on the association of Sir2 with HMR-E and HML-E silencers, nor with mating type genes a1 and α2 (Figure 6A), which are silenced by the spreading of Sir proteins (Rusche et al. 2002, 2003). Neither did these mutations affect the chromatin association of Sir2 with telomeric or HMR-based reporter genes, which are also silenced by the spreading of the Sirs and silent chromatin (Figure 6B). Since spreading of the Sirs requires the Sir2 deacetylase activity (Rusche et al. 2002), this result also rules out Mcm10 playing a role in the activation of Sir2. While it may seem counterintuitive that silencing can be disrupted without affecting Sir association, these findings are consistent with a recent study showing that the association of Sir proteins with silent regions are uncoupled from transcriptional silencing at these regions (Kirchmaier and Rine 2006).

The findings that Mcm10 interacts with chromatin only during S phase, but can interact with Sir2 in other phases of the cell cycle, imply that the Mcm10/Sir2 interaction occurs away from the chromatin. A consistent model is that Mcm10 stabilizes the complex formation between Sir2 and additional factors that modify Sir2 in such a way as to make it more competent for silencing (Figure 7). If Mcm10 or other MCMs are defective, unmodified or improperly associated, then Sir2 will be incorporated into heterochromatin and silencing will be reduced. One potential player in such a mechanism may be the Cdc7-Dbf4 kinase which has also been implicated in silencing (Axelrod and Rine 1991; Rehman et al. 2006). In Schizosaccharomyces pombe the homolog of Cdc7-Dbf4 has been shown to phosphorylate the homolog of HP-1 in a DNA replication-independent manner (Bailis et al. 2003). Cdc7-Dbf4 is also able to phosphorylate the Mcm2–7 complex, in a Mcm10-dependent manner (Lee et al. 2003). Since Mcm10 has been shown to physically interact with both HP-1 and Mcm proteins (Merchant et al. 1997; Christensen and Tye 2003), it is conceivable that in budding yeast Mcm10 is required for Cdc7-Dbf4 to phosphorylate one of the SIRs, in lieu of HP-1, which is not found in budding yeast. This model is also consistent with data showing that Mcm10 is required to maintain an interaction between Cdc17 and Pol12, and that maintenance of this complex is necessary for Pol12 phosphorylation (Ricke and Bielinsky 2006). This idea is also consistent with what is already known about the function of Mcm10 as a stabilizing factor for larger complexes, such as the pre-RC and the polymerase-α/primase complex.

Figure 7.—

Figure 7.—

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Model for MCM function in silencing. (A) Mcm10 stabilizes the interactions between Sir2 and Mcm2–7 proteins. This complex can be acted upon by a set of modifying factors. The modified version of Sir2 is then assembled into functional silent chromatin. (B) If MCM10 is mutated, it cannot stabilize the complex in A and therefore fewer of the Sir2 molecules are modified, resulting in weaker silencing.

This study raises interesting possibilities on the nature of the relationship between silencing and replication. Past studies have implicated DNA replication factors in connection with transcriptional silencing, however several other studies have shown that the process of replication is not required for silencing (Miller and Nasmyth 1984; Kirchmaier and Rine 2001; Li et al. 2001; Lau et al. 2002; Martins-Taylor et al. 2004). This apparent contradiction suggests that DNA replication factors may have nonreplication functions. Indeed, this has been clearly demonstrated with the ORC (Bell et al. 1993; Foss et al. 1993; Micklem et al. 1993; Ehrenhofer-Murray et al. 1995; Loo et al. 1995; Triolo and Sternglanz 1996; Dillin and Rine 1997; Fox et al. 1997; Zhang et al. 2002; Hou et al. 2005; Hsu et al. 2005). In addition, recent work has shown a genetic interaction between Sir2 and members of the pre-RC where deletion of SIR2 rescues temperature-sensitive pre-RC mutants (Pappas et al. 2004; Crampton et al. 2008). This finding suggests that Sir2 plays a role in regulating replication. It is not yet known whether the interactions shown in this study are relevant for both replication and silencing. Notably, second site suppressors of mcm10-1 fail to rescue its silencing defect (Liachko and Tye 2005). Also, several silencing defective mcm10 mutants do not exhibit replication defects (Figure 5). These observations, along with the finding that the Mcm–Sir2 interaction persists outside of S phase (Figure 2A) argue that Mcm10's silencing function may be separate from its replication function. Future studies in this area should further elucidate the connection between DNA replication and silent chromatin.

Acknowledgments

We thank the Bretscher, Huffaker, Roberts, and Kamakaka labs for providing antibodies and strains. We also thank Amy Lyndaker for help with ChIP and Justin Donato and Tim Christensen for helpful discussions and critical reading of the manuscript. This project is supported by National Science Foundation MCB-0453773 and National Institutes of Health (NIH) GM-072557. I.L. is supported by NIH training grant 3 T32 GM-07617-25S2.

References

  1. Axelrod, A., and J. Rine, 1991. A role for CDC7 in repression of transcription at the silent mating-type locus HMR in Saccharomyces cerevisiae. Mol. Cell. Biol. 11 1080–1091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bailis, J., P. Bernard, R. Antonelli, R. Allshire and S. Forsburg, 2003. Hsk1-Dfp1 is required for heterochromatin-mediated cohesion at centromeres. Nat. Cell Biol. 5 1111–1116. [DOI] [PubMed] [Google Scholar]
  3. Bell, S., R. Kobayashi and B. Stillman, 1993. Yeast origin recognition complex functions in transcriptional silencing and DNA replication. Science 262 1844–1849. [DOI] [PubMed] [Google Scholar]
  4. Burke, T. W., J. G. Cook, M. Asano and J. R. Nevins, 2001. Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1. J. Biol. Chem. 276 15397–15408. [DOI] [PubMed] [Google Scholar]
  5. Christensen, T. W., and B. K. Tye, 2003. Drosophila Mcm10 interacts with members of the prereplication complex and is required for proper chromosome condensation. Mol. Biol. Cell 14 2206–2215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cook, C. R., G. Kung, F. C. Peterson, B. F. Volkman and M. Lei, 2003. A novel zinc finger is required for Mcm10 homocomplex assembly. J. Biol. Chem. 278 36051–36058. [DOI] [PubMed] [Google Scholar]
  7. Crampton, A., F. Chang, D. L. Pappas, Jr., R. L. Frisch and M. Weinreich, 2008. An ARS element inhibits DNA replication through a SIR2-dependent mechanism. Mol. Cell 30 156–166. [DOI] [PubMed] [Google Scholar]
  8. Das-Bradoo, S., R. M. Ricke and A.-K. Bielinsky, 2006. Interaction between PCNA and diubiquitinated Mcm10 is essential for cell growth in budding yeast. Mol. Cell. Biol. 26 4806–4817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dillin, A., and J. Rine, 1997. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics 147 1053–1062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Donato, J. J., S. C. C. Chung and B. K. Tye, 2006. Genome-wide hierarchy of replication origin usage in Saccharomyces cerevisiae. PLoS Genet. 2 e141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Douglas, N. L., S. K. Dozier and J. J. Donato, 2005. Dual roles for Mcm10 in DNA replication initiation and silencing at the mating-type loci. Mol. Biol. Rep. V32 197–204. [DOI] [PubMed] [Google Scholar]
  12. Dziak, R., D. Leishman, M. Radovic, B. K. Tye and K. Yankulov, 2003. Evidence for a role of MCM (mini-chromosome maintenance)5 in transcriptional repression of sub-telomeric and Ty-proximal genes in Saccharomyces cerevisiae. J. Biol. Chem. 278 27372–27381. [DOI] [PubMed] [Google Scholar]
  13. Ehrenhofer-Murray, A. E., M. Gossen, D. T. Pak, M. R. Botchan and J. Rine, 1995. Separation of origin recognition complex functions by cross-species complementation. Science 270 1671–1674. [DOI] [PubMed] [Google Scholar]
  14. Ehrenhofer-Murray, A. E., R. T. Kamakaka and J. Rine, 1999. A role for the replication proteins PCNA, RF-C, Polymerase-ɛ and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae. Genetics 153 1171–1182. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fields, S., and O. Song, 1989. A novel genetic system to detect protein-protein interactions. Nature 340 245–246. [DOI] [PubMed] [Google Scholar]
  16. Forsburg, S., 2004. Eukaryotic MCM proteins: beyond replication initiation. Microbiol. Mol. Biol. Rev. 68 109–131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Foss, M., F. J. McNally, P. Laurenson and J. Rine, 1993. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science 262 1838–1844. [DOI] [PubMed] [Google Scholar]
  18. Fox, C. A., A. E. Ehrenhofer-Murray, S. Loo and J. Rine, 1997. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science 276 1547–1551. [DOI] [PubMed] [Google Scholar]
  19. Goldfarb, T., and E. Alani, 2004. Chromatin immunoprecipitation to investigate protein-DNA interactions during genetic recombination. Methods Mol. Biol. 262 223–237. [DOI] [PubMed] [Google Scholar]
  20. Homesley, L., M. Lei, Y. Kawasaki, S. Sawyer, T. Christensen et al., 2000. Mcm10 and the MCM2–7 complex interact to initiate DNA synthesis and to release replication factors from origins. Genes Dev. 14 913–926. [PMC free article] [PubMed] [Google Scholar]
  21. Hoppe, G. J., J. C. Tanny, A. D. Rudner, S. A. Gerber, S. Danaie et al., 2002. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol. 22 4167–4180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Horton, R. M., H. D. Hunt, S. N. Ho, J. K. Pullen and L. R. Pease, 1989. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77 61–68. [DOI] [PubMed] [Google Scholar]
  23. Hou, Z., D. A. Bernstein, C. A. Fox and J. L. Keck, 2005. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc. Natl. Acad. Sci. USA 102 8489–8494. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Hsu, H.-C., B. Stillman and R.-M. Xu, 2005. Structural basis for origin recognition complex 1 protein-silence information regulator 1 protein interaction in epigenetic silencing. Proc. Natl. Acad. Sci. USA 102 8519–8524. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Imai, S., C. Armstrong, M. Kaeberlein and L. Guarente, 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403 795–800. [DOI] [PubMed] [Google Scholar]
  26. Ishimi, Y., 1997. A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex. J. Biol. Chem. 272 24508–24513. [DOI] [PubMed] [Google Scholar]
  27. Kawasaki, Y., S.-I. Hiraga and A. Sugino, 2000. Interactions between Mcm10p and other replication factors are required for proper initiation and elongation of chromosomal DNA replication in Saccharomyces cerevisiae. Genes Cells 5 975–989. [DOI] [PubMed] [Google Scholar]
  28. Kirchmaier, A. L., and J. Rine, 2001. DNA replication-independent silencing in S. cerevisiae. Science 291 646–650. [DOI] [PubMed] [Google Scholar]
  29. Kirchmaier, A. L., and J. Rine, 2006. Cell cycle requirements in assembling silent chromatin in Saccharomyces cerevisiae. Mol. Cell. Biol. 26 852–862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kyrion, G., K. Liu, C. Liu and A. Lustig, 1993. RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev. 7 1146–1159. [DOI] [PubMed] [Google Scholar]
  31. Lau, A., H. Blitzblau and S. P. Bell, 2002. Cell-cycle control of the establishment of mating-type silencing in S. cerevisiae. Genes Dev. 16 2935–2945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lee, J.-K., and J. Hurwitz, 2000. Isolation and characterization of various complexes of the minichromosome maintenance proteins of Schizosaccharomyces pombe. J. Biol. Chem. 275 18871–18878. [DOI] [PubMed] [Google Scholar]
  33. Lee, J.-K., Y.-S. Seo and J. Hurwitz, 2003. The Cdc23 (Mcm10) protein is required for the phosphorylation of minichromosome maintenance complex by the Dfp1-Hsk1 kinase. Proc. Natl. Acad. Sci. USA 100 2334–2339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Lei, M., Y. Kawasaki and B. Tye, 1996. Physical interactions among Mcm proteins and effects of Mcm dosage on DNA replication in Saccharomyces cerevisiae. Mol. Cell. Biol. 16 5081–5090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Li, Y.-C., T.-H. Cheng and M. R. Gartenberg, 2001. Establishment of transcriptional silencing in the absence of DNA replication. Science 291 650–653. [DOI] [PubMed] [Google Scholar]
  36. Liachko, I., and B. K. Tye, 2005. Mcm10 is required for the maintenance of transcriptional silencing in Saccharomyces cerevisiae. Genetics 171 503–515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Liang, D., J. Hodson and S. Forsburg, 1999. Reduced dosage of a single fission yeast MCM protein causes genetic instability and S phase delay. J. Cell Sci. 112 559–567. [DOI] [PubMed] [Google Scholar]
  38. Loo, S., C. Fox, J. Rine, R. Kobayashi, B. Stillman et al., 1995. The origin recognition complex in silencing, cell cycle progression, and DNA replication. Mol. Biol. Cell 6 741–756. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Maine, G. T., P. Sinha and B.-K. Tye, 1984. Mutants of S. cerevisiae defective in the maintenance of minichromosomes. Genetics 106 365–385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Martins-Taylor, K., M. L. Dula and S. G. Holmes, 2004. Heterochromatin spreading at yeast telomeres occurs in M phase. Genetics 168 65–75. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. McNally, F. J., and J. Rine, 1991. A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae. Mol. Cell. Biol. 11 5648–5659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Merchant, A., Y. Kawasaki, Y. Chen, M. Lei and B. Tye, 1997. A lesion in the DNA replication initiation factor Mcm10 induces pausing of elongation forks through chromosomal replication origins in Saccharomyces cerevisiae. Mol. Cell. Biol. 17 3261–3271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Micklem, G., A. Rowley, J. Harwood, K. Nasmyth and J. Diffley, 1993. Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. Nature 366 87–89. [DOI] [PubMed] [Google Scholar]
  44. Miller, A., and K. Nasmyth, 1984. Role of DNA replication in the repression of silent mating type loci in yeast. Nature 312 247–251. [DOI] [PubMed] [Google Scholar]
  45. Moretti, P., K. Freeman, L. Coodly and D. Shore, 1994. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 8 2257–2269. [DOI] [PubMed] [Google Scholar]
  46. Okorokov, A., A. Waugh, J. Hodgkinson, A. Murthy, H. Hong et al., 2007. Hexameric ring structure of human MCM10 DNA replication factor. EMBO Rep. 8 925–930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Orr-Weaver, T., J. Szostak and R. Rothstein, 1981. Yeast transformation: a model system for the study of recombination. Proc. Natl. Acad. Sci. USA 78 6354–6358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Pappas, Jr., D. L., R. Frisch and M. Weinreich, 2004. The NAD+-dependent Sir2p histone deacetylase is a negative regulator of chromosomal DNA replication. Genes Dev. 18 769–781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Pillus, L., and J. Rine, 1989. Epigenetic inheritance of transcriptional states in S. cerevisiae. Cell 59 637–647. [DOI] [PubMed] [Google Scholar]
  50. Rehman, M. A., G. Fourel, A. Mathews, D. Ramdin, M. Espinosa et al., 2006. Differential requirement of DNA replication factors for subtelomeric ACS proto-silencers in S.cerevisiae. Genetics 174 1801–1810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Ricke, R. M., and A.-K. Bielinsky, 2004. Mcm10 regulates the stability and chromatin association of DNA Polymerase-α. Mol. Cell 16 173–185. [DOI] [PubMed] [Google Scholar]
  52. Ricke, R. M., and A.-K. Bielinsky, 2006. A conserved Hsp10-like domain in Mcm10 is required to stabilize the catalytic subunit of DNA Polymerase-α in budding yeast. J. Biol. Chem. 281 18414–18425. [DOI] [PubMed] [Google Scholar]
  53. Rusche, L. N., A. L. Kirchmaier and J. Rine, 2002. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell 13 2207–2222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Rusche, L. N., A. L. Kirchmaier and J. Rine, 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72 481–516. [DOI] [PubMed] [Google Scholar]
  55. Sawyer, S. L., I. H. Cheng, W. Chai and B. K. Tye, 2004. Mcm10 and Cdc45 cooperate in origin activation in Saccharomyces cerevisiae. J. Mol. Biol. 340 195–202. [DOI] [PubMed] [Google Scholar]
  56. Sherman, F., 1991. Getting started with yeast. Methods Enzymol. 194 3–21. [DOI] [PubMed] [Google Scholar]
  57. Thon, G., P. Bjerling, C. M. Bunner and J. Verhein-Hansen, 2002. Expression-state boundaries in the mating-type region of fission yeast. Genetics 161 611–622. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Triolo, T., and R. Sternglanz, 1996. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature 381 251–253. [DOI] [PubMed] [Google Scholar]
  59. Tye, B. K., 1999. Mcm proteins in DNA replication. Annu. Rev. Biochem. 68 649–686. [DOI] [PubMed] [Google Scholar]
  60. Tye, B. K., and S. Sawyer, 2000. The hexameric eukaryotic MCM helicase: building symmetry from nonidentical parts. J. Biol. Chem. 275 34833–34836. [DOI] [PubMed] [Google Scholar]
  61. Yang, X., J. Gregan, K. Lindner, H. Young and S. E. Kearsey, 2005. Nuclear distribution and chromatin association of DNA polymerase α-primase is affected by TEV protease cleavage of Cdc23 (Mcm10) in fission yeast. BMC Mol. Biol. 6 13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Zhang, Z., M. K. Hayashi, O. Merkel, B. Stillman and R.-M. Xu, 2002. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J. 21 4600–4611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Zhang, Z., K. Shibahara and B. Stillman, 2000. PCNA connects DNA replication to epigenetic inheritance in yeast. Nature 408 221–225. [DOI] [PubMed] [Google Scholar]

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