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"10.1083%2Fjcb.200602108" . @prefix ns4: . ns4:contains _:b1663933 , _:b1663979 , _:b1663966 , _:b1664022 . _:b1663933 rdf:type ns4:Section . @prefix dc: . _:b1663933 dc:title "introduction" ; ns4:contains _:b1663934 , _:b1663935 , _:b1663952 , _:b1663953 , _:b1663954 , _:b1663955 , _:b1663956 , _:b1663957 , _:b1663958 , _:b1663959 , _:b1663960 , _:b1663961 , _:b1663962 , _:b1663963 , _:b1663964 , _:b1663965 , _:b1663936 , _:b1663937 , _:b1663938 , _:b1663939 , _:b1663940 , _:b1663941 , _:b1663942 , _:b1663943 , _:b1663944 , _:b1663945 , _:b1663946 , _:b1663947 , _:b1663948 , _:b1663949 , _:b1663950 , _:b1663951 . _:b1663934 rdf:type ns1:Context ; rdf:value "In late mitosis and early G1, origins are licensed for replication by loading complexes of the minichromosome maintenance proteins 2\u20137 (Mcm2\u20137), thus, forming a \u201Cprereplicative complex\u201D (Diffley, >>2004<<; Blow and Dutta, 2005)." ; ns1:mentions . _:b1663935 rdf:type ns1:Context ; rdf:value "In late mitosis and early G1, origins are licensed for replication by loading complexes of the minichromosome maintenance proteins 2\u20137 (Mcm2\u20137), thus, forming a \u201Cprereplicative complex\u201D (Diffley, 2004; Blow and Dutta, >>2005<<). Licensing involves the coordinated action of the origin recognition complex (ORC) Cdc6 and Cdt1 proteins (Gillespie et al., 2001), which probably act to clamp Mcm2\u20137 around the DNA. Mcm2\u20137 are displaced from replication origins as they" ; ns1:mentions . _:b1663936 rdf:type ns1:Context ; rdf:value "Licensing involves the coordinated action of the origin recognition complex (ORC) Cdc6 and Cdt1 proteins (Gillespie et al., >>2001<<), which probably act to clamp Mcm2\u20137 around the DNA." ; ns1:mentions . _:b1663937 rdf:type ns1:Context ; rdf:value "Mcm2\u20137 are displaced from replication origins as they initiate, and they have been suggested to provide a helicase activity to unwind DNA ahead of the replication fork (Labib and Diffley, >>2001<<). To prevent replication origins from firing more than once in a single S phase, the ability to license new origins is prevented from late G1 through to midmitosis (Diffley, 2004; Blow and Dutta, 2005). This means that whatever the" ; ns1:mentions . _:b1663938 rdf:type ns1:Context ; rdf:value "To prevent replication origins from firing more than once in a single S phase, the ability to license new origins is prevented from late G1 through to midmitosis (Diffley, >>2004<<; Blow and Dutta, 2005)." ; ns1:mentions . _:b1663939 rdf:type ns1:Context ; rdf:value "To prevent replication origins from firing more than once in a single S phase, the ability to license new origins is prevented from late G1 through to midmitosis (Diffley, 2004; Blow and Dutta, >>2005<<). This means that whatever the problems encountered by replication forks during S phase, only previously licensed sites can be used. If two converging replication forks stall irreversibly during S phase, the DNA between them will probably" ; ns1:mentions . _:b1663940 rdf:type ns1:Context ; rdf:value "cerevisiae, humans, and Xenopus laevis, has demonstrated that Mcm2\u20137 complexes are loaded onto DNA in an \u223C20-fold excess over the number of DNA-bound ORC molecules and over the number of replication origins (Burkhart et al., >>1995<<; Lei et al., 1996; Rowles et al., 1996; Donovan et al., 1997; Mahbubani et al., 1997; Edwards et al., 2002)." ; ns1:mentions . _:b1663941 rdf:type ns1:Context ; rdf:value "humans, and Xenopus laevis, has demonstrated that Mcm2\u20137 complexes are loaded onto DNA in an \u223C20-fold excess over the number of DNA-bound ORC molecules and over the number of replication origins (Burkhart et al., 1995; Lei et al., >>1996<<; Rowles et al., 1996; Donovan et al., 1997; Mahbubani et al., 1997; Edwards et al., 2002)." ; ns1:mentions . _:b1663942 rdf:type ns1:Context ; rdf:value "laevis, has demonstrated that Mcm2\u20137 complexes are loaded onto DNA in an \u223C20-fold excess over the number of DNA-bound ORC molecules and over the number of replication origins (Burkhart et al., 1995; Lei et al., 1996; Rowles et al., >>1996<<; Donovan et al., 1997; Mahbubani et al., 1997; Edwards et al., 2002)." ; ns1:mentions . _:b1663943 rdf:type ns1:Context ; rdf:value "that Mcm2\u20137 complexes are loaded onto DNA in an \u223C20-fold excess over the number of DNA-bound ORC molecules and over the number of replication origins (Burkhart et al., 1995; Lei et al., 1996; Rowles et al., 1996; Donovan et al., >>1997<<; Mahbubani et al., 1997; Edwards et al., 2002)." ; ns1:mentions . _:b1663944 rdf:type ns1:Context ; rdf:value "are loaded onto DNA in an \u223C20-fold excess over the number of DNA-bound ORC molecules and over the number of replication origins (Burkhart et al., 1995; Lei et al., 1996; Rowles et al., 1996; Donovan et al., 1997; Mahbubani et al., >>1997<<; Edwards et al., 2002)." ; ns1:mentions . _:b1663945 rdf:type ns1:Context ; rdf:value "in an \u223C20-fold excess over the number of DNA-bound ORC molecules and over the number of replication origins (Burkhart et al., 1995; Lei et al., 1996; Rowles et al., 1996; Donovan et al., 1997; Mahbubani et al., 1997; Edwards et al., >>2002<<). However, normal replication rates are maintained when the number of Mcm2\u20137 molecules is reduced to 1\u20132 per origin (Mahbubani et al., 1997; Edwards et al., 2002; Cortez et al., 2004; Oehlmann et al., 2004; Tsao et al., 2004)." ; ns1:mentions . _:b1663946 rdf:type ns1:Context ; rdf:value "However, normal replication rates are maintained when the number of Mcm2\u20137 molecules is reduced to 1\u20132 per origin (Mahbubani et al., >>1997<<; Edwards et al., 2002; Cortez et al., 2004; Oehlmann et al., 2004; Tsao et al., 2004)." ; ns1:mentions . _:b1663947 rdf:type ns1:Context ; rdf:value "However, normal replication rates are maintained when the number of Mcm2\u20137 molecules is reduced to 1\u20132 per origin (Mahbubani et al., 1997; Edwards et al., >>2002<<; Cortez et al., 2004; Oehlmann et al., 2004; Tsao et al., 2004)." ; ns1:mentions . _:b1663948 rdf:type ns1:Context ; rdf:value "However, normal replication rates are maintained when the number of Mcm2\u20137 molecules is reduced to 1\u20132 per origin (Mahbubani et al., 1997; Edwards et al., 2002; Cortez et al., >>2004<<; Oehlmann et al., 2004; Tsao et al., 2004)." ; ns1:mentions . _:b1663949 rdf:type ns1:Context ; rdf:value "However, normal replication rates are maintained when the number of Mcm2\u20137 molecules is reduced to 1\u20132 per origin (Mahbubani et al., 1997; Edwards et al., 2002; Cortez et al., 2004; Oehlmann et al., >>2004<<; Tsao et al., 2004)." ; ns1:mentions . _:b1663950 rdf:type ns1:Context ; rdf:value "However, normal replication rates are maintained when the number of Mcm2\u20137 molecules is reduced to 1\u20132 per origin (Mahbubani et al., 1997; Edwards et al., 2002; Cortez et al., 2004; Oehlmann et al., 2004; Tsao et al., >>2004<<). This observation, termed the \u201CMCM paradox\u201D (Hyrien et al., 2003), has led to speculation on the possible function of these extra complexes, particularly as MCM proteins do not exclusively colocalize with sites of DNA synthesis in S" ; ns1:mentions . _:b1663951 rdf:type ns1:Context ; rdf:value "This observation, termed the \u201CMCM paradox\u201D (Hyrien et al., >>2003<<), has led to speculation on the possible function of these extra complexes, particularly as MCM proteins do not exclusively colocalize with sites of DNA synthesis in S phase (Madine et al., 1995; Krude et al., 1996; Dimitrova et al.," ; ns1:mentions . _:b1663952 rdf:type ns1:Context ; rdf:value "the \u201CMCM paradox\u201D (Hyrien et al., 2003), has led to speculation on the possible function of these extra complexes, particularly as MCM proteins do not exclusively colocalize with sites of DNA synthesis in S phase (Madine et al., >>1995<<; Krude et al., 1996; Dimitrova et al., 1999)." ; ns1:mentions . _:b1663953 rdf:type ns1:Context ; rdf:value "(Hyrien et al., 2003), has led to speculation on the possible function of these extra complexes, particularly as MCM proteins do not exclusively colocalize with sites of DNA synthesis in S phase (Madine et al., 1995; Krude et al., >>1996<<; Dimitrova et al., 1999)." ; ns1:mentions . _:b1663954 rdf:type ns1:Context ; rdf:value "has led to speculation on the possible function of these extra complexes, particularly as MCM proteins do not exclusively colocalize with sites of DNA synthesis in S phase (Madine et al., 1995; Krude et al., 1996; Dimitrova et al., >>1999<<)." ; ns1:mentions . _:b1663955 rdf:type ns1:Context ; rdf:value "There is evidence that Mcm2\u20137 complexes are found on DNA at significant distances from where ORC is bound (Ritzi et al., >>1998<<; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., 2004). It has been suggested that these distant multiple MCM complexes could cooperatively pump double-stranded DNA and, thus, unwind it (Laskey and Madine, 2003)." ; ns1:mentions . _:b1663956 rdf:type ns1:Context ; rdf:value "There is evidence that Mcm2\u20137 complexes are found on DNA at significant distances from where ORC is bound (Ritzi et al., 1998; Edwards et al., >>2002<<; Harvey and Newport, 2003; Danis et al., 2004). It has been suggested that these distant multiple MCM complexes could cooperatively pump double-stranded DNA and, thus, unwind it (Laskey and Madine, 2003)." ; ns1:mentions . _:b1663957 rdf:type ns1:Context ; rdf:value "There is evidence that Mcm2\u20137 complexes are found on DNA at significant distances from where ORC is bound (Ritzi et al., 1998; Edwards et al., 2002; Harvey and Newport, >>2003<<; Danis et al., 2004). It has been suggested that these distant multiple MCM complexes could cooperatively pump double-stranded DNA and, thus, unwind it (Laskey and Madine, 2003)." ; ns1:mentions . _:b1663958 rdf:type ns1:Context ; rdf:value "There is evidence that Mcm2\u20137 complexes are found on DNA at significant distances from where ORC is bound (Ritzi et al., 1998; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., >>2004<<). It has been suggested that these distant multiple MCM complexes could cooperatively pump double-stranded DNA and, thus, unwind it (Laskey and Madine, 2003)." ; ns1:mentions . _:b1663959 rdf:type ns1:Context ; rdf:value "It has been suggested that these distant multiple MCM complexes could cooperatively pump double-stranded DNA and, thus, unwind it (Laskey and Madine, >>2003<<). More recently, a role for excess MCM proteins in checkpoint activation has been proposed, based on the observation that cells partially depleted of Mcm7 display a reduction in replication checkpoint signaling (Cortez et al., 2004; Tsao" ; ns1:mentions . _:b1663960 rdf:type ns1:Context ; rdf:value "More recently, a role for excess MCM proteins in checkpoint activation has been proposed, based on the observation that cells partially depleted of Mcm7 display a reduction in replication checkpoint signaling (Cortez et al., >>2004<<; Tsao et al., 2004)." ; ns1:mentions . _:b1663961 rdf:type ns1:Context ; rdf:value "a role for excess MCM proteins in checkpoint activation has been proposed, based on the observation that cells partially depleted of Mcm7 display a reduction in replication checkpoint signaling (Cortez et al., 2004; Tsao et al., >>2004<<). A third possibility that has been suggested is that excess Mcm2\u20137 can provide replication origins for use under certain contingencies, such as incomplete DNA replication (Lucas et al., 2000; Edwards et al., 2002; Hyrien et al., 2003;" ; ns1:mentions . _:b1663962 rdf:type ns1:Context ; rdf:value "A third possibility that has been suggested is that excess Mcm2\u20137 can provide replication origins for use under certain contingencies, such as incomplete DNA replication (Lucas et al., >>2000<<; Edwards et al., 2002; Hyrien et al., 2003; Blow and Dutta, 2005)." ; ns1:mentions . _:b1663963 rdf:type ns1:Context ; rdf:value "A third possibility that has been suggested is that excess Mcm2\u20137 can provide replication origins for use under certain contingencies, such as incomplete DNA replication (Lucas et al., 2000; Edwards et al., >>2002<<; Hyrien et al., 2003; Blow and Dutta, 2005)." ; ns1:mentions . _:b1663964 rdf:type ns1:Context ; rdf:value "A third possibility that has been suggested is that excess Mcm2\u20137 can provide replication origins for use under certain contingencies, such as incomplete DNA replication (Lucas et al., 2000; Edwards et al., 2002; Hyrien et al., >>2003<<; Blow and Dutta, 2005)." ; ns1:mentions . _:b1663965 rdf:type ns1:Context ; rdf:value "that has been suggested is that excess Mcm2\u20137 can provide replication origins for use under certain contingencies, such as incomplete DNA replication (Lucas et al., 2000; Edwards et al., 2002; Hyrien et al., 2003; Blow and Dutta, >>2005<<). These different proposals are not mutually exclusive." ; ns1:mentions . _:b1663966 rdf:type ns4:Section ; dc:title "materials and methods" ; ns4:contains _:b1663967 , _:b1663976 , _:b1663977 , _:b1663978 , _:b1663972 , _:b1663973 , _:b1663974 , _:b1663975 , _:b1663968 , _:b1663969 , _:b1663970 , _:b1663971 . _:b1663967 rdf:type ns1:Context ; rdf:value "X. laevis egg extracts were prepared as previously described (Chong et al., >>1997<<) and supplemented with 250 \u03BCg/ml cycloheximide, 25 mM phosphocreatine, 15 \u03BCg/ml creatine phosphokinase, and 300 \u03BCM CaCl2 before use." ; ns1:mentions . _:b1663968 rdf:type ns1:Context ; rdf:value "Demembranated X. laevis sperm nuclei (Chong et al., >>1997<<) were added to extract to a final concentration of 10\u201315 ng DNA/\u03BCl and incubated at 23\u00B0C." ; ns1:mentions . _:b1663969 rdf:type ns1:Context ; rdf:value "For replication assays, extracts were supplemented with \u03B1-[32P]dATP, and DNA synthesis was measured by trichloroacetic acid precipitation, as previously described (Chong et al., >>1997<<). To obtain minimally licensed DNA samples, recombinant geminin lacking the destruction box (McGarry and Kirschner, 1998; Tada et al., 2001) was added to a final concentration of 10 ng/\u03BCl. The appropriate geminin addition time was" ; ns1:mentions . _:b1663970 rdf:type ns1:Context ; rdf:value "To obtain minimally licensed DNA samples, recombinant geminin lacking the destruction box (McGarry and Kirschner, >>1998<<; Tada et al., 2001) was added to a final concentration of 10 ng/\u03BCl." ; ns1:mentions . _:b1663971 rdf:type ns1:Context ; rdf:value "To obtain minimally licensed DNA samples, recombinant geminin lacking the destruction box (McGarry and Kirschner, 1998; Tada et al., >>2001<<) was added to a final concentration of 10 ng/\u03BCl." ; ns1:mentions . _:b1663972 rdf:type ns1:Context ; rdf:value "The appropriate geminin addition time was determined for each extract to produce minimal licensing, as previously described (Oehlmann et al., >>2004<<). Chromatin was isolated and subjected to Western blot analysis, as previously described (Oehlmann et al., 2004)." ; ns1:mentions . _:b1663973 rdf:type ns1:Context ; rdf:value "Chromatin was isolated and subjected to Western blot analysis, as previously described (Oehlmann et al., >>2004<<)." ; ns1:mentions . _:b1663974 rdf:type ns1:Context ; rdf:value "Anti-Cdc45 antibody (Mimura and Takisawa, >>1998<<) was a gift from H. Takisawa (Osaka University, Osaka, Japan)." ; ns1:mentions . _:b1663975 rdf:type ns1:Context ; rdf:value "DNA was spread on glass slides according to the previously described standard conditions (Blow et al., >>2001<<). Slides were rehydrated with HPLC pure water and incubated for 2 h in blocking solution containing PBS, 1% (wt/vol) BSA, and 0.05% (vol/vol) TWEEN 20." ; ns1:mentions . _:b1663976 rdf:type ns1:Context ; rdf:value "Aliquots (10 \u03BCl) were subsequently removed from the sample at the desired time points, reactions were stopped, and the DNA was processed for electrophoresis on 0.7% agarose gels, as previously described (Luciani et al., >>2004<<). HindIII-digested \u03BB-phage DNA (New England Biolabs) was end-labeled with \u03B1-[32P]dATP and loaded for comparison (12.5 ng per lane). Alkaline agarose gels were exposed to autoradiography film (Kodak), which was scanned using a scanner" ; ns1:mentions . _:b1663977 rdf:type ns1:Context ; rdf:value "C. elegans RNAi feeding was performed as previously described, using MCM5 (R10E4.4), MCM6 (ZK632.1), and MCM7 (F32D1.10) from the genome-wide RNAi library (Fraser et al., >>2000<<; Kamath et al., 2003). MCM RNAi-expressing bacteria were titrated with bacteria expressing RNAi against GFP." ; ns1:mentions . _:b1663978 rdf:type ns1:Context ; rdf:value "C. elegans RNAi feeding was performed as previously described, using MCM5 (R10E4.4), MCM6 (ZK632.1), and MCM7 (F32D1.10) from the genome-wide RNAi library (Fraser et al., 2000; Kamath et al., >>2003<<). MCM RNAi-expressing bacteria were titrated with bacteria expressing RNAi against GFP." ; ns1:mentions . _:b1663979 rdf:type ns4:Section ; dc:title "results" ; ns4:contains _:b1664008 , _:b1664009 , _:b1664010 , _:b1664011 , _:b1664012 , _:b1664013 , _:b1664014 , _:b1664015 , _:b1664000 , _:b1664001 , _:b1664002 , _:b1664003 , _:b1664004 , _:b1664005 , _:b1664006 , _:b1664007 , _:b1664016 , _:b1664017 , _:b1664018 , _:b1664019 , _:b1664020 , _:b1664021 , _:b1663980 , _:b1663981 , _:b1663982 , _:b1663983 , _:b1663992 , _:b1663993 , _:b1663994 , _:b1663995 , _:b1663996 , _:b1663997 , _:b1663998 , _:b1663999 , _:b1663984 , _:b1663985 , _:b1663986 , _:b1663987 , _:b1663988 , _:b1663989 , _:b1663990 , _:b1663991 . _:b1663980 rdf:type ns1:Context ; rdf:value "When demembranated sperm nuclei are incubated in X. laevis egg extracts, an average of 10\u201320 Mcm2\u20137 complexes are loaded onto each replication origin before entry into S phase (Mahbubani et al., >>1997<<; Edwards et al., 2002; Oehlmann et al., 2004); we call this DNA \u201Cmaximally licensed." ; ns1:mentions . _:b1663981 rdf:type ns1:Context ; rdf:value "When demembranated sperm nuclei are incubated in X. laevis egg extracts, an average of 10\u201320 Mcm2\u20137 complexes are loaded onto each replication origin before entry into S phase (Mahbubani et al., 1997; Edwards et al., >>2002<<; Oehlmann et al., 2004); we call this DNA \u201Cmaximally licensed." ; ns1:mentions . _:b1663982 rdf:type ns1:Context ; rdf:value "demembranated sperm nuclei are incubated in X. laevis egg extracts, an average of 10\u201320 Mcm2\u20137 complexes are loaded onto each replication origin before entry into S phase (Mahbubani et al., 1997; Edwards et al., 2002; Oehlmann et al., >>2004<<); we call this DNA \u201Cmaximally licensed." ; ns1:mentions . _:b1663983 rdf:type ns1:Context ; rdf:value "If the Cdt1 inhibitor geminin is added to the extract shortly after the sperm DNA, the number of DNA-bound MCM complexes can be limited to the minimum required to support approximately normal replication kinetics (Oehlmann et al., >>2004<<); we call this DNA \u201Cminimally licensed.\u201D To examine the role of excess Mcm2\u20137 complexes, we first investigated whether minimum licensing causes an alteration in the spacing between adjacent replication origins." ; ns1:mentions . _:b1663984 rdf:type ns1:Context ; rdf:value "which were caused by bidirectional replication from origins at the center of each track, and the spacing between replication origins was determined by measuring the distance between the centers of adjacent tracks (Herrick et al., >>2000<<; Blow et al., 2001). Fig. 1 A shows that there was no significant difference in the average interorigin distance between the two samples (15.8 kb for maximum licensing; 17.1 kb for minimum licensing)." ; ns1:mentions . _:b1663985 rdf:type ns1:Context ; rdf:value "by bidirectional replication from origins at the center of each track, and the spacing between replication origins was determined by measuring the distance between the centers of adjacent tracks (Herrick et al., 2000; Blow et al., >>2001<<). Fig. 1 A shows that there was no significant difference in the average interorigin distance between the two samples (15.8 kb for maximum licensing; 17.1 kb for minimum licensing)." ; ns1:mentions . _:b1663986 rdf:type ns1:Context ; rdf:value "Under normal circumstances, clusters of 3\u20137 adjacent origins initiate at similar times, with different clusters being activated at different stages of S phase (Blow et al., >>2001<<). We observed no major difference between minimally and maximally licensed DNA in the clustering of replication origins, with an average of 6.1 origins per cluster for maximally licensed DNA and 4.8 for minimally licensed DNA. Therefore," ; ns1:mentions . _:b1663987 rdf:type ns1:Context ; rdf:value "that, at this concentration, aphidicolin slows replication forks by approximately threefold, but that the major effect on replication is to induce an ATR-dependent checkpoint that suppresses further initiation events (Luciani et al., >>2004<<). Therefore, we also supplemented extracts with caffeine, which is an ATR kinase inhibitor (Fig." ; ns1:mentions . _:b1663988 rdf:type ns1:Context ; rdf:value "Consistent with a previous study (Luciani et al., >>2004<<), the addition of caffeine completely rescued the aphidicolin-induced inhibition of replication with maximally licensed DNA." ; ns1:mentions . _:b1663989 rdf:type ns1:Context ; rdf:value "Replication forks in X. laevis normally progress at \u223C10 bp/s (Callan, >>1972<<; Mahbubani et al., 1992; Strausfeld et al., 1994; Walter and Newport, 1997), but are slowed approximately threefold by 10 \u03BCM aphidicolin (Luciani et al., 2004)." ; ns1:mentions . _:b1663990 rdf:type ns1:Context ; rdf:value "Replication forks in X. laevis normally progress at \u223C10 bp/s (Callan, 1972; Mahbubani et al., >>1992<<; Strausfeld et al., 1994; Walter and Newport, 1997), but are slowed approximately threefold by 10 \u03BCM aphidicolin (Luciani et al., 2004)." ; ns1:mentions . _:b1663991 rdf:type ns1:Context ; rdf:value "Replication forks in X. laevis normally progress at \u223C10 bp/s (Callan, 1972; Mahbubani et al., 1992; Strausfeld et al., >>1994<<; Walter and Newport, 1997), but are slowed approximately threefold by 10 \u03BCM aphidicolin (Luciani et al., 2004)." ; ns1:mentions . _:b1663992 rdf:type ns1:Context ; rdf:value "Replication forks in X. laevis normally progress at \u223C10 bp/s (Callan, 1972; Mahbubani et al., 1992; Strausfeld et al., 1994; Walter and Newport, >>1997<<), but are slowed approximately threefold by 10 \u03BCM aphidicolin (Luciani et al., 2004)." ; ns1:mentions . _:b1663993 rdf:type ns1:Context ; rdf:value "Replication forks in X. laevis normally progress at \u223C10 bp/s (Callan, 1972; Mahbubani et al., 1992; Strausfeld et al., 1994; Walter and Newport, 1997), but are slowed approximately threefold by 10 \u03BCM aphidicolin (Luciani et al., >>2004<<). Fork rate is not significantly affected by the presence of caffeine (Luciani et al., 2004)." ; ns1:mentions . _:b1663994 rdf:type ns1:Context ; rdf:value "Fork rate is not significantly affected by the presence of caffeine (Luciani et al., >>2004<<). To replicate at normal rates in the presence of aphidicolin and caffeine, maximally licensed DNA must use more replication forks than normal. Minimally licensed DNA, in contrast, does not appear capable of using more replication forks." ; ns1:mentions . _:b1663995 rdf:type ns1:Context ; rdf:value "Cdc45 loads onto replication forks (probably binding Mcm2\u20137) just before initiation and moves with the forks as they elongate (Hopwood and Dalton, >>1996<<; Aparicio et al., 1997, 1999; Zou and Stillman, 1998; Mimura and Takisawa, 1998)." ; ns1:mentions . _:b1663996 rdf:type ns1:Context ; rdf:value "Cdc45 loads onto replication forks (probably binding Mcm2\u20137) just before initiation and moves with the forks as they elongate (Hopwood and Dalton, 1996; Aparicio et al., >>1997<<, 1999; Zou and Stillman, 1998; Mimura and Takisawa, 1998)." ; ns1:mentions . _:b1663997 rdf:type ns1:Context ; rdf:value "Cdc45 loads onto replication forks (probably binding Mcm2\u20137) just before initiation and moves with the forks as they elongate (Hopwood and Dalton, 1996; Aparicio et al., 1997, >>1999<<; Zou and Stillman, 1998; Mimura and Takisawa, 1998)." ; ns1:mentions . _:b1663998 rdf:type ns1:Context ; rdf:value "Cdc45 loads onto replication forks (probably binding Mcm2\u20137) just before initiation and moves with the forks as they elongate (Hopwood and Dalton, 1996; Aparicio et al., 1997, 1999; Zou and Stillman, >>1998<<; Mimura and Takisawa, 1998)." ; ns1:mentions . _:b1663999 rdf:type ns1:Context ; rdf:value "Cdc45 loads onto replication forks (probably binding Mcm2\u20137) just before initiation and moves with the forks as they elongate (Hopwood and Dalton, 1996; Aparicio et al., 1997, 1999; Zou and Stillman, 1998; Mimura and Takisawa, >>1998<<). Fig. 2 A shows that both maximally and minimally licensed chromatin contained similar quantities of Cdc45 during an undisturbed S phase, as expected from their similar replication rates." ; ns1:mentions . _:b1664000 rdf:type ns1:Context ; rdf:value "Consistent with a previous study (Edwards et al., >>2002<<), the amount of Cdc45 on maximally licensed chromatin increased \u223C20-fold when extract was treated with a combination of aphidicolin and caffeine." ; ns1:mentions . _:b1664001 rdf:type ns1:Context ; rdf:value "of chromatin-bound Cdc45 was also seen when both maximally and minimally licensed chromatin were treated with caffeine, which is consistent with the acceleration of the origin firing that caffeine causes (Marheineke and Hyrien, >>2004<<; Shechter et al., 2004)." ; ns1:mentions . _:b1664002 rdf:type ns1:Context ; rdf:value "Cdc45 was also seen when both maximally and minimally licensed chromatin were treated with caffeine, which is consistent with the acceleration of the origin firing that caffeine causes (Marheineke and Hyrien, 2004; Shechter et al., >>2004<<)." ; ns1:mentions . _:b1664003 rdf:type ns1:Context ; rdf:value "2 B, shaded bars), caused, in part, by increased quantities of Mcm2\u20137 being loaded onto the DNA (Mahbubani et al., >>1997<<). On the minimally licensed chromatin, however, Cdc45 remained at a fairly constant level of 3\u20135 ng (Fig. 2 B, open bars). This level of Cdc45 on minimally licensed chromatin corresponds to 1\u20132 molecules of Cdc45 per 10-kb DNA, or 1\u20132" ; ns1:mentions . _:b1664004 rdf:type ns1:Context ; rdf:value "This level of Cdc45 on minimally licensed chromatin corresponds to 1\u20132 molecules of Cdc45 per 10-kb DNA, or 1\u20132 molecules of Cdc45 per molecule of ORC (Rowles et al., >>1996<<). If there is a single molecule of Cdc45 at each replication fork, these results suggest that under normal conditions a single molecule of ORC allows, on average, a single pair of replication forks to initiate; the number of forks can be" ; ns1:mentions . _:b1664005 rdf:type ns1:Context ; rdf:value "Because recent studies have shown that caffeine can accelerate origin firing (Marheineke and Hyrien, >>2004<<; Shechter et al., 2004), we repeated the fluorescent fiber-labeling experiments using extracts supplemented with caffeine." ; ns1:mentions . _:b1664006 rdf:type ns1:Context ; rdf:value "Because recent studies have shown that caffeine can accelerate origin firing (Marheineke and Hyrien, 2004; Shechter et al., >>2004<<), we repeated the fluorescent fiber-labeling experiments using extracts supplemented with caffeine." ; ns1:mentions . _:b1664007 rdf:type ns1:Context ; rdf:value "Within expected error, this is consistent with each strand being elongated by two forks, each moving at 10 nt/s, as previously reported (Callan, >>1972<<; Mahbubani et al., 1992; Strausfeld et al., 1994; Walter and Newport, 1997; Luciani et al., 2004)." ; ns1:mentions . _:b1664008 rdf:type ns1:Context ; rdf:value "Within expected error, this is consistent with each strand being elongated by two forks, each moving at 10 nt/s, as previously reported (Callan, 1972; Mahbubani et al., >>1992<<; Strausfeld et al., 1994; Walter and Newport, 1997; Luciani et al., 2004)." ; ns1:mentions . _:b1664009 rdf:type ns1:Context ; rdf:value "Within expected error, this is consistent with each strand being elongated by two forks, each moving at 10 nt/s, as previously reported (Callan, 1972; Mahbubani et al., 1992; Strausfeld et al., >>1994<<; Walter and Newport, 1997; Luciani et al., 2004)." ; ns1:mentions . _:b1664010 rdf:type ns1:Context ; rdf:value "Within expected error, this is consistent with each strand being elongated by two forks, each moving at 10 nt/s, as previously reported (Callan, 1972; Mahbubani et al., 1992; Strausfeld et al., 1994; Walter and Newport, >>1997<<; Luciani et al., 2004)." ; ns1:mentions . _:b1664011 rdf:type ns1:Context ; rdf:value "expected error, this is consistent with each strand being elongated by two forks, each moving at 10 nt/s, as previously reported (Callan, 1972; Mahbubani et al., 1992; Strausfeld et al., 1994; Walter and Newport, 1997; Luciani et al., >>2004<<)." ; ns1:mentions . _:b1664012 rdf:type ns1:Context ; rdf:value "Note that, consistent with a previous work (Luciani et al., >>2004<<), there was no sign of caffeine reducing fork stability, as we did not observe buildup of low molecular weight products." ; ns1:mentions . _:b1664013 rdf:type ns1:Context ; rdf:value "It is known that Cdks are required for the initiation of replication forks in the X. laevis system, but not for fork elongation (Strausfeld et al., >>1994<<; Luciani et al., 2004)." ; ns1:mentions . _:b1664014 rdf:type ns1:Context ; rdf:value "It is known that Cdks are required for the initiation of replication forks in the X. laevis system, but not for fork elongation (Strausfeld et al., 1994; Luciani et al., >>2004<<). It is also known that Cdks act on individual origins very shortly before the origin fires (Strausfeld et al., 1994; Luciani et al., 2004). Therefore, we predicted that if Cdks were inhibited at the start of S phase, when only the very" ; ns1:mentions . _:b1664015 rdf:type ns1:Context ; rdf:value "It is also known that Cdks act on individual origins very shortly before the origin fires (Strausfeld et al., >>1994<<; Luciani et al., 2004)." ; ns1:mentions . _:b1664016 rdf:type ns1:Context ; rdf:value "It is also known that Cdks act on individual origins very shortly before the origin fires (Strausfeld et al., 1994; Luciani et al., >>2004<<). Therefore, we predicted that if Cdks were inhibited at the start of S phase, when only the very first origins had fired, dormant origin firing would be prevented and no rescue of DNA replication would take place. To inhibit Cdks, we" ; ns1:mentions . _:b1664017 rdf:type ns1:Context ; rdf:value "To inhibit Cdks, we used roscovitine, which is a purine analogue that inhibits initiation in the X. laevis system (Meijer et al., >>1997<<; Luciani et al., 2004)." ; ns1:mentions . _:b1664018 rdf:type ns1:Context ; rdf:value "To inhibit Cdks, we used roscovitine, which is a purine analogue that inhibits initiation in the X. laevis system (Meijer et al., 1997; Luciani et al., >>2004<<). A model of the predicted behavior is shown in Fig. 4 A. The model on the left shows initiation occurring at dormant origins when replication occurs in the presence of aphidicolin and caffeine. The model on the right shows that if" ; ns1:mentions . _:b1664019 rdf:type ns1:Context ; rdf:value "Consistent with previous work (Luciani et al., >>2004<<), the addition of roscovitine in early S phase allowed existing forks to elongate, but the replication rate subsequently trailed off as these clustered nascent strands fused with one another." ; ns1:mentions . _:b1664020 rdf:type ns1:Context ; rdf:value "This result is explained by the inability of actinomycin D to activate a strong ATR-dependent checkpoint response, despite strong inhibition of replication (Hekmat-Nejad et al., >>2000<<). Dormant origins in such cases can fire and promote significant recovery from replication inhibition without the need for checkpoint alleviation by caffeine. Consistent with this interpretation, treatment of X. laevis egg extracts with" ; ns1:mentions . _:b1664021 rdf:type ns1:Context ; rdf:value "Consistent with this interpretation, treatment of X. laevis egg extracts with actinomycin D greatly enhances Cdc45 loading (Edwards et al., >>2002<<)." ; ns1:mentions . _:b1664022 rdf:type ns4:Section ; dc:title "discussion" ; ns4:contains _:b1664056 , _:b1664057 , _:b1664058 , _:b1664052 , _:b1664053 , _:b1664054 , _:b1664055 , _:b1664048 , _:b1664049 , _:b1664050 , _:b1664051 , _:b1664044 , _:b1664045 , _:b1664046 , _:b1664047 , _:b1664040 , _:b1664041 , _:b1664042 , _:b1664043 , _:b1664036 , _:b1664037 , _:b1664038 , _:b1664039 , _:b1664032 , _:b1664033 , _:b1664034 , _:b1664035 , _:b1664028 , _:b1664029 , _:b1664030 , _:b1664031 , _:b1664024 , _:b1664025 , _:b1664026 , _:b1664027 , _:b1664023 . _:b1664023 rdf:type ns1:Context ; rdf:value "DNA fiber autoradiography studies have shown an increase in the density of replication origins after replication has been inhibited by FdUrd, which is a thymidylate synthase inhibitor (Ockey and Saffhill, >>1976<<; Taylor, 1977), or by treatment with ultraviolet light (Griffiths and Ling, 1985, 1987, 1989; Painter, 1985)." ; ns1:mentions . _:b1664024 rdf:type ns1:Context ; rdf:value "DNA fiber autoradiography studies have shown an increase in the density of replication origins after replication has been inhibited by FdUrd, which is a thymidylate synthase inhibitor (Ockey and Saffhill, 1976; Taylor, >>1977<<), or by treatment with ultraviolet light (Griffiths and Ling, 1985, 1987, 1989; Painter, 1985)." ; ns1:mentions . _:b1664025 rdf:type ns1:Context ; rdf:value "in the density of replication origins after replication has been inhibited by FdUrd, which is a thymidylate synthase inhibitor (Ockey and Saffhill, 1976; Taylor, 1977), or by treatment with ultraviolet light (Griffiths and Ling, >>1985<<, 1987, 1989; Painter, 1985). Similarly, reduced nucleotide availability has been shown to increase the frequency of initiation at origins that are not normally used (Anglana et al., 2003)." ; ns1:mentions . _:b1664026 rdf:type ns1:Context ; rdf:value "in the density of replication origins after replication has been inhibited by FdUrd, which is a thymidylate synthase inhibitor (Ockey and Saffhill, 1976; Taylor, 1977), or by treatment with ultraviolet light (Griffiths and Ling, 1985, >>1987<<, 1989; Painter, 1985). Similarly, reduced nucleotide availability has been shown to increase the frequency of initiation at origins that are not normally used (Anglana et al., 2003)." ; ns1:mentions . _:b1664027 rdf:type ns1:Context ; rdf:value "density of replication origins after replication has been inhibited by FdUrd, which is a thymidylate synthase inhibitor (Ockey and Saffhill, 1976; Taylor, 1977), or by treatment with ultraviolet light (Griffiths and Ling, 1985, 1987, >>1989<<; Painter, 1985). Similarly, reduced nucleotide availability has been shown to increase the frequency of initiation at origins that are not normally used (Anglana et al., 2003)." ; ns1:mentions . _:b1664028 rdf:type ns1:Context ; rdf:value "origins after replication has been inhibited by FdUrd, which is a thymidylate synthase inhibitor (Ockey and Saffhill, 1976; Taylor, 1977), or by treatment with ultraviolet light (Griffiths and Ling, 1985, 1987, 1989; Painter, >>1985<<). Similarly, reduced nucleotide availability has been shown to increase the frequency of initiation at origins that are not normally used (Anglana et al., 2003)." ; ns1:mentions . _:b1664029 rdf:type ns1:Context ; rdf:value "Similarly, reduced nucleotide availability has been shown to increase the frequency of initiation at origins that are not normally used (Anglana et al., >>2003<<). Therefore, we believe that dormant origins are present in many metazoans, where they can potentially provide a role in responding to replicative stresses." ; ns1:mentions . _:b1664030 rdf:type ns1:Context ; rdf:value "It is known from work in the X. laevis system that replication forks initiate from sites where Mcm2\u20137, and not ORC, are bound (Hua and Newport, >>1998<<; Rowles et al., 1999; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., 2004)." ; ns1:mentions . _:b1664031 rdf:type ns1:Context ; rdf:value "It is known from work in the X. laevis system that replication forks initiate from sites where Mcm2\u20137, and not ORC, are bound (Hua and Newport, 1998; Rowles et al., >>1999<<; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., 2004)." ; ns1:mentions . _:b1664032 rdf:type ns1:Context ; rdf:value "It is known from work in the X. laevis system that replication forks initiate from sites where Mcm2\u20137, and not ORC, are bound (Hua and Newport, 1998; Rowles et al., 1999; Edwards et al., >>2002<<; Harvey and Newport, 2003; Danis et al., 2004)." ; ns1:mentions . _:b1664033 rdf:type ns1:Context ; rdf:value "It is known from work in the X. laevis system that replication forks initiate from sites where Mcm2\u20137, and not ORC, are bound (Hua and Newport, 1998; Rowles et al., 1999; Edwards et al., 2002; Harvey and Newport, >>2003<<; Danis et al., 2004)." ; ns1:mentions . _:b1664034 rdf:type ns1:Context ; rdf:value "It is known from work in the X. laevis system that replication forks initiate from sites where Mcm2\u20137, and not ORC, are bound (Hua and Newport, 1998; Rowles et al., 1999; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., >>2004<<). Based on previous studies, Mcm2\u20137 may be spread several kilobases around the ORC that loaded them, to form what we term a \u201Clicense group\u201D (Ritzi et al., 1998; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., 2004)." ; ns1:mentions . _:b1664035 rdf:type ns1:Context ; rdf:value "Based on previous studies, Mcm2\u20137 may be spread several kilobases around the ORC that loaded them, to form what we term a \u201Clicense group\u201D (Ritzi et al., >>1998<<; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., 2004)." ; ns1:mentions . _:b1664036 rdf:type ns1:Context ; rdf:value "Based on previous studies, Mcm2\u20137 may be spread several kilobases around the ORC that loaded them, to form what we term a \u201Clicense group\u201D (Ritzi et al., 1998; Edwards et al., >>2002<<; Harvey and Newport, 2003; Danis et al., 2004)." ; ns1:mentions . _:b1664037 rdf:type ns1:Context ; rdf:value "Based on previous studies, Mcm2\u20137 may be spread several kilobases around the ORC that loaded them, to form what we term a \u201Clicense group\u201D (Ritzi et al., 1998; Edwards et al., 2002; Harvey and Newport, >>2003<<; Danis et al., 2004)." ; ns1:mentions . _:b1664038 rdf:type ns1:Context ; rdf:value "Based on previous studies, Mcm2\u20137 may be spread several kilobases around the ORC that loaded them, to form what we term a \u201Clicense group\u201D (Ritzi et al., 1998; Edwards et al., 2002; Harvey and Newport, 2003; Danis et al., >>2004<<). Each site containing bound Mcm2\u20137 is a candidate replication origin that can potentially initiate replication (Fig. 7 A). The wide dispersal of Mcm2\u20137 increases the usefulness of these candidate origins in dealing with replicative" ; ns1:mentions . _:b1664039 rdf:type ns1:Context ; rdf:value "Consistent with previous studies (Edwards et al., >>2002<<; Marheineke and Hyrien, 2004; Shechter et al., 2004), our results with caffeine suggest a role for ATM\u2013ATR in preventing more than one origin in a license group from initiating replication." ; ns1:mentions . _:b1664040 rdf:type ns1:Context ; rdf:value "Consistent with previous studies (Edwards et al., 2002; Marheineke and Hyrien, >>2004<<; Shechter et al., 2004), our results with caffeine suggest a role for ATM\u2013ATR in preventing more than one origin in a license group from initiating replication." ; ns1:mentions . _:b1664041 rdf:type ns1:Context ; rdf:value "Consistent with previous studies (Edwards et al., 2002; Marheineke and Hyrien, 2004; Shechter et al., >>2004<<), our results with caffeine suggest a role for ATM\u2013ATR in preventing more than one origin in a license group from initiating replication." ; ns1:mentions . _:b1664042 rdf:type ns1:Context ; rdf:value "Abolishing this inhibitory signal with caffeine in the absence of replication stress causes a decrease in origin spacing, but does not significantly increase overall replication rates. In contrast to Shechter et al. (>>2004<<), we find that if we restrict our analysis to extracts that replicate DNA efficiently (as should be the case if extracts recapitulate the behavior of intact eggs), inhibition of ATM and ATR kinases does not greatly accelerate the" ; ns1:mentions . _:b1664043 rdf:type ns1:Context ; rdf:value "to extracts that replicate DNA efficiently (as should be the case if extracts recapitulate the behavior of intact eggs), inhibition of ATM and ATR kinases does not greatly accelerate the replication-timing program (Luciani et al., >>2004<<; this study). Dormant origins are therefore not just late-firing origins, as confirmed by our experiments with roscovitine (Fig." ; ns1:mentions . _:b1664044 rdf:type ns1:Context ; rdf:value "Our results do not rule out a role for Mcm2\u20137 in checkpoint activation; indeed, the recently reported phosphorylation of Mcm2\u20137 proteins by ATR (Cortez et al., >>2004<<; Tsao et al., 2004) may contribute to the inhibition of dormant origins that we propose." ; ns1:mentions . _:b1664045 rdf:type ns1:Context ; rdf:value "Our results do not rule out a role for Mcm2\u20137 in checkpoint activation; indeed, the recently reported phosphorylation of Mcm2\u20137 proteins by ATR (Cortez et al., 2004; Tsao et al., >>2004<<) may contribute to the inhibition of dormant origins that we propose." ; ns1:mentions . _:b1664046 rdf:type ns1:Context ; rdf:value "Origin spacing is therefore largely independent of the number of Mcm2\u20137 complexes bound to DNA and is determined by the location of ORC binding. In X. laevis, regular ORC spacing (Blow et al., >>2001<<; Oehlmann et al., 2004), coupled with the repression of excess Mcm2\u20137 within license groups, can reliably support complete genome replication, with dormant origins used as a backup only if problems are encountered by forks originating" ; ns1:mentions . _:b1664047 rdf:type ns1:Context ; rdf:value "In X. laevis, regular ORC spacing (Blow et al., 2001; Oehlmann et al., >>2004<<), coupled with the repression of excess Mcm2\u20137 within license groups, can reliably support complete genome replication, with dormant origins used as a backup only if problems are encountered by forks originating from primary origins." ; ns1:mentions . _:b1664048 rdf:type ns1:Context ; rdf:value "This is reminiscent of the \u201CJesuit model\u201D for selection of replication initiation sites, which suggests that DNA contains many potential initiation sites, but some sites are repressed, while others are activated (DePamphilis, >>1999<<)." ; ns1:mentions . _:b1664049 rdf:type ns1:Context ; rdf:value "Replication origins in metazoans can take two different forms (DePamphilis, >>1999<<; Gilbert, 2001; Machida et al., 2005)." ; ns1:mentions . _:b1664050 rdf:type ns1:Context ; rdf:value "Replication origins in metazoans can take two different forms (DePamphilis, 1999; Gilbert, >>2001<<; Machida et al., 2005)." ; ns1:mentions . _:b1664051 rdf:type ns1:Context ; rdf:value "Replication origins in metazoans can take two different forms (DePamphilis, 1999; Gilbert, 2001; Machida et al., >>2005<<). At some replication origins, such as the origin near the lamin B2 gene, replication initiates reproducibly at a tightly defined locus; at other origins, such as the origin near the dihydrofolate reductase gene, replication can initiate" ; ns1:mentions . _:b1664052 rdf:type ns1:Context ; rdf:value "In the case of origins with large initiation zones, such as the dihydrofolate reductase origin, each zone may consist of multiple sites containing bound Mcm2\u20137 (Alexandrow et al., >>2002<<), with only one of these candidate origins initiating during S phase." ; ns1:mentions . _:b1664053 rdf:type ns1:Context ; rdf:value "It remains unclear how certain candidate origins might be selected for preferential initiation, though some difference in the underlying chromatin would be an attractive possibility (Machida et al., >>2005<<). In the case of X. laevis, initiation can occur at some variable distance away from where ORC is bound (Harvey and Newport, 2003) and can be directed toward specific DNA sequences by DNA-bound transcription factors (Danis et al., 2004)." ; ns1:mentions . _:b1664054 rdf:type ns1:Context ; rdf:value "In the case of X. laevis, initiation can occur at some variable distance away from where ORC is bound (Harvey and Newport, >>2003<<) and can be directed toward specific DNA sequences by DNA-bound transcription factors (Danis et al., 2004)." ; ns1:mentions . _:b1664055 rdf:type ns1:Context ; rdf:value "In the case of X. laevis, initiation can occur at some variable distance away from where ORC is bound (Harvey and Newport, 2003) and can be directed toward specific DNA sequences by DNA-bound transcription factors (Danis et al., >>2004<<). Because this occurs without changing the localization of ORC, it presumably happens by increasing the initiation probability of certain candidate origins." ; ns1:mentions . _:b1664056 rdf:type ns1:Context ; rdf:value "Interestingly, transcription factor binding induced histone acetylation at the favored origins (Danis et al., >>2004<<), supporting the case for chromatin modification being involved in candidate origin selection." ; ns1:mentions . _:b1664057 rdf:type ns1:Context ; rdf:value "Somatic cells undergo a transition called the origin decision point (ODP) in the middle of G1, where initiation is directed to occur at specific preferred sequences rather than at more randomly distributed sites (Wu and Gilbert, >>1996<<). Because the ODP occurs after Mcm2\u20137 have bound to DNA and the origins have been functionally licensed (Dimitrova et al., 2002), it is possible that the ODP represents the stage when certain candidate origins are selected to" ; ns1:mentions . _:b1664058 rdf:type ns1:Context ; rdf:value "Because the ODP occurs after Mcm2\u20137 have bound to DNA and the origins have been functionally licensed (Dimitrova et al., >>2002<<), it is possible that the ODP represents the stage when certain candidate origins are selected to preferentially support initiation." ; ns1:mentions . _:b331088836 rdf:type ns1:RelevantBibliographicResource . @prefix xsd: . _:b331088836 ns1:RelevantScore "61"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b331088837 rdf:type ns1:RelevantBibliographicResource ; ns1:RelevantScore "42"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b331088838 rdf:type ns1:RelevantBibliographicResource ; ns1:RelevantScore "22"^^xsd:nonNegativeInteger ; ns1:hasRelevantPaperId . _:b331088839 rdf:type ns1:RelevantBibliographicResource ; 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