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Nuclear Position Leaves Its Mark on Replication Timing

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The functional significance of this program is not understood, but, in general, transcriptionally active chromatin replicates early in S phase, whereas hypoacetylated, transcriptionally inactive chromatin replicates later... During metazoan development, multiple origins, encompassing megabase domains of chromosomes, exhibit replication timing switches that precede gene activation and accompany changes in chromatin structure (Selig et al. 1992)... These early- and late-replicating chromosomal domains are localized to distinct spatial compartments of the metazoan nucleus where DNA synthesis can be observed to take place at defined times during S phase... While many laboratories have catalogued the replication timing of various genes and related this to their transcriptional activity and overall chromatin structure, very few studies have addressed the problem of what actually regulates replication timing... The authors wisely chose to restrict their analysis to G1 phase cells, to avoid potential movements that might take place during S phase; movements which they later confirm can be quite dynamic... By dividing the nucleus into five concentric zones, they found that early origins were localized randomly throughout the nucleus, while late origins were preferentially localized to the most peripheral zone, albeit not as frequently as telomeres... One potential caveat to this result is that the late replicating plasmid was nearly three times larger than the early replicating plasmid (24 kb vs. 9.4 kb)... However, others have shown that plasmid size per se does not influence replication timing (Friedman et al. 1996; Donaldson et al. 1998a) or the mobility of sequences in yeast nuclei (Marshall et al. 1997)... Therefore, the simplest interpretation is that sequences flanking ARS1412, previously shown to delay replication timing, target ARS1412 to the nuclear periphery... The target is not a unique site on the periphery as the ARS1412 plasmids did not colocalize with chromosomal ARS1412 or with telomeric clusters... Both HP1 and PcG chromodomain proteins have been shown to dissociate during mitosis and reassociate shortly thereafter... Although S. cerevisiae nuclei do not break down during mitosis, partial release of Sir3 and Sir4 from telomere clusters during mitosis has been observed (Laroche et al. 2000)... Often, the exceptions in nature provide the key to common threads linking similar mechanisms... The demonstration that both telomeric and nontelomeric origins localize to the periphery suggests that such a common thread will be found (Heun et al. 2001)... Surely, further investigations into the gene products that regulate peripheral localization and replication timing at the ARS1412 locus will provide valuable clues.

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A, Telomere-dependent late replication. yKu binds both telomere DNA and proteins that extend from nuclear pores (Mlp1 and Mlp2; anchored to the pore through NUP145) to mediate the clustering of telomeres at the periphery (for simplicity, only one telomere is shown). yKu and the telomere binding protein Rap1 recruit Sir proteins. The increased local concentration of Sir proteins seeds the propagation of Sir complexes into the adjacent chromatin where they interact with and stabilize hypoacetylated nucleosomes (dark blue N, hypoacetylated; light blue N, acetylated), creating a silenced chromosomal domain. It has been proposed (Dimitrova and Gilbert 1999; Stevenson and Gottschling 1999) that such silenced domains set thresholds for the initiation of replication by restricting the access of initiation factors to origin-bound prereplication complexes, consisting of the origin recognition complex (ORC), Cdc6, and the Mcm complex. The nature of the limiting initiation factor(s) is unknown, but is likely to include the B-type cyclin-Cdk (Donaldson et al. 1998b) and Dbf4/Cdc7 (Donaldson et al. 1998a) protein kinases and/or Cdc45 (Aparicio et al. 1999). If the concentration of any one of these initiation factors is limiting at the onset of S phase, initiation would be restricted to those replication origins located within the most accessible domains. As the concentrations of initiation factors increase during S phase, the less accessible later initiating origins can then fire. B, Similar microenvironments may form at multiple sites in mammalian nuclei. See text for details.
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Figure 1: A, Telomere-dependent late replication. yKu binds both telomere DNA and proteins that extend from nuclear pores (Mlp1 and Mlp2; anchored to the pore through NUP145) to mediate the clustering of telomeres at the periphery (for simplicity, only one telomere is shown). yKu and the telomere binding protein Rap1 recruit Sir proteins. The increased local concentration of Sir proteins seeds the propagation of Sir complexes into the adjacent chromatin where they interact with and stabilize hypoacetylated nucleosomes (dark blue N, hypoacetylated; light blue N, acetylated), creating a silenced chromosomal domain. It has been proposed (Dimitrova and Gilbert 1999; Stevenson and Gottschling 1999) that such silenced domains set thresholds for the initiation of replication by restricting the access of initiation factors to origin-bound prereplication complexes, consisting of the origin recognition complex (ORC), Cdc6, and the Mcm complex. The nature of the limiting initiation factor(s) is unknown, but is likely to include the B-type cyclin-Cdk (Donaldson et al. 1998b) and Dbf4/Cdc7 (Donaldson et al. 1998a) protein kinases and/or Cdc45 (Aparicio et al. 1999). If the concentration of any one of these initiation factors is limiting at the onset of S phase, initiation would be restricted to those replication origins located within the most accessible domains. As the concentrations of initiation factors increase during S phase, the less accessible later initiating origins can then fire. B, Similar microenvironments may form at multiple sites in mammalian nuclei. See text for details.

Mentions: So what prompted Heun et al. 2001 to examine the subnuclear positions of early and late replicating origins? Again, telomeres provide a useful paradigm (Fig. 1 A). The 32 S. cerevisiae telomeres are clustered into 6–10 sites at the nuclear periphery. Telomere clusters provide a well developed model for a subnuclear compartment whose integrity is required to seed the assembly of silent chromatin (reviewed in Cockell and Gasser 1999). Telomeres are tethered to the nuclear envelope through an interaction between the telomeric DNA-bound yKu heterodimer (Laroche et al. 1998) and proteins (Mlp1 and Mlp2) that extend from the nuclear pore via an interaction with the pore protein NUP145 (Galy et al. 2000). Both Ku and another telomere-bound protein (Rap1), recruit Sir proteins to the telomere clusters, creating microenvironments with high local concentrations of Sir proteins. Mutations that either disrupt the localization of telomeres (mutations in NUP145, yKu, or Mlp1/Mlp2 double mutants), or that cause Sir proteins to disperse throughout the nucleus (Rap1 mutations) also relieve telomeric silencing. Silencing under these conditions can be restored by overexpressing Sir proteins. Hence, Sir proteins are limiting in the overall nucleus but become concentrated at telomere clusters to a level sufficient to seed the assembly of silent chromatin (Fig. 1 A). In fact, a reporter gene flanked by a crippled silencer can be silenced, in a Sir-dependent fashion, by anchorage to the nuclear periphery (Andrulis et al. 1998), suggesting that the entire nuclear periphery constitutes a zone of high Sir concentration. How might this increase in local concentration of chromatin regulators influence replication timing? It has been proposed (Stevenson and Gottschling 1999) that silent chromatin could restrict the access of replication proteins to origins (Fig. 1 A). These could be initiation factors that accumulate during S phase until their levels overcome the restriction imposed by silent chromatin. In support of this model, high concentrations of a transcriptional activator can overcome telomeric silencing of a reporter gene (Aparicio and Gottschling 1994).


Nuclear Position Leaves Its Mark on Replication Timing
A, Telomere-dependent late replication. yKu binds both telomere DNA and proteins that extend from nuclear pores (Mlp1 and Mlp2; anchored to the pore through NUP145) to mediate the clustering of telomeres at the periphery (for simplicity, only one telomere is shown). yKu and the telomere binding protein Rap1 recruit Sir proteins. The increased local concentration of Sir proteins seeds the propagation of Sir complexes into the adjacent chromatin where they interact with and stabilize hypoacetylated nucleosomes (dark blue N, hypoacetylated; light blue N, acetylated), creating a silenced chromosomal domain. It has been proposed (Dimitrova and Gilbert 1999; Stevenson and Gottschling 1999) that such silenced domains set thresholds for the initiation of replication by restricting the access of initiation factors to origin-bound prereplication complexes, consisting of the origin recognition complex (ORC), Cdc6, and the Mcm complex. The nature of the limiting initiation factor(s) is unknown, but is likely to include the B-type cyclin-Cdk (Donaldson et al. 1998b) and Dbf4/Cdc7 (Donaldson et al. 1998a) protein kinases and/or Cdc45 (Aparicio et al. 1999). If the concentration of any one of these initiation factors is limiting at the onset of S phase, initiation would be restricted to those replication origins located within the most accessible domains. As the concentrations of initiation factors increase during S phase, the less accessible later initiating origins can then fire. B, Similar microenvironments may form at multiple sites in mammalian nuclei. See text for details.
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Related In: Results  -  Collection

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Figure 1: A, Telomere-dependent late replication. yKu binds both telomere DNA and proteins that extend from nuclear pores (Mlp1 and Mlp2; anchored to the pore through NUP145) to mediate the clustering of telomeres at the periphery (for simplicity, only one telomere is shown). yKu and the telomere binding protein Rap1 recruit Sir proteins. The increased local concentration of Sir proteins seeds the propagation of Sir complexes into the adjacent chromatin where they interact with and stabilize hypoacetylated nucleosomes (dark blue N, hypoacetylated; light blue N, acetylated), creating a silenced chromosomal domain. It has been proposed (Dimitrova and Gilbert 1999; Stevenson and Gottschling 1999) that such silenced domains set thresholds for the initiation of replication by restricting the access of initiation factors to origin-bound prereplication complexes, consisting of the origin recognition complex (ORC), Cdc6, and the Mcm complex. The nature of the limiting initiation factor(s) is unknown, but is likely to include the B-type cyclin-Cdk (Donaldson et al. 1998b) and Dbf4/Cdc7 (Donaldson et al. 1998a) protein kinases and/or Cdc45 (Aparicio et al. 1999). If the concentration of any one of these initiation factors is limiting at the onset of S phase, initiation would be restricted to those replication origins located within the most accessible domains. As the concentrations of initiation factors increase during S phase, the less accessible later initiating origins can then fire. B, Similar microenvironments may form at multiple sites in mammalian nuclei. See text for details.
Mentions: So what prompted Heun et al. 2001 to examine the subnuclear positions of early and late replicating origins? Again, telomeres provide a useful paradigm (Fig. 1 A). The 32 S. cerevisiae telomeres are clustered into 6–10 sites at the nuclear periphery. Telomere clusters provide a well developed model for a subnuclear compartment whose integrity is required to seed the assembly of silent chromatin (reviewed in Cockell and Gasser 1999). Telomeres are tethered to the nuclear envelope through an interaction between the telomeric DNA-bound yKu heterodimer (Laroche et al. 1998) and proteins (Mlp1 and Mlp2) that extend from the nuclear pore via an interaction with the pore protein NUP145 (Galy et al. 2000). Both Ku and another telomere-bound protein (Rap1), recruit Sir proteins to the telomere clusters, creating microenvironments with high local concentrations of Sir proteins. Mutations that either disrupt the localization of telomeres (mutations in NUP145, yKu, or Mlp1/Mlp2 double mutants), or that cause Sir proteins to disperse throughout the nucleus (Rap1 mutations) also relieve telomeric silencing. Silencing under these conditions can be restored by overexpressing Sir proteins. Hence, Sir proteins are limiting in the overall nucleus but become concentrated at telomere clusters to a level sufficient to seed the assembly of silent chromatin (Fig. 1 A). In fact, a reporter gene flanked by a crippled silencer can be silenced, in a Sir-dependent fashion, by anchorage to the nuclear periphery (Andrulis et al. 1998), suggesting that the entire nuclear periphery constitutes a zone of high Sir concentration. How might this increase in local concentration of chromatin regulators influence replication timing? It has been proposed (Stevenson and Gottschling 1999) that silent chromatin could restrict the access of replication proteins to origins (Fig. 1 A). These could be initiation factors that accumulate during S phase until their levels overcome the restriction imposed by silent chromatin. In support of this model, high concentrations of a transcriptional activator can overcome telomeric silencing of a reporter gene (Aparicio and Gottschling 1994).

View Article: PubMed Central

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

The functional significance of this program is not understood, but, in general, transcriptionally active chromatin replicates early in S phase, whereas hypoacetylated, transcriptionally inactive chromatin replicates later... During metazoan development, multiple origins, encompassing megabase domains of chromosomes, exhibit replication timing switches that precede gene activation and accompany changes in chromatin structure (Selig et al. 1992)... These early- and late-replicating chromosomal domains are localized to distinct spatial compartments of the metazoan nucleus where DNA synthesis can be observed to take place at defined times during S phase... While many laboratories have catalogued the replication timing of various genes and related this to their transcriptional activity and overall chromatin structure, very few studies have addressed the problem of what actually regulates replication timing... The authors wisely chose to restrict their analysis to G1 phase cells, to avoid potential movements that might take place during S phase; movements which they later confirm can be quite dynamic... By dividing the nucleus into five concentric zones, they found that early origins were localized randomly throughout the nucleus, while late origins were preferentially localized to the most peripheral zone, albeit not as frequently as telomeres... One potential caveat to this result is that the late replicating plasmid was nearly three times larger than the early replicating plasmid (24 kb vs. 9.4 kb)... However, others have shown that plasmid size per se does not influence replication timing (Friedman et al. 1996; Donaldson et al. 1998a) or the mobility of sequences in yeast nuclei (Marshall et al. 1997)... Therefore, the simplest interpretation is that sequences flanking ARS1412, previously shown to delay replication timing, target ARS1412 to the nuclear periphery... The target is not a unique site on the periphery as the ARS1412 plasmids did not colocalize with chromosomal ARS1412 or with telomeric clusters... Both HP1 and PcG chromodomain proteins have been shown to dissociate during mitosis and reassociate shortly thereafter... Although S. cerevisiae nuclei do not break down during mitosis, partial release of Sir3 and Sir4 from telomere clusters during mitosis has been observed (Laroche et al. 2000)... Often, the exceptions in nature provide the key to common threads linking similar mechanisms... The demonstration that both telomeric and nontelomeric origins localize to the periphery suggests that such a common thread will be found (Heun et al. 2001)... Surely, further investigations into the gene products that regulate peripheral localization and replication timing at the ARS1412 locus will provide valuable clues.

No MeSH data available.