RESEARCH ARTICLE

Cyclin-A–CDK2-mediated phosphorylation of CIZ1 blocksreplisome formation and initiation of mammalian DNA replication

Nikki A. Copeland*, Heather E. Sercombe, Rosemary H. C. Wilson` and Dawn Coverley§

ABSTRACT

CIZ1 is a nuclear matrix protein that cooperates with cyclin A2 (encoded

by CCNA2) and CDK2 to promote mammalian DNA replication. We

show here that cyclin-A–CDK2 also negatively regulates CIZ1 activity

by phosphorylation at threonines 144, 192 and 293. Phosphomimetic

mutants do not promote DNA replication in cell-free and cell-based

assays, and also have a dominant-negative effect on replisome

formation at the level of PCNA recruitment. Phosphorylation blocks

direct interaction with cyclin-A–CDK2 and recruitment of endogenous

cyclin A to the nuclear matrix. In contrast, phosphomimetic CIZ1

retains the ability to bind to the nuclear matrix, and its interaction with

CDC6 is not affected. Phospho-T192-specific antibodies confirm that

CIZ1 is phosphorylated during S phase and G2, and show that

phosphorylation at this site occurs at post-initiation concentrations of

cyclin-A–CDK2. Taken together, the data suggest that CIZ1 is a

kinase sensor that promotes initiation of DNA replication at low

kinase levels, when in a hypophosphorylated state that is permissive

for cyclin-A–CDK2 interaction and delivery to licensed origins, but

blocks delivery at higher kinase levels when it is phosphorylated.

KEY WORDS: CIZ1, Cyclin A, Cyclin dependent kinase 2, DNAreplication, Phosphorylation, Replisome

INTRODUCTIONEukaryotic DNA replication is initiated at multiple replication

origins that fire in a temporally and spatially regulated process.

Multiple layers of regulation ensure that the entire genome is

duplicated completely and only once in each S phase. The initiation

proteins and the principles of their regulation by the combined

activities of cyclin dependent kinases (CDKs) and Dbf4–Cdc7,

also referred to as Dbf4-dependent kinase (DDK), are conserved

among eukaryotes (Araki, 2010; Labib, 2010). Sites of initiation

are specified by the pre-replication complex (pre-RC), which

includes ORC, CDC6 and CDT1, leading to recruitment of the

replicative helicase complex containing MCM2–7, CDC45 and

GINS (CMG complex) (Ilves et al., 2010; Pacek et al., 2006). DDK

activates the CMG complex leading to localised DNA unwinding

(Heller et al., 2011), and in yeast this is followed by CDK-mediated

phosphorylation of GINS subunits SLD2 and SLD3, recruitment of

DPB11 and polymerase e to form the pre-initiation complex (pre-

IC), and activation of MCM helicase activity (Heller et al., 2011;

Muramatsu et al., 2010; Tanaka et al., 2007; Zegerman and Diffley,

2007). Subsequent recruitment of PCNA and polymerases a and dcomplete the replisome and enable initiation of DNA replication.

In mammals, replication origin licensing and initiation of DNA

replication require the sequential activities of cyclin-E–CDK2

(cyclin E is encoded by CCNE1 and CCNE2), which supports

MCM complex assembly, and cyclin-A–CDK2, which activates

DNA synthesis (Coverley et al., 2002; Geng et al., 2007; Geng

et al., 2003). Importantly, cyclin-A–CDK2 plays additional

inhibitory roles at lower and higher concentrations than that

which activates DNA synthesis (Copeland et al., 2010; Coverley

et al., 2002), illustrating tight control over initiation and implying a

complicated array of substrates. In recent years, studies in

mammalian cells have identified replication factors that have

evolved with little homology to the ‘core’ replication proteins

identified in yeasts, yet are required as drivers of the initiation

process. These include CIP1-interacting zinc finger protein 1

(CIZ1) and geminin coiled-coil containing protein 1 (GEMC1, also

known as GMNC), which acts under the regulation of cyclin-E–

CDK2 to promote TopBP1-mediated recruitment of CDC45 to

chromatin (Balestrini et al., 2010). We identified the DNA

replication role of CIZ1 using a cell-free system that reconstitutes

spatially organized replication of chromatin, using isolated intact

nuclei as a template (Coverley et al., 2005). Consistent with a role

in DNA replication at the interface with its nuclear organisation,

CIZ1 is normally immobilized in the nucleus after removal of

chromatin, soluble proteins and membranes (Ainscough et al.,

2007), indicating association with an underlying nuclear matrix. A

dysfunctional nuclear matrix is thought to be a defining feature of

cancer cells (Munkley et al., 2011; Zink et al., 2004), and aberrant

nuclear architecture is one of the most overt visible indicators of

pathogenesis. Related to this, aberrant expression of alternatively

spliced CIZ1 transcripts is now implicated in a range of adult and

paediatric cancers (den Hollander et al., 2006; Higgins et al., 2012;

Rahman et al., 2007; Rahman et al., 2010; Warder and Keherly,

2003), in some cases specifying altered sub-nuclear localisation. In

addition, CIZ1 has been associated with the apparently unrelated

human disorders Alzheimer’s disease and cervical dystonia

(Dahmcke et al., 2008; Xiao et al., 2012).

CIZ1 interacts with cyclin E or cyclin A through distinct sites, in

a two-step process that reflects the order of cyclin expression in late

G1 phase (Copeland et al., 2010). This work suggests that CIZ1

acts to temporally and spatially coordinate cyclin function during

the assembly and activation of the DNA replication machinery.

Interaction with cyclin-A–CDK2 is through a conserved cyclin-

binding motif at Cy-ii (K321) in CIZ1, and mutation of this site

prevents both cyclin-A–CDK2 interaction and CIZ1-mediated

activation of DNA replication (Copeland et al., 2010). Previous

University of York, Department of Biology, Heslington, York YO10 5DD, UK.*Present address: Lancaster University, Faculty of Health and Medicine,Biomedical and Life Sciences, Lancaster LA1 4YQ, UK. `Present address: TheUniversity of Oxford, Wellcome Trust Centre for Human Genetics, RooseveltDrive, Oxford OX3 7BN, UK.

§Author for correspondence (dawn.coverley@york.ac.uk)

Received 9 September 2014; Accepted 23 February 2015

� 2015. Published by The Company of Biologists Ltd | Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1518

Jou

rna

lo

fC

ell

Sci

en

ce

results also hint at a complex regulatory relationship between CIZ1and cyclin-A–CDK2. Titration of recombinant cyclin-A–CDK2

into cytosolic extracts normally elicits a biphasic response in DNAreplication assays, promoting initiation within a narrow range ofkinase concentrations (Copeland et al., 2010; Coverley et al.,2002); however, when supplemented with recombinant CIZ1, this

range is extended both below and above the peak concentration(Coverley et al., 2005). Moreover, when assayed at the peak activeconcentration of cyclin-A–CDK2, recombinant CIZ1 also elicits a

biphasic response but this is extended by mutation of a putativeCDK phosphorylation site (Coverley et al., 2005). Here, we showthat CIZ1 is a direct substrate for cyclin-A–CDK2, and we identify

sites for which phosphorylation downregulates the functionalinteraction, impacting on both cyclin A delivery to the nuclearmatrix and the formation of a functional replisome.

RESULTSPhosphomimetic mutation of CIZ1 inhibits DNA replicationThere are 14 putative CDK phosphorylation sites (S/TP) in the

full-length (845-amino-acid) form of murine CIZ1, specified by

the reference sequence NP082688 (accessed 24 April 2014). Sixare within the minimal functional replication domain referred to

as N471 (Fig. 1A) and are highly conserved in mammals(supplementary material Fig. S1). None of these are specifiedby sequences that have been reported to be alternatively spliced indisease contexts (Dahmcke et al., 2008; den Hollander et al.,

2006; Higgins et al., 2012; Rahman et al., 2007; Rahman et al.,2010; Warder and Keherly, 2003; Xiao et al., 2012). Toinvestigate how phosphorylation might regulate the function of

CIZ1 in initiation of DNA replication, phosphomimetic aspartatemutations in each of the six sites were analysed in cell-free DNAreplication experiments. When incubated in mid G1 phase

extracts, 18% of late G1 phase template nuclei incorporatedlabelled nucleotides, indicating the fraction that was in S phaseprior to isolation and establishing the background of this assay.

Parallel incubation in S phase extract increased the fraction to30% (by inducing licensed nuclei to enter S phase), and this wasincreased further to 44% by recombinant CIZ1-N471 (Fig. 1B).This illustrates the positive influence of CIZ1 on initiation, and

defines the fraction of nuclei in this population that is capable of

Fig. 1. Phosphomimetic mutation of CIZ1 inhibits DNA replication. (A) Schematic of murine CIZ1, showing translated exons (numbered) and those that encodethe DNA replication domain present in CIZ1 fragment N471 (exons 2–9 and part of 10, shown in yellow and red box) (Copeland et al., 2010). The nuclear matrix anchordomain-containing fragment (exon 10–17; grey box) is also shown (Ainscough et al., 2007). Reported CIZ1 spicing events (Dahmcke et al., 2008; Greaves et al.,2012; Higgins et al., 2012; Rahman et al., 2007) are shaded in dark grey in exons 4, 6, 8 and 14. Putative phosphorylation sites in N471 are shown in black. Knowncyclin-binding domains are shown with blue ovals; dark blue identifes the regulatory site required for DNA replication function, which mediates both cyclin E and cyclinA interactions, and light blue indicates cyclin A interactions only (Copeland et al., 2010). (B) Cell-free DNA replication assay showing the proportion of G1 nucleithat incorporate biotin–dUTP when incubated in G1 or S phase cytosolic extract with or without 0.05 nmol l21 CIZ1-N471. Data show the mean6s.d. (n53).Representative images show total DNA (blue) and nascent DNA (magenta). Scale bar: 10 mm. (C) Cell-free DNA replication in G1 nuclei incubated with S phaseextract in the absence (grey bars) or presence (black bars) of 0.05 nM recombinant CIZ1-N471 or derived phosphomimetic mutants. WT, wild type. Data are plotted asthe mean percentage initiation6s.d. (n54); ***P,0.001. (D) Initiation of DNA replication in G1 nuclei incubated in S phase extract, showing a concentration-dependent

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1519

Jou

rna

lo

fC

ell

Sci

en

ce

initiation in vitro. Analysis of the phosphomimetic mutantproteins revealed that three of the six putative CDK

phosphorylation sites in N471 suppress initiation of DNAreplication in vitro (Fig. 1C). At the optimal concentration(0.05 nM), mutation of threonine residues at positions 144, 192and 293 reduced activity relative to wild-type N471, and this was

confirmed over a broad concentration range (0.02–0.5 nM,Fig. 1D). Importantly, phosphomimetic mutation at each ofthese sites not only blocked the ability of N471 to boost

initiation, it also suppressed initiation in nuclei that wouldnormally respond to S phase extract. This contrasts withindividual alanine mutations at these sites, all of which

promoted initiation of DNA replication to a similar degree aswild-type CIZ1 (supplementary material Fig. S2).

To establish whether phosphorylation at multiple sites has a

cooperative effect, N471 with three phosphomimetic mutations(T144D, T192D and T293D; N471-DDD) was tested under thesame conditions as the single mutants (Fig. 1D). As expected,N471-DDD failed to promote initiation and, in fact, suppressed

initiation to a greater extent than any of the single mutations. Thedata clearly demonstrate that phosphomimetic CIZ1 mutantsreduce initiation of DNA replication in licensed nuclei and

identify a dominant inhibitory effect.

CDK-mediated phosphorylation of CIZ1 regulates itsinteraction with cyclin AIn vitro kinase assays confirmed that CIZ1 is a substrate forrecombinant cyclin-A–CDK2 and cyclin-E–CDK2 in vitro

(supplementary material Fig. S3A). However, as the interactionbetween CIZ1 and these two cyclins appears to be sequential in

vivo (Copeland et al., 2010), we reasoned that it is unlikely thatcyclin-E–CDK2 would mediate inhibitory phosphorylation events

that suppress interaction with cyclin A, and therefore the abilityof CIZ1 to promote initiation. For this reason, and the likelihoodthat site specificity would not be faithfully recapitulated in a two-

component purified system, in vitro kinase assays were focussedon cyclin-A–CDK2 only. This generated kinetic analysis ofphosphorylation of CIZ1 species with alanine mutations at each

of the six putative CDK sites (Fig. 2A,B), providing insight intothe relationship between them. This revealed two distinct effects– a low-level reduction in phosphorylation rate relative to that ofthe wild type for alanine mutations at T138, T144 and T187, and

a more severe reduction for alanine mutations in the C-terminalresidues T192, T293 and S331. The data imply a hierarchy ofmodifications in which phosphorylation at all of the C-terminal

sites facilities phosphorylation at one or more of the N-terminalsites. Efficient phosphorylation does not distinguish betweenfunctional and non-functional sites, where ‘function’ is defined

by reduced initiation activity of phosphomimetic equivalents,as only two of the three high impact sites downregulate activityin replication assays. Lack of impact of phosphomimetic

S331 in replication assays (Fig. 1C) does not contradict thisinterpretation, but argues that phosphorylation at this site alone isnot sufficient.

Consistent with a fundamental regulatory role for the threonine

residue at T293, proteomic analysis of wild-type CIZ1 showedthat T293 is phosphorylated by cyclin-A–CDK2 in vitro

(supplementary material Fig. S3B), but phosphorylation(s) at

other sites were not detected in this system.To begin to dissect the role of phosphorylation in regulation of

CIZ1 function, protein interaction studies were performed. Direct

interaction with both endogenous cyclin A (Fig. 2C) and

recombinant cyclin-A–CDK2 (Fig. 2D) was confirmed usingCIZ1-N471 immobilized by a GST tag. Consistent with the idea

that CDK phosphorylation reduces the stability of the cyclin-A–CDK2–CIZ1 ternary complex, the amount of cyclin A recoveredthrough interaction with CIZ1-N471 was modulated by titration ofATP into the reaction, and stabilized by the presence of the CDK

inhibitor roscovitine (Fig. 2D). However, single phosphomimeticmutation of N471 did not significantly weaken the CIZ1–cyclin-Acomplex (supplementary material Fig. S3C), requiring instead

phosphomimetic mutation of all three of the functionally implicatedregulatory sites in triple mutant CIZ1-N471-DDD (Fig. 2E). Thisshows that phosphorylation of CIZ1 at multiple sites is required to

regulate interaction with cyclin-A–CDK2, potentially modulatinginitiation of DNA replication by influencing the targeting of cyclin-A–CDK2 to chromatin (Copeland et al., 2010).

CIZ1 interacts with the pre-RC protein CDC6Direct interaction between CIZ1 and cyclin A requires motifswithin the 80 amino acids encoded by the active N471 fragment

of CIZ1, but absent from the inactive fragment N391 (Fig. 2A)(Copeland et al., 2010). In contrast, both N471 and N391 interactwith endogenous CDC6 in S phase HeLa cell cytosolic extract,

whereas neither recovered MCM2 or PCNA under the sameconditions (Fig. 2F). Moreover, direct interaction between N471and recombinant CDC6 was not significantly impaired by

individual phosphomimetic mutations (Fig. 2G) or by triplemutant N471-DDD (Fig. 2H), a conclusion supported byreciprocal binding reactions in which GST–CDC6 was used as

bait for CIZ1 (Fig. 2I). This shows for the first time directinteraction between CIZ1 and CDC6 but, more importantly, itshows contrasting interaction profiles, which suggest that CDC6and cyclin A associate with CIZ1 through distinct sites and are

not regulated in the same way. Thus, CIZ1 could associate withlicensed replication origins through CDC6, independently ofCIZ1 phosphorylation status.

Phosphorylation regulates CIZ1 DNA replication activity butnot subnuclear localizationThe majority of the CIZ1 protein in NIH3T3 cells exists in nuclearfoci that are immobilized on a DNase-I- and high-salt-resistantnuclear matrix (Ainscough et al., 2007). Therefore, directinteraction with CDC6 raises the possibility that CIZ1 might

play a role in the recruitment of DNA replication complexes to thenuclear matrix, where replication proteins and their regulators arebelieved to function in mammalian cells, and initiation and

elongation take place (Anachkova et al., 2005; Djeliova et al.,2001; Pospelov et al., 1982). Neither of the CIZ1 fragments N471or N391 encode nuclear-matrix-binding domains; therefore, in

order to probe the effects of CIZ1 phosphorylation onimmobilization and function in cell-based assays, we used full-length protein incorporating nuclear-matrix-binding sequences,

with and without mutation at the three key sites. When transfectedinto cycling NIH3T3 cells (Fig. 3A), unphosphorylatable GFP–CIZ1-AAA boosts the number of cells engaged in DNA synthesis(P,0.001), whereas GFP alone (control) has no significant effect

on DNA replication, compared with that of untransfected cells.Importantly, phosphomimetic GFP–CIZ1-DDD reduced thenumber of replicating cells to below the level in untransfected

populations (P50.013), consistent with a dominant-negativephenotype that inhibits DNA replication at licensed origins.

Wild-type GFP–CIZ1, and also AAA and DDD derivatives,

were detected in the nuclear matrix fraction after DNase I

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1520

Jou

rna

lo

fC

ell

Sci

en

ce

digestion and elution of chromatin and associated proteins

(Fig. 3B), localised in subnuclear foci (Fig. 3C). We concludetherefore that CIZ1 phosphorylation does not regulate its functionin DNA replication by affecting its immobilization on the nuclear

matrix.

Cyclin A fails to colocalize with phosphomimetic CIZ1 on thenuclear matrixTo evaluate the effect on cyclin A recruitment, asynchronous 3T3cells were transfected with GFP–CIZ1 or derived DDD and AAA

mutants, and nuclear matrix fractions were isolated by DNase I

extraction of chromatin. Endogenous cyclin A was dramaticallyreduced in the nuclear matrix fraction from cells transfected withGFP–CIZ1-DDD, suggesting that phosphorylated CIZ1 recruits

cyclin A much less efficiently than wild-type or AAA does(Fig. 3D). Moreover, the low-level residual endogenous cyclin Aprotein that was detected by immunofluorescence in chromatin-

depleted GFP–CIZ1-DDD transfected nuclei failed to colocalisewith recombinant GFP-tagged protein (Fig. 3E). In contrast,colocalization was apparent in the chromatin-depleted nuclei

Fig. 2. Phosphorylation of CIZ1 regulates its interaction with cyclin A. (A) Schematic of the replication-active fragment CIZ1-N471 and inactive CIZ1-N391(Copeland et al., 2010). Putative phosphorylation sites are shown in black. (B) Rate of phosphorylation of recombinant CIZ1-N471 and derived alanine mutantsby recombinant cyclin-A–CDK2, quantified by densitometry. Data show the mean6s.d. (n53). Inset, representative autoradiograph of incorporatedradiolabelled ATP for wild type (WT) and the T293A mutant. (C) Protein interaction assays using immobilised GST–CIZ1-N471 and HeLa S phase cytosolicextract, in the presence of increasing concentrations of ATP, as indicated. Recovery of endogenous cyclin A was monitored by western blotting, showing that0.1 mM ATP destabilised cyclin A recovery. GST was used as a negative control. (D) Protein interaction assays performed as in C, except that recombinant0.5 mg cyclin-A–CDK2 was added to reactions and roscovitine (RV) was included as indicated. (E) Protein interaction assays showing the effect of triplephosphomimetic mutant (DDD; T144D, T192D, T293D) on the ability of CIZ1-N471 to recover recombinant cyclin-A–CDK2. (F) Protein interaction assayscomparing the interaction of N471 and the inactive fragment N391 with endogenous proteins in S phase HeLa nuclear extracts. Recovered CDC6, MCM2 andPCNA are detected by western blotting and are shown relative to 5% (v/v) of the input extract. (G) Protein interaction assay using CIZ1-N471 and derivedphosphomimetic mutants, and recombinant CDC6. All mutants recovered CDC6. (H) As in G, except that triple mutant DDD was used as bait for recombinantCDC6. (I) Protein interaction assay using GST–CDC6 as bait to report on the interaction with CIZ1-N471 or CIZ1-N471-DDD phosphomimetic mutant,as indicated.

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1521

Jou

rna

lo

fC

ell

Sci

en

ce

population transfected with GFP–CIZ1 or GFP–CIZ1-AAA.Analysis of the extent of colocalisation with cyclin A in

populations of nuclei is shown in supplementary material Fig.S4, revealing very low levels of overlap with CIZ1-DDD that aresignificantly different (P,0.01) to the overlap with CIZ1 orCIZ1-AAA. The data support the premise that CIZ1 facilitates

cyclin A recruitment to the nuclear matrix, but only when in ahypophosphorylated state.

Endogenous CIZ1 is phosphorylated in S phaseAn affinity-purified phosphospecific antibody, raised against aphosphorylated peptide encompassing position phospho-T293,

was validated using in vitro kinase and phosphatase treatment ofrecombinant CIZ1 and derived mutants (supplementary materialFig. S3D). Western blot analysis of detergent-insoluble nuclear

protein (chromatin and nuclear matrix) harvested from

chemically synchronised 3T3 cells (Fig. 4A) shows that CIZ1phospho-T293 is evident in S phase, peaks during G2 and is lost

in nocodazole-arrested cells, although CIZ1 protein itself remainspresent (Fig. 4B). Similar results were seen when 3T3 cells weresynchronised by contact inhibition and serum depletion, theninduced to re-enter the cell cycle (Fig. 4C). Progression through

G1 and S phase was monitored by EdU incorporation (Fig. 4D),indicating entry to S phase between 16 and 22 hours, whereasCIZ1 phospho-T293 is evident from 20 hours and accumulates

through S phase. Cell-cycle-dependent phosphorylation in intactcells synchronized by this physiologically relevant method isstrong evidence that CIZ1 activity is normally regulated by

phosphorylation at this site.The data suggest that CIZ1 promotes DNA replication in a

hypo-phosphorylated state and inhibits DNA replication in a

hyper-phosphorylated state. Consistent with this, using a cell-free

Fig. 3. CIZ1 phosphorylation sitemutants retain nuclear matrixbinding. (A) DNA replication inasynchronous 3T3 cells, monitored byincorporation of BrdU into nascentDNA, after transfection with GFPempty vector control or GFP–CIZ1-derived triple mutations at T144, T192and T293 to generate GFP–CIZ1-AAA or GFP–CIZ1-DDD (green). Theproportion of BrdU-positive cells in theuntransfected fraction of the same cellpopulations (grey) are shown forcomparison. Data show themean6s.d. (n54); *P,0.05;***P,0.001. Images show arepresentative nucleus; total DNA(blue), GFP–CIZ1 (green) andnascent DNA (magenta). (B) Westernblot of total protein, DNase-I-solublechromatin-associated proteins(supernatant, verified by co-fractionation of histone H3) andDNase-I-resistant nuclear-matrix-associated proteins (NM, verified byco-fractionation of lamin A), preparedfrom cells transfected with GFP–CIZ1or the derived mutants, as indicated.(C) Images of 3T3 cells transfectedwith GFP–CIZ1 and triple mutants, asindicated (green). Unextracted nuclei(total), detergent-resistant protein(chromatin and nuclear-matrix-associated) and DNase-I-resistantprotein (nuclear-matrix-associated)are shown. DNA is blue. (D) Westernblot of the nuclear matrix fraction of3T3 cells, transfected with GFP–CIZ1or triple mutants, showingrecombinant CIZ1, endogenous cyclinA and lamin A. (E) Endogenous cyclinA (magenta) in 3T3 cells transfectedwith GFP–CIZ1 or derived triplemutants (green), after extraction withDNase I to reveal the nuclear-matrix-associated fraction. Colocalisation isshown in the right panel in white, asdetermined by BioImage XD3. Imagesare composites showing nuclei takenfrom different fields. Scale bars:10 mm.

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1522

Jou

rna

lo

fC

ell

Sci

en

ce

assay under conditions that induce a biphasic response to cyclin-A–CDK2 in isolated G1 nuclei (Copeland et al., 2010; Coverleyet al., 2002), we saw no increase in the phosphorylation of

endogenous CIZ1 at T293 at the activating concentration ofcyclin-A–CDK2 (0.1 ng/ml, Fig. 4E,F), indicating that initiationof DNA replication is not accompanied by detectable

phosphorylation at this site. In contrast, a tenfold higherconcentration of cyclin-A–CDK2 (1 ng/ml), which fails toactivate DNA synthesis (Fig. 4E), did phosphorylate CIZ1 atT293 (Fig. 4F), supporting the idea that phosphorylation of CIZ1

occurs after initiation and plays a role in suppressing re-initiation.

Phosphorylation of CIZ1 prevents recruitment of cyclin Aand PCNATo look at how phosphorylation of CIZ1 influences the DNAreplication machinery, we monitored the recruitment of selected

replication factors in 3T3 cells synchronised by release fromquiescence, after transfection with phosphomimetic GFP–CIZ1N471-DDD or unphosphorylatable GFP–CIZ1N471-AAA(Fig. 5A). Cells entered S phase with tight synchrony after

16 hours for control and transfected populations, except thoseexpressing DDD (Fig. 5B). This reinforces results withunsynchronised cells and with isolated nuclei, and shows that

DDD has a potent dominant-negative effect on initiation. Westernblot analysis at 24 hours after release from quiescence shows thatrecombinant CIZ1 is expressed at similar levels for all three

constructs, and that they are present in the detergent-resistant(chromatin/nuclear matrix-associated) fraction at similar levels

(Fig. 5C). CDC6, MCM2 and CDT1 levels are similar,suggesting that pre-RC formation is unperturbed and thereforenot responsible for the observed reduction in DNA replication.

CDC45 levels are also similar, indicating that its recruitment, andby implication that of MCM2–7 and GINS (the CMG complex),is also not blocked. However, consistent with weakened cyclin A

interaction in vitro (Fig. 2) and loss of cyclin A from the nuclearmatrix fraction (Fig. 3), there is a marked decrease in cyclin Arecruitment in the presence of GFP–CIZ1N471-DDD. This isaccompanied by failure to complete replisome assembly as

evidenced by reduced PCNA recruitment. This suggests thatcyclin-A–CDK2 positively regulates late steps in the transitionfrom G1 to S phase, and implicates CIZ1 in the execution of this

process.

DISCUSSIONCell cycle progression is governed by cyclin-dependent proteinkinases as they reach levels that exceed thresholds required tophosphorylate their substrates. Temporal separation of replicationlicensing and activation of DNA synthesis prevents replicated

DNA from re-establishing licensed origins (Blow and Dutta,2005) and is controlled by both positive and negativephosphorylation events. Within this process, an array of

substrates have been documented; MCM complex assembly inG1 phase is dependent upon cyclin-E–CDK2 (Coverley et al.,2002; Geng et al., 2007; Mailand and Diffley, 2005), and

recruitment of GEMC1 and the candidate functional orthologuesof lower eukaryote proteins SLD2 (an orthologue of mammalian

Fig. 4. Phosphorylated CIZ1 T293 accumulates during S phase. (A) Flow cytometry of propidium-iodide-stained 3T3 cells confirms synchrony in G0, G1, Sphase, G2 and nocodazole-arrested cells. An asynchronous population is shown for reference. (B) Synchronised populations were fractionated, and thechromatin and nuclear matrix (NM) fraction was analysed by western blotting for phospho-T293 CIZ1, endogenous CIZ1, cyclin A and actin. Noc, nocodazole.(C) 3T3 cells were synchronised by contact inhibition in G0, then released into the cell cycle and harvested at the indicated times. Western blot showsphosphoT293 CIZ1, endogenous CIZ1, cyclin A and actin in the chromatin and nuclear matrix fraction. (D) Cells from C were monitored for incorporation of EdUto determine the proportion of cells in S phase for each time point. (E) Cell-free DNA replication assay illustrating the effect of 0.1 ng/ml cyclin-A–CDK2 on theinitiation of DNA replication in G1 nuclei incubated in G1 cytosolic extract [the previously determined optimal concentration (Copeland et al., 2010; Coverleyet al., 2002)], and failure of 1 ng/ml cyclin-A–CDK2 to promote the same outcome. Data show the mean6s.d. (n53). (F) Western blot of parallel reactions

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1523

Jou

rna

lo

fC

ell

Sci

en

ce

RecQ4) and SLD3 (an orthologue of mammalian treslin) is

promoted by CDK activity (Abe et al., 2011; Balestrini et al.,2010; Kumagai et al., 2010; Kumagai et al., 2011; Piergiovanniand Costanzo, 2010; Sangrithi et al., 2005). The proteins forwhich phosphorylation promotes and inhibits DNA replication in

mammalian cells are still to be fully elucidated, but some keyevents have been found to correlate with defined kinase activitythresholds (Coudreuse and Nurse, 2010; Spencer et al., 2013). In

the case of cyclin-A–CDK2, distinct positive and negative eventscan be ordered along a concentration gradient that reflectsincreasing endogenous kinase levels in late G1 phase – lower

concentrations switch off pre-RC assembly by phosphorylatingand inactivating CDC6, higher concentrations activate DNAsynthesis, and still higher concentrations phosphorylate MCM2

and are associated with loss of ability to promote initiation(Coverley et al., 2002). This is consistent with studies of DNApolymerase a, where CDK-mediated phosphorylation promotesinitiation at low levels, but inhibits activity at high concentrations

(Schub et al., 2001; Voitenleitner et al., 1997; Voitenleitneret al., 1999). Thus, cyclin-A–CDK2 both activates and inhibitsinitiation by regulating components of the pre-RC and the

replisome. However, this level of analysis is not capable ofreporting on localized environments within the highly organizednucleus of higher eukaryotes, because global levels measured in

cell lysates mask localised peaks and troughs established byimmobilization of kinase at sites of action.

In fact, individual replication factories might experiencechanges in local kinase concentration in an asynchronous

manner, guided by delivery or receptor proteins that spatiallylimit kinase-regulated events. We find that CIZ1 is both adelivery factor that mediates the nuclear matrix recruitment of

cyclin-A–CDK2, and is itself phosphorylated by cyclin-A–CDK2

at multiple sites that inhibit its function in DNA replication.Notably, direct interaction with the pre-RC protein CDC6 isunaffected by CIZ1 phosphorylation. This raises the possibilitythat CDC6 is a receptor for CIZ1, and their interaction brings

licensed origins and the nuclear matrix into close proximity.CDC6 was previously suggested to be a chromatin-associatedreceptor for cyclin E (Furstenthal et al., 2001), which is also a

direct interaction partner of CIZ1 (Copeland et al., 2010).However, this earlier study did not apply nuclease digestiontechniques and so was not able to distinguish between recruitment

to chromatin verses the nuclear matrix. Nevertheless, whenconsidered alongside our previous work, which showed that CIZ1interacts sequentially with cyclins E and A (Copeland et al.,

2010), the data suggest that CIZ1 (and cyclin E) might cooperatewith CDC6 to bring activating kinases to replication origins.

Based on the data presented here, which shows that CIZ1mediates the regulated recruitment of cyclin A to the nuclear

matrix, and independent data sets that identify nuclear-matrix-binding sites in the C-terminal part of CIZ1 (Ainscough et al.,2007), we suggest that CIZ1 contributes nuclear matrix localization

to the events leading to initiation. On the assumption that bothcyclin A interaction and nuclear matrix interaction domains arepresent and active within the same molecule, our integrated model

proposes the following. In late G1 phase when kinase levels arelow, CIZ1 exists in a hypophosphorylated state that is permissivefor interaction with cyclin-A–CDK2 and localization of cyclin-A–CDK2 activity to nuclear-matrix-associated sites of initiation

(Fig. 6). As kinase levels rise during early S phase, cyclin-A–CDK2 phosphorylates CIZ1 at three sites (T144, T192 and T293),inactivating its DNA-replication-promoting activity by preventing

Fig. 5. Phosphomimetic CIZ1 mutants prevent replisome assembly. (A) Schematic showing experimental design in which quiescent 3T3 cells weretransfected with GFP–CIZ1, the derived triple mutants AAA and DDD or GFP alone, and stimulated to re-enter the cell cycle. R denotes the restriction point;arrows indicate the time points at which nuclei with nascent DNA were scored (based on incorporation of EdU). Replication complex assembly was monitored bywestern blotting at 24 hours post transfection. (B) Proportion of GFP-expressing cells that entered S phase at the indicated time points, compared with thatof untransfected (GFP-negative) cells. WT, wild type. Data show the mean6s.d. (n53). (C) Total protein and detergent-resistant fraction [chromatin and nuclearmatrix (NM)-associated proteins] at 24 hours, showing recombinant GFP–CIZ1, endogenous cyclin A and actin, plus markers of the pre-RC (CDT1, CDC6,MCM2), the pre-IC (MCM2, CDC45) (Heller et al., 2011; Ilves et al., 2010) and the replisome (PCNA).

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1524

Jou

rna

lo

fC

ell

Sci

en

ce

further interaction with cyclin-A–CDK2. This describes anegative-feedback loop that could limit cyclin-A–CDK2

recruitment to origins to within a narrow local range of CDKactivity. Thus, CIZ1 appears to function as a nuclear-matrix-associated kinase sensor, which could influence replisomeformation independently at individual sites.

MATERIALS AND METHODSCell culture, synchrony and transfectionMouse 3T3 and HeLa cells were cultured in Dulbecco’s modified Eagles

Media (D-MEM) containing 10% (v/v) fetal calf serum (FCS) and

penicillin-streptomycin-glutamine (all Gibco). Synchronised populations

of 3T3 cells were generated by contact inhibition and serum starvation in

G0 followed by release into fresh medium prior to the isolation of nuclei

or cytosolic extracts for cell-free analysis, or chromatin for analysis of

CIZ1 phosphorylation (Coverley et al., 2002). S phase and G2 cells were

produced using a double thymidine block (2.5 mM) followed by release

into fresh medium for 1 hour or 10 hours, respectively, and G2/M phase

cells were produced by addition of 0.02 mg/ml nocodazole to S phase

cells for 12 hours prior to isolation. For transfection of asynchronous

populations of 3T3 cells, 15-cm dishes at ,80% confluence were

transfected with 5 ml of vector as indicated (2.5 mg) using nucleofector

kit R (Lonza) and cultured for the indicated times. Where indicated,

synchronous cells were transfected after contact inhibition and serum

starvation in quiescence with 5 ml of vector as indicated (2.5 mg) using

nucleofector kit R (Lonza), plated into fresh medium to re-enter the cell

cycle and cultured for up to 24 hours after release.

Flow cytometryGrowing cells were harvested, fixed overnight in 20% ethanol at 220 C

and stained with 100 mg/ml propidium iodide in PBS containing 0.5% (v/

v) Triton X-100. Cell cycle profiles were determined using a BD

FACScanto flow cytometer and FACSDiva software. Data were collected

for 10,000 cells with consistent gating applied for all samples.

Cell-free DNA replication assaysCytosolic extracts were prepared from early S phase HeLa cells by

Dounce homogenisation in hypotonic buffer (10 mM HEPES pH 7.8,

5 mM potassium acetate, 0.5 mM MgCl2, 1 mM DTT) followed by

centrifugation to remove insoluble material (Krude et al., 1997). G1

nuclei were isolated at 17 hours after release from quiescence and used as

substrates in cell-free DNA replication assays. Evaluation of the

composition of nuclei populations was described previously, and

consists of (1) nuclei that incorporate labelled nucleotides in the

absence of CDK (in a pre-restriction point early G1 phase cytosolic

extract, isolated at 15 hours after release) and which were in S phase at

the time of isolation, (2) nuclei that respond to CDK (supplied by S phase

extract or recombinant kinase) and which are ‘licensed’ late G1 phase

nuclei, and (3) those that do not respond and are therefore not licensed

(early G1 or G0). For each independent experiment, at least 100 nuclei

were scored for the presence of fluorescent DNA replication foci and

expressed as a percentage of the total population. All experiments were

performed with n§3, as indicated. Calculation of the percentage

initiation in the licensed fraction was as described previously

(Coverley et al., 2005).

Cellular fractionationCells were washed twice in cold PBS, then cytoskeleton (CSK) buffer

[10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 1 mM MgCl2,

1 mM DTT, with EDTA-free complete protease inhibitors (Roche)].

Detergent-insoluble fractions were prepared by inclusion of Triton X-100

(0.1% v/v) in CSK buffer and incubation on ice for 5 minutes, followed

by centrifugation at 6000 g for 5 minutes. Further inclusion of 0.5 M

NaCl followed by centrifugation generates a high-salt-resistant fraction.

The nuclear matrix fraction was obtained by washing the high-salt-

resistant pellet twice in DNase I buffer (10 mM Tris-HCl pH 7.4, 10 mM

MgCl2, 5 mM CaCl2) before digestion with RNase-free DNase I (Roche)

at 37 C for 1 hour, and a further wash with 0.5 M NaCl in CSK buffer

(Munkley et al., 2011). For immunofluorescence analysis, cells were

treated on coverslips and DNase I efficiency was monitored by staining

Fig. 6. Model showing the effect of phosphorylation of CIZ1 on cyclin A recruitment and replisome assembly. (A) During G1 phase, CIZ1 associates withCDC6, facilitating recruitment of the pre-RC to the nuclear matrix. In late G1, cyclin-A–CDK2 binds to hypo-phosphorylated CIZ1, leading to phosphorylation anddisplacement of CDC6, recruitment of PCNA and production of an active replisome. As cyclin A levels rise, CIZ1 is itself phosphorylated so that it can nolonger recruit cyclin A, preventing further initiation at the same site. A, cyclin A; K2, CDK2. (B) Phosphomimetic CIZ1-DDD retains the ability to associate withCDC6 but does not recruit cyclin-A–CDK2, forming an unproductive complex with a dominant inhibitory effect on initiation. Loading of components of the pre-RC(CDT1, CDC6, MCM2) and pre-IC (CDC45), but failure to recruit PCNA, indicates that completion of the replisome is blocked under these circumstances.

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1525

Jou

rna

lo

fC

ell

Sci

en

ce

residual nuclei with Hoechst 33258. For interaction studies with

endogenous CDC6, S3 HeLa cells were resuspended in buffer A

[50 mM HEPES-KOH pH 7.8, 0.5 mM ATP, 5 mM MgCl2, 10 mM

CaCl2, 1 mM EDTA, 1 mM EGTA, 5 mM magnesium acetate, 10% (v/

v) glycerol, 1 mM DTT and 16Halt protease inhibitors (Pierce)]. Cells

were Dounce homogenised, and nuclei were enriched by centrifugation at

6000 g, then resuspended in two volumes of the same buffer

supplemented with 450 mM KCl and 0.02% (v/v) NP40. Soluble

extract was removed after centrifugation at 10,000 g, diluted in three

volumes of buffer A and incubated with GST–CIZ1-N471, GST–CIZ1-

N391 or GST alone, immobilised on glutathione–Sepharose, as indicated,

for 1 hour at 4 C. Beads were washed five times, in ten times bead

volume buffer A containing 100 mM KCl and 0.02% (v/v) NP40, and

analysed by western blotting.

ImmunofluorescenceCells on coverslips were extracted as described previously and

immunostained to reveal chromatin and nuclear matrix or just matrix-

associated proteins (Munkley et al., 2011). BrdU (GE Bioscience) or EdU

Click IT reactions (Invitrogen) were used as recommended to identify

replicating cells. Colocalisation experiments using cells expressing GFP–

CIZ1 constructs were performed using a Zeiss 510 confocal microscope,

with 1 Airy unit pin-hole for all fluorophores. Images were captured

using multitrack mode, setting imaging parameters for GFP–CIZ1 using

palette range finder to set parameters that were applied for all images.

Post acquisition, images were prepared using Adobe Photoshop CS5 and

colocalisation was determined using BioImage XD (http://www.

openbioimage.org). Colocalisation was determined using constant

parameters for all images. Percentage colocalisation refers to the total

percentage of CIZ1 and cyclin A colocalised pixels in each image.

Population data for each construct was used to generate a box and

whisker plot using SPSS statistics 21, showing the distribution of the

extent of colocalisation for each construct.

AntibodiesMonoclonal antibodies against cyclin A (CY-1A, Sigma Aldrich), actin

(AC15, Sigma Aldrich), PCNA (sc56, Santa Cruz Biotechnology), CDC6

(sc-9964), anti-BM28 (Becton Dickinson) and lamin A (sc-20680), and

polyclonal antibodies against CDC45 (Santa Cruz Biotechnology, sc-

20685), histone H3 (Abcam, ab1791) and CDT1 (Santa Cruz

Biotechnology, sc-28262) were used as directed for western blotting

and/or immunofluorescence. CIZ1 was detected with anti-CIZ1 polyclonal

antibody 1793 (Coverley et al., 2005) or a rabbit polyclonal antibody raised

against purified bacterially expressed recombinant ECIZ1-N471 for this

study (Covalab) (Fig. 4 only). For western blots, goat anti-mouse-IgG

conjugated to peroxidase (POD) and goat anti-rabbit-IgG–POD (both

Sigma Aldrich) were used with an ECL detection system (GE Lifescience).

For immunofluorescence, Alexa-FluorH-488-conjugated goat anti-mouse-

IgG (H+L) (A10667) and Alexa-FluorH-568-conjugated goat anti-rabbit-

IgG (H+L) (A11036) (both Invitrogen) were used. Phosphospecific anti-

CIZ1 phospho-T293 (anti-pT293) was produced by immunisation of

rabbits with TAPKQTQTpTPDRL peptide, where pT indicates

phosphothreonine (Covalabs). Antibodies were purified by sequential

subtraction on unphosphorylated peptide columns and enrichment on a

phosphopeptide column, to purify phosphospecific anti-CIZ1 antibodies.

Site-directed mutagenesisSingle amino acid substitutions were created with the Stratagene

QuikChange method, using pGEX-ECIZ1 N471 or pEGFP-ECIZ1 as

templates (Copeland et al., 2010). For multiple mutations, each site was

mutated in separate reactions and all vectors were sequence verified

(Eurofins).

Protein production and binding assaysAll CIZ1 fragments and derived mutants were expressed as GST fusions

in pGEX6P3 in Escherichia coli Rosetta (DE3) and purified as described

previously (Coverley et al., 2002; Coverley et al., 2005). GST–CDC6 was

expressed in BL21 (DE3) E. coli and the tag was removed by digestion

with PreScission protease (GE). For binding studies, proteins were

immobilised on glutathione beads (as indicated) incubated with cell

extracts or purified recombinant proteins for 1 hour at 4 C in binding

buffer (10 mM HEPES pH 7.8, 135 mM KCl, 20 mM MgCl2, 10 mM

CaCl2, 0.04% NP40, 1 mM DTT, with EDTA-free complete protease

inhibitor cocktail). ATP (Sigma Aldrich) and/or 100 mM roscovitine

(Cell Signaling Technology/New England Biolabs) were included as

indicated. Beads were washed five times in cold binding buffer and

analysed by western blotting.

In vitro protein kinase assaysAssays were performed in 50 mM HEPES KOH pH 7.8, 20 mM MgCl210 mM ATP, 1.5 ml [c-33P]ATP (Perkin Elmer), 1 mM DTT. CIZ1 was

used at 1 mM, and cyclin-A–CDK2 or cyclin-E–CDK2 were used at

50 nM under pseudo-first conditions. For samples treated with l protein

phosphatase (P0753S, New England Biolabs), reactions were performed

according to the manufacturer’s instructions. Samples were separated by

SDS-PAGE, and gels were dried and developed on CL-XPosure Film

(Thermofisher). Densitometry was performed using NIH ImageJ.

Statistical analysisSignificant differences in DNA replication activity and colocalisation

analysis were performed by one-way analysis of variance (ANOVA)

followed by Tukey’s test post-hoc using IBM SPSS statistics 21. All

significant results are shown in figures as appropriate. ***P,0.001,

**P,0.01 and *P,0.05.

Phosphoproteomic analysisIn vitro kinase assays were performed using cyclin-A–CDK2 and CIZ1-

N471 fragments and analysed by SDS-PAGE, and in-gel proteolytic

digestion was performed after reduction and S-carbamidomethylation

with iodoacetamide. Gel pieces were rehydrated in 25 mM ammonium

bicarbonate and digested with sequencing-grade modified porcine trypsin

at 0.004 mg/ml (Promega) overnight at 37 C. Eluted peptides were

vacuum desiccated and resuspended in 1 M glycolic acid in 80% aqueous

acetonitrile (v/v), 5% trifluoroacetic acid (v/v). Phosphopeptides were

selectively enriched using manually packed titanium microcolumns

(Larsen et al., 2005). Enriched phosphopeptides were purified by Poros

Oligo R3 reversed-phase a material (Larsen et al., 2005) and eluted

directly onto a ground steel MALDI target plate with a freshly prepared

10 mg/ml solution of 2,5-dihydroxybenzoic acid (Sigma-Aldrich) in 50%

aqueous acetonitrile (v/v), 1% phosphoric acid (v/v).

Positive-ion MALDI mass spectra were obtained using an ultraflex III

mass spectrometer (Bruker, Bramen, Germany) in reflectron mode,

equipped with a Nd:YAG smart beam laser. Mass spectrometry (MS)

spectra were acquired over a mass range of 800–4000 m/z. Final mass

spectra were externally calibrated against an adjacent spot containing

six peptides of known m/z [des-Arg1-bradykinin, 904.681; angiotensin

I, 1296.685; Glu1-fibrinopeptide B, 1750.677; ACTH (1–17 clip),

2093.086; ACTH (18–39 clip), 2465.198; ACTH (7–38 clip),

3657.929]. Peptides were manually selected for MS/MS fragmentation,

which was performed in LIFT mode without the introduction of a

collision gas. Fragmentation spectra were acquired manually with laser

intensity and number of summed spectra optimised for each acquisition.

The default calibration was used for MS/MS spectra, which were

baseline-subtracted and smoothed (Savitsky-Golay, width 0.15 m/z,

cycles 4); monoisotopic peak detection used a SNAP averaging algorithm

(C 4.9384, N 1.3577, O 1.4773, S 0.0417, H 7.7583) with a minimum S/N

of 6. Bruker flexAnalysis software (version 3.3) was used to perform the

spectral processing and peak list generation for both the MS and MS/MS

spectra. Tandem mass spectral data were submitted to database searching

using a locally running copy of the Mascot program (Matrix Science Ltd,

version 2.3), through the Bruker ProteinScape interface (version 2.1). All

spectral data were searched against an in-house database containing the

expected protein sequence. Search criteria specified: Enzyme, trypsin;

Fixed modifications, carbamidomethyl (C); Variable modifications,

oxidation (M) and phosphorylation (S,T); Peptide tolerance, 250 ppm;

MS/MS tolerance, 0.5 Da; Instrument, MALDI-TOF-TOF.

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1526

Jou

rna

lo

fC

ell

Sci

en

ce

AcknowledgementsWe thank Adam Dowle and Jerry Thomas for technical support with MS andanalysis. We are grateful to Clive Price, Emma Hesketh and Justin Ainscough forcritical comments on the manuscript.

Competing interestsThe authors declare no competing or financial interests.

Author contributionsN.A.C. and D.C. designed experiments. N.A.C., H.E.S. and R.H.C.W. performedexperiments. N.A.C. analysed data. N.A.C. and D.C. wrote the manuscript.

FundingThis work was supported by Yorkshire Cancer Research [grant number Y252 toD.C]; and the North West Cancer Research [grant numbers CR879 and CR891 toN.A.C]. D.C. is supported by the Higher Education Funding Council; and R.W. andH.S. studentships were supported by the Biotechnology and Biological SciencesResearch Council.

Supplementary materialSupplementary material available online athttp://jcs.biologists.org/lookup/suppl/doi:10.1242/jcs.161919/-/DC1

ReferencesAbe, T., Yoshimura, A., Hosono, Y., Tada, S., Seki, M. and Enomoto, T. (2011).

The N-terminal region of RECQL4 lacking the helicase domain is both essentialand sufficient for the viability of vertebrate cells. Role of the N-terminal region ofRECQL4 in cells. Biochim. Biophys. Acta 1813, 473-479.

Ainscough, J. F., Rahman, F. A., Sercombe, H., Sedo, A., Gerlach, B. andCoverley, D. (2007). C-terminal domains deliver the DNA replication factor Ciz1to the nuclear matrix. J. Cell Sci. 120, 115-124.

Anachkova, B., Djeliova, V. and Russev, G. (2005). Nuclear matrix support ofDNA replication. J. Cell. Biochem. 96, 951-961.

Araki, H. (2010). Cyclin-dependent kinase-dependent initiation of chromosomalDNA replication. Curr. Opin. Cell Biol. 22, 766-771.

Balestrini, A., Cosentino, C., Errico, A., Garner, E. and Costanzo, V. (2010).GEMC1 is a TopBP1-interacting protein required for chromosomal DNAreplication. Nat. Cell Biol. 12, 484-491.

Blow, J. J. and Dutta, A. (2005). Preventing re-replication of chromosomal DNA.Nat. Rev. Mol. Cell Biol. 6, 476-486.

Copeland, N. A., Sercombe, H. E., Ainscough, J. F. and Coverley, D. (2010).Ciz1 cooperates with cyclin-A-CDK2 to activate mammalian DNA replication invitro. J. Cell Sci. 123, 1108-1115.

Coudreuse, D. and Nurse, P. (2010). Driving the cell cycle with a minimal CDKcontrol network. Nature 468, 1074-1079.

Coverley, D., Laman, H. and Laskey, R. A. (2002). Distinct roles for cyclins E andA during DNA replication complex assembly and activation. Nat. Cell Biol. 4,523-528.

Coverley, D., Marr, J. and Ainscough, J. (2005). Ciz1 promotes mammalianDNA replication. J. Cell Sci. 118, 101-112.

Dahmcke, C. M., Buchmann-Møller, S., Jensen, N. A. and Mitchelmore, C.(2008). Altered splicing in exon 8 of the DNA replication factor CIZ1 affectssubnuclear distribution and is associated with Alzheimer’s disease. Mol. Cell.Neurosci. 38, 589-594.

den Hollander, P., Rayala, S. K., Coverley, D. and Kumar, R. (2006). Ciz1, aNovel DNA-binding coactivator of the estrogen receptor alpha, confershypersensitivity to estrogen action. Cancer Res. 66, 11021-11029.

Djeliova, V., Russev, G. and Anachkova, B. (2001). Dynamics of association oforigins of DNA replication with the nuclear matrix during the cell cycle. NucleicAcids Res. 29, 3181-3187.

Furstenthal, L., Kaiser, B. K., Swanson, C. and Jackson, P. K. (2001). Cyclin Euses Cdc6 as a chromatin-associated receptor required for DNA replication.J. Cell Biol. 152, 1267-1278.

Geng, Y., Yu, Q., Sicinska, E., Das, M., Schneider, J. E., Bhattacharya, S.,Rideout, W. M., Bronson, R. T., Gardner, H. and Sicinski, P. (2003). Cyclin Eablation in the mouse. Cell 114, 431-443.

Geng, Y., Lee, Y. M., Welcker, M., Swanger, J., Zagozdzon, A., Winer, J. D.,Roberts, J. M., Kaldis, P., Clurman, B. E. and Sicinski, P. (2007). Kinase-independent function of cyclin E. Mol. Cell 25, 127-139.

Greaves, E. A., Copeland, N. A., Coverley, D. and Ainscough, J. F. (2012).Cancer-associated variant expression and interaction of CIZ1 with cyclin A1 indifferentiating male germ cells. J. Cell Sci. 125, 2466-2477.

Heller, R. C., Kang, S., Lam, W. M., Chen, S., Chan, C. S. and Bell, S. P. (2011).Eukaryotic origin-dependent DNA replication in vitro reveals sequential action ofDDK and S-CDK kinases. Cell 146, 80-91.

Higgins, G., Roper, K. M., Watson, I. J., Blackhall, F. H., Rom, W. N., Pass, H.I., Ainscough, J. F. and Coverley, D. (2012). Variant Ciz1 is a circulating

biomarker for early-stage lung cancer. Proc. Natl. Acad. Sci. USA 109, E3128-E3135.

Ilves, I., Petojevic, T., Pesavento, J. J. and Botchan, M. R. (2010). Activation ofthe MCM2-7 helicase by association with Cdc45 and GINS proteins. Mol. Cell37, 247-258.

Krude, T., Jackman, M., Pines, J. and Laskey, R. A. (1997). Cyclin/Cdk-dependent initiation of DNA replication in a human cell-free system. Cell 88,109-119.

Kumagai, A., Shevchenko, A., Shevchenko, A. and Dunphy, W. G. (2010).Treslin collaborates with TopBP1 in triggering the initiation of DNA replication.Cell 140, 349-359.

Kumagai, A., Shevchenko, A., Shevchenko, A. and Dunphy, W. G. (2011).Direct regulation of Treslin by cyclin-dependent kinase is essential for the onsetof DNA replication. J. Cell Biol. 193, 995-1007.

Labib, K. (2010). How do Cdc7 and cyclin-dependent kinases trigger theinitiation of chromosome replication in eukaryotic cells? Genes Dev. 24, 1208-1219.

Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P. and Jorgensen,T. J. (2005). Highly selective enrichment of phosphorylated peptides frompeptide mixtures using titanium dioxide microcolumns. Mol. Cell Proteomics 4,873-886.

Mailand, N. and Diffley, J. F. (2005). CDKs promote DNA replication originlicensing in human cells by protecting Cdc6 from APC/C-dependent proteolysis.Cell 122, 915-926.

Munkley, J., Copeland, N. A., Moignard, V., Knight, J. R., Greaves, E.,Ramsbottom, S. A., Pownall, M. E., Southgate, J., Ainscough, J. F. andCoverley, D. (2011). Cyclin E is recruited to the nuclear matrix duringdifferentiation, but is not recruited in cancer cells. Nucleic Acids Res. 39, 2671-2677.

Muramatsu, S., Hirai, K., Tak, Y. S., Kamimura, Y. and Araki, H. (2010). CDK-dependent complex formation between replication proteins Dpb11, Sld2, Pol(epsilon, and GINS in budding yeast. Genes Dev. 24, 602-612.

Pacek, M., Tutter, A. V., Kubota, Y., Takisawa, H. and Walter, J. C. (2006).Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding duringeukaryotic DNA replication. Mol. Cell 21, 581-587.

Piergiovanni, G. and Costanzo, V. (2010). GEMC1 is a novel TopBP1-interactingprotein involved in chromosomal DNA replication. Cell Cycle 9, 3686-3690.

Pospelov, V., Anachkova, B. and Russev, G. (1982). Organization of the newlyreplicated chromatin in the vicinity of the replication fork. Biochim. Biophys. Acta699, 241-246.

Rahman, F., Ainscough, J. F., Copeland, N. and Coverley, D. (2007). Cancer-associated missplicing of exon 4 influences the subnuclear distribution of theDNA replication factor CIZ1. Hum. Mutat. 28, 993-1004.

Rahman, F. A., Aziz, N. and Coverley, D. (2010). Differential detection ofalternatively spliced variants of Ciz1 in normal and cancer cells using a customexon-junction microarray. BMC Cancer 10, 482.

Sangrithi, M. N., Bernal, J. A., Madine, M., Philpott, A., Lee, J., Dunphy, W. G.and Venkitaraman, A. R. (2005). Initiation of DNA replication requires theRECQL4 protein mutated in Rothmund-Thomson syndrome. Cell 121, 887-898.

Schub, O., Rohaly, G., Smith, R. W., Schneider, A., Dehde, S., Dornreiter, I.and Nasheuer, H. P. (2001). Multiple phosphorylation sites of DNA polymerasealpha-primase cooperate to regulate the initiation of DNA replication in vitro.J. Biol. Chem. 276, 38076-38083.

Spencer, S. L., Cappell, S. D., Tsai, F. C., Overton, K. W., Wang, C. L. andMeyer, T. (2013). The proliferation-quiescence decision is controlled by abifurcation in CDK2 activity at mitotic exit. Cell 155, 369-383.

Tanaka, S., Umemori, T., Hirai, K., Muramatsu, S., Kamimura, Y. and Araki, H.(2007). CDK-dependent phosphorylation of Sld2 and Sld3 initiates DNAreplication in budding yeast. Nature 445, 328-332.

Voitenleitner, C., Fanning, E. and Nasheuer, H. P. (1997). Phosphorylation ofDNA polymerase alpha-primase by cyclin A-dependent kinases regulatesinitiation of DNA replication in vitro. Oncogene 14, 1611-1615.

Voitenleitner, C., Rehfuess, C., Hilmes, M., O’Rear, L., Liao, P. C., Gage, D. A.,Ott, R., Nasheuer, H. P. and Fanning, E. (1999). Cell cycle-dependentregulation of human DNA polymerase alpha-primase activity byphosphorylation. Mol. Cell. Biol. 19, 646-656.

Warder, D. E. and Keherly, M. J. (2003). Ciz1, Cip1 interacting zinc finger protein1 binds the consensus DNA sequence ARYSR(0-2)YYAC. J. Biomed. Sci. 10,406-417.

Xiao, J., Uitti, R. J., Zhao, Y., Vemula, S. R., Perlmutter, J. S., Wszolek, Z. K.,Maraganore, D. M., Auburger, G., Leube, B., Lehnhoff, K. et al. (2012).Mutations in CIZ1 cause adult onset primary cervical dystonia. Ann. Neurol. 71,458-469.

Zegerman, P. and Diffley, J. F. (2007). Phosphorylation of Sld2 and Sld3 bycyclin-dependent kinases promotes DNA replication in budding yeast. Nature445, 281-285.

Zink, D., Fischer, A. H. and Nickerson, J. A. (2004). Nuclear structure in cancercells. Nat. Rev. Cancer 4, 677-687.

RESEARCH ARTICLE Journal of Cell Science (2015) 128, 1518–1527 doi:10.1242/jcs.161919

1527

Jou

rna

lo

fC

ell

Sci

en

ce