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S phase

The S phase, or synthesis phase, is a critical stage of the eukaryotic cell cycle during which the cell's DNA is precisely duplicated to produce two identical copies of each chromosome, ensuring genetic continuity for daughter cells upon division.^[1] This replication occurs semi-conservatively, transforming the DNA content from 2n to 4n, and is confined to interphase, following the G1 phase and preceding the G2 phase.^[2] In typical mammalian cells, the S phase duration ranges from 8 to 12 hours, comprising roughly half of the total ~24-hour cell cycle in rapidly dividing human cells.^[1]^[2] The primary process in S phase involves the activation of thousands of replication origins across the genome, where the origin recognition complex (ORC) and minichromosome maintenance (MCM) proteins initiate bidirectional DNA synthesis by DNA polymerases, resulting in the formation of tightly associated sister chromatids.^[2] Centrosomes and centrioles (in animal cells) also duplicate during this phase to support subsequent mitosis.^[3] Progression into S phase is gated by the G1/S checkpoint, often called the restriction point, which integrates extracellular growth signals and internal assessments of DNA integrity before committing to replication.^[2]^[4] S phase entry and execution are tightly regulated by cyclin-dependent kinases (CDKs), particularly CDK2 complexed with cyclin E, which phosphorylate targets to license replication origins in G1 and trigger firing in S phase, while ubiquitin ligases and checkpoints prevent over-replication or proceed in the face of damage.^[5] DNA damage detected during S phase activates repair pathways, such as those involving p53, which can halt progression or induce arrest to maintain genomic stability.^[2] Dysregulation of S phase, as seen in cancer, can lead to genomic instability, highlighting its role in both normal proliferation and disease.^[4]

Overview

Definition and role

The S phase, or synthesis phase, is the second stage of the eukaryotic cell cycle, occurring after the G1 phase and before the G2 phase, during which the cell's entire genome undergoes semiconservative replication to produce two identical copies of each DNA molecule. This process doubles the DNA content from 2C to 4C, preparing the cell for subsequent division while maintaining genetic stability.^[6] The primary role of S phase is to ensure genetic continuity across generations by duplicating the genome exactly once per cell cycle, thereby preventing catastrophic errors such as mutations, gene amplification, or aneuploidy that could arise from incomplete or over-replication. This duplication is crucial for the equitable segregation of sister chromatids during mitosis, where the replicated chromosomes are distributed to daughter cells. S phase is temporally coordinated with the preceding G1 phase, which assesses cellular readiness, and the following G2 phase, which verifies replication fidelity before mitosis. The existence of distinct cell cycle phases, including S phase, was first established in the 1950s through pioneering radiolabeling experiments using phosphorus-32 on root tip cells of Vicia faba, conducted by Alma Howard and Stephen Pelc. These studies revealed a discrete period of DNA synthesis intervening between mitosis and a subsequent postsynthetic gap, laying the foundation for understanding the ordered progression of eukaryotic cell division. In human somatic cells, S phase typically lasts 8–10 hours and involves replicating approximately 6 billion base pairs of diploid DNA at a rate of approximately 20–50 base pairs per second per replication fork, facilitated by thousands of origins of replication firing in a coordinated manner.^[7]^[8]^[9]

Timing and coordination with cell cycle

The S phase occurs immediately following the G1 phase and precedes the G2 phase in the eukaryotic cell cycle, during which DNA replication ensures genome duplication prior to cell division. Its temporal placement is tightly coordinated to maintain genomic integrity, with the phase's onset triggered by the successful completion of G1 growth and readiness checks. In mammalian somatic cells, S phase typically lasts 8–10 hours, while in rapidly dividing early Drosophila embryos, it is dramatically shorter, completing in approximately 3–4 minutes due to high replication fork speeds and dense origin firing. This variability in duration across organisms and cell types is largely influenced by the density of replication origins, with higher densities enabling faster coverage of the genome and shorter overall S phase times.^[7]^[10] Integration with cell cycle checkpoints ensures orderly progression, beginning with the restriction point in late G1, where cells commit irreversibly to entering S phase upon receiving sufficient growth signals and achieving a critical size threshold. This commitment prevents reversal even if external stimuli are withdrawn, linking G1 competence to S phase initiation. At the downstream end, coordination with the G2/M transition is enforced by the DNA replication checkpoint, which halts mitotic entry if replication remains incomplete, thereby blocking progression until all genomic regions are duplicated and damage is resolved. These checkpoints collectively synchronize S phase with the broader cycle, averting errors like aneuploidy.^[11]^[12] The timing of S phase onset and exit is governed by cell cycle oscillators, particularly the periodic fluctuations in cyclin levels, which rise to promote entry into DNA synthesis and decline to facilitate progression to G2. These oscillations create a temporal framework that aligns replication with other cycle events, ensuring S phase neither overlaps with mitosis nor lags behind preparatory phases. Experimental quantification of S phase dynamics often employs flow cytometry combined with thymidine analogs like BrdU, which incorporate into newly synthesized DNA, allowing real-time tracking of progression through bivariate analysis of DNA content and analog incorporation. This approach reveals cell-to-cell variability and average durations, providing insights into synchronization mechanisms without disrupting cycle flow.^[13]^[14]

Regulation

Molecular triggers for entry

The transition into S phase is gated by the restriction point in late G1, an irreversible commitment to cell cycle progression that depends on sufficient growth factors and nutrient availability to ensure cellular resources for DNA replication.^[15] This checkpoint integrates extracellular signals, such as mitogens, which activate signaling pathways leading to the accumulation of D-type cyclins and their associated cyclin-dependent kinases (CDKs), thereby promoting passage through the restriction point.^[16] Once crossed, cells become independent of external stimuli and proceed to prepare for DNA synthesis. A critical preparatory step is the assembly of the pre-replication complex (pre-RC) during G1 phase, which licenses replication origins for subsequent activation. The origin recognition complex (ORC) binds to specific DNA sequences at potential origins, recruiting Cdc6 and Cdt1 to load the MCM2-7 helicase as a double hexamer, forming the pre-RC.^[17] This licensing is tightly regulated to occur only in G1; in S, G2, and M phases, mechanisms including CDK-mediated phosphorylation of Cdc6, Cdt1 degradation, and geminin binding to Cdt1 prevent re-licensing, ensuring genome duplication happens once per cycle.^[18] Entry into S phase is further triggered by the activation of E2F transcription factors, which drive expression of genes essential for DNA replication. In early G1, the retinoblastoma protein (Rb) binds and represses E2F; however, sequential phosphorylation of Rb by cyclin D-CDK4/6 and then cyclin E-CDK2 complexes releases E2F, allowing it to transcribe S-phase genes such as those encoding DNA polymerase and thymidine kinase.^[19] This transcriptional program, in coordination with pre-RC licensing, initiates origin firing at designated sites, with mammalian cells activating approximately 30,000 to 50,000 origins to replicate the genome.^[20]

Control by cyclins and kinases

The progression of S phase is primarily orchestrated by cyclin-dependent kinases (CDKs), which form complexes with specific cyclins to drive DNA replication initiation and elongation while preventing aberrant re-replication.^[21] These enzymes phosphorylate key substrates, including components of the pre-replication complex and transcription factors, ensuring timely and controlled DNA synthesis.^[22] A pivotal complex is cyclin E bound to CDK2, which peaks in activity during late G1 and early S phase to trigger origin firing. This complex phosphorylates the retinoblastoma protein (Rb), leading to the release of E2F transcription factors that activate genes essential for S phase entry, such as those encoding DNA polymerase and thymidine kinase.^[23] Additionally, cyclin E-CDK2 phosphorylates CDC6, facilitating the loading of the MCM helicase onto origins and promoting the onset of DNA replication.^[23] The activity of this complex is modulated by cyclin E levels and CDK2's phosphorylation state, where activating phosphorylation on threonine 160 by CAK enhances kinase function; mathematically, CDK2 activity can be approximated as proportional to the product of cyclin E concentration and its phosphorylated state:

\text{CDK2 activity} \propto [\text{Cyclin E}] \times (\text{phosphorylation state})

This relationship underscores the tight regulation required for precise S phase initiation.^[22] Following entry, cyclin A-CDK2 sustains replication fork progression throughout S phase and enforces a barrier against re-replication. Cyclin A associates with CDK2 to phosphorylate substrates like CDC6, exporting it from the nucleus and inhibiting new pre-replication complex assembly at licensed origins.^[24] This phosphorylation also targets Cdt1, a licensing factor, rendering it incapable of reloading MCM complexes and thus preventing DNA from being replicated more than once per cycle.^[25] By maintaining high activity during S phase, cyclin A-CDK2 ensures unidirectional progression of replication forks without untimely origin reactivation.^[25] To safeguard against uncontrolled entry, inhibitory mechanisms counteract CDK activity, particularly under cellular stress. CDK inhibitors such as p21 (CDKN1A) and p27 (CDKN1B) bind to cyclin E-CDK2 and cyclin A-CDK2 complexes, blocking their kinase activity and halting S phase progression in response to DNA damage or nutrient deprivation.^[26] For instance, p21 and p27 levels rise during stress, sequestering cyclins and preventing phosphorylation of pro-replicative targets.^[27] Complementing this, geminin accumulates in early S phase to sequester Cdt1, further inhibiting pre-replication complex reformation independently of direct CDK inhibition.^[28] This cyclin-CDK framework is highly conserved across eukaryotes, with variations reflecting species-specific adaptations. In budding yeast (Saccharomyces cerevisiae), the S phase-promoting cyclins Clb5 and Clb6 pair with Cdk1 (the ortholog of metazoan CDK2) to drive origin firing and replication progression, mirroring the roles of cyclin E/A-CDK2 in mammals.^[29] Deletion of CLB5 delays S phase onset, while Clb6 provides partial redundancy, highlighting their functional equivalence.^[30] Despite these differences in cyclin nomenclature, the core mechanism—cyclin oscillation driving CDK-mediated phosphorylation for S phase control—remains invariant from yeast to humans, ensuring genomic stability.^[21]

DNA replication process

Initiation of replication

The initiation of DNA replication begins with the recognition of replication origins by the origin recognition complex (ORC), a heterohexameric protein that binds specifically to AT-rich DNA sequences in eukaryotic genomes. In budding yeast, ORC preferentially associates with autonomously replicating sequences (ARS) characterized by an AT-rich composition, which facilitates initial DNA unwinding and serves as a platform for subsequent protein recruitment.^[31] Once bound, ORC recruits the Cdc6 ATPase and Cdt1 proteins during the G1 phase of the cell cycle, enabling the loading of the MCM2-7 helicase complex onto double-stranded DNA in a head-to-head orientation, forming the pre-replicative complex (pre-RC).^[32] This encircles the DNA without unwinding it, positioning two MCM2-7 hexamers for bidirectional replication potential. Upon entry into S phase, activation of the pre-RC occurs through phosphorylation by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), which remodel the MCM2-7 complex and promote the recruitment of additional factors.^[33] DDK primarily phosphorylates MCM2-7 subunits, facilitating the loading of Cdc45 and the GINS complex to assemble the active CMG (Cdc45-MCM2-7-GINS) helicase, which encircles and unwinds the DNA at the origin.^[34] As the helicase progresses, replication protein A (RPA) binds to the exposed single-stranded DNA (ssDNA), stabilizing it and preventing secondary structure formation to support downstream priming and synthesis.^[35] This unwinding generates a bubble of ssDNA, marking the transition from licensing to active replication fork establishment.^[32] Primer synthesis is initiated by the DNA polymerase α-primase complex, which synthesizes short RNA-DNA hybrid primers on the exposed ssDNA templates.^[36] Primase within the complex first polymerizes approximately 10 nucleotides of RNA using NTP substrates, followed by extension with about 20 nucleotides of DNA by the polymerase α subunit, creating a chimeric primer of roughly 30 nucleotides total.^[37] These primers provide the 3'-OH end required for subsequent elongation by replicative polymerases. On the leading strand, DNA polymerase ε binds and begins continuous synthesis from the primer in the 5' to 3' direction, while on the lagging strand, DNA polymerase δ initiates discontinuous Okazaki fragment synthesis from additional primers generated periodically.^[38] The initial rate of replication fork progression is coordinated by the CMG helicase unwinding rate and polymerase synthesis, typically 1-2 kb/min (≈17-33 bp/s) in mammalian cells.^[39]

Elongation and fork progression

During the elongation phase of DNA replication, the leading strand is synthesized continuously in the 5' to 3' direction by DNA polymerase ε (Pol ε), which advances in tandem with the CMG helicase complex to replicate the parental template ahead of the fork. This process allows Pol ε to incorporate nucleotides without frequent dissociation, achieving high processivity of up to approximately 100 kb per binding event in eukaryotes. The lagging strand, in contrast, is replicated discontinuously by DNA polymerase δ (Pol δ) in short segments known as Okazaki fragments, each typically 100-200 nucleotides long in human cells. Pol δ synthesizes these fragments in the opposite direction to fork progression, initiating from RNA primers laid down by Pol α-primase. Maturation of Okazaki fragments on the lagging strand involves the coordinated removal of RNA primers and gap filling to enable seamless ligation. RNase H specifically cleaves the RNA-DNA hybrid at the 5' end of each fragment, while flap endonuclease 1 (FEN1) excises the remaining ribonucleotides through endonucleolytic cleavage of displaced flaps generated by Pol δ's strand displacement activity. The resulting nicks are then sealed by DNA ligase I, which catalyzes phosphodiester bond formation in an ATP-dependent manner, completing the lagging strand synthesis. Replication fork progression relies on accessory proteins that maintain replisome stability and coordinate unwinding with synthesis. The fork protection complex (FPC), comprising Timeless, Tipin, and Claspin, associates with the CMG helicase and polymerases to prevent fork collapse and ensure coupling between helicase unwinding and DNA synthesis. In eukaryotes, the CMG helicase unwinds the double helix at a rate of approximately 50 base pairs per second, enabling bidirectional fork movement from each origin. Fork progression can be impeded by obstacles such as encounters with the transcription machinery or nucleosomes, which temporarily slow the replisome and increase the risk of stalling. Transcription-replication conflicts arise when RNA polymerase complexes block fork advance, particularly in highly transcribed regions, leading to reduced fork speeds. Similarly, nucleosomes ahead of the fork resist unwinding, and insufficient histone supply or assembly behind the fork further decelerates progression by disrupting chromatin dynamics. The overall time required for S phase completion can be estimated using the relation between genome size, fork speed, and the number of active origins, as replication proceeds bidirectionally from multiple sites:

t = \frac{\text{genome size}}{2 \times \text{fork speed} \times \text{number of origins}}

This formula highlights how increased origin firing or faster forks reduce replication duration, ensuring timely genome duplication.

Termination and completion

As replication forks from adjacent origins converge during the final stages of S phase in eukaryotes, termination occurs without dedicated terminus sites, unlike in prokaryotes where specific ter sequences direct bidirectional fork meeting. Instead, eukaryotic forks merge stochastically across the genome, leading to the formation of catenated daughter DNA molecules due to unreleased intertwinings from replication. Decatenation is primarily mediated by topoisomerase II, which resolves these catenanes by introducing transient double-strand breaks and strand passage, ensuring the segregation of newly replicated chromosomes in the subsequent G2 and M phases.^[40] Any unreplicated gaps remaining after fork convergence, often arising from DNA lesions or replication stress that stalled forks earlier, are typically filled through post-replicative mechanisms such as translesion synthesis (TLS). TLS employs specialized low-fidelity polymerases, including DNA polymerase ζ (Pol ζ), which acts as an extender to complete synthesis across damaged templates after an initial lesion-bypassing polymerase inserts nucleotides opposite the damage. This process minimizes persistent single-stranded DNA gaps that could otherwise trigger genomic instability, although it introduces a higher mutation risk compared to replicative polymerases.^[41] Completion of S phase is marked by signals that halt further origin firing, including the deactivation of late-firing and dormant origins through rising cyclin-dependent kinase (CDK) activity that phosphorylates and inhibits pre-replication complex components like Cdc6 and Cdt1, preventing relicensing. Concurrently, chromatin undergoes decondensation facilitated by CDK2-mediated histone H1 phosphorylation, which loosens higher-order structures and signals readiness for G2 entry by promoting nuclear reorganization and gene expression appropriate for the post-replicative state. The TRESLIN-MTBP complex further couples replication completion to G2/M transition by inhibiting premature progression until synthesis is fully resolved.^[42]^[43] The overall fidelity of eukaryotic DNA replication achieves an error rate of approximately 1 mistake per 10^9 to 10^10 bases incorporated, primarily through the combined actions of 3'→5' exonuclease proofreading by replicative polymerases (which corrects ~99% of initial mismatches) and post-replicative mismatch repair (MMR) systems that excise and replace erroneous segments. This multi-layered error correction ensures genome stability despite the immense scale of replication, with human cells duplicating ~6 × 10^9 base pairs per S phase.^[44]

Biosynthetic accompaniments

Histone synthesis and supply

During S phase, the canonical core histones H2A, H2B, H3, and H4 are synthesized in large quantities to package newly replicated DNA into chromatin, while replication-dependent variants of the linker histone H1 are also produced primarily during this period.^[45] These histones are encoded by gene clusters that lack introns and polyadenylation signals, ensuring their expression is tightly coupled to DNA replication. In mammalian cells, this process demands the production of approximately 400 million core histone molecules per cell division to form the required number of nucleosomes for the duplicated genome.^[46] Transcriptional activation of these histone genes occurs specifically at the G1/S transition through S-phase promoters that respond to cell cycle signals. The key regulators include the transcription factor HiNF-P (histone nuclear factor P), which binds to these promoters, and NPAT (nuclear protein ataxia-telangiectasia locus), which is phosphorylated by cyclin E-CDK2 to recruit HiNF-P and initiate a cascade of coactivators within histone locus bodies.^[47] This upregulation ensures a burst of histone mRNA synthesis that peaks in early to mid-S phase. Histone mRNAs are stabilized by a conserved 3' stem-loop structure bound by stem-loop binding protein (SLBP), which protects them from degradation and coordinates their processing and export during active replication.^[48] Excess histones produced during S phase are temporarily stored in the nucleus by acidic chaperones to prevent toxicity and maintain supply. In mammalian cells, the chaperone NASP (nuclear acidic protein) forms reservoirs of soluble H3-H4 dimers, buffering fluctuations in histone demand.^[49] For delivery to replication sites, ASF1 acts as an intermediary chaperone that binds newly synthesized H3-H4 and transfers them to CAF-1 (chromatin assembly factor 1), which is recruited to replication forks via PCNA to facilitate timely deposition.^[50] Following S phase completion, histone mRNAs are rapidly degraded through oligouridylation of the 3' stem-loop, decapping, and exonucleolytic decay, ensuring synthesis ceases and excess proteins are cleared.^[48]

Nucleosome replication and assembly

During nucleosome replication in S phase, parental nucleosomes ahead of the replication fork are disassembled to allow replisome progression, with existing histones recycled onto daughter DNA strands. Parental (H3-H4)₂ tetramers are recycled symmetrically to both daughter DNA strands behind the replication fork. The N-terminal histone-binding domain of Mcm2 within the MCM2-7 helicase complex binds and chaperones these parental tetramers, countering a weak leading-strand bias to ensure even distribution.^[51] This recycling ensures efficient reuse of pre-existing histones, preventing depletion and maintaining chromatin structure during replication. The process is tightly coupled to fork movement, with Mcm2 facilitating histone handover without requiring additional chaperones in some contexts. Newly synthesized histones, supplied in coordination with DNA replication to double chromatin content, are deposited onto the nascent strands to complement recycled parental histones. The chromatin assembly factor 1 (CAF-1) complex plays a central role, binding to proliferating cell nuclear antigen (PCNA) at replication forks and depositing (H3-H4)₂ tetramers onto newly synthesized DNA. This PCNA-dependent mechanism targets histone deposition precisely to sites of DNA synthesis, ensuring balanced nucleosome formation on both leading and lagging strands. Following tetramer placement, H2A-H2B dimers are incorporated by chaperones such as NAP1 or FACT to complete octamer assembly. Nucleosome assembly proceeds in a stepwise manner: first, the (H3-H4)₂ tetramer binds to DNA, wrapping approximately 120 base pairs around it, followed by the addition of two H2A-H2B dimers to form the full octamer that encompasses about 147 base pairs of DNA. This sequential pathway maintains nucleosome integrity and spacing, with one nucleosome typically assembled per 147-200 base pairs to achieve proper chromatin compaction. The stoichiometry reflects the core particle structure, where the histone octamer stabilizes the DNA wrap through electrostatic interactions. Replication-coupled assembly specifically incorporates the canonical histone variant H3.1, distinguishing it from replication-independent variants like H3.3. H3.1 is chaperoned by CAF-1 for deposition during S phase, ensuring that newly formed nucleosomes contain this variant on nascent DNA. This variant-specific integration supports the structural fidelity of replicated chromatin, with H3.1's unique sequence features aiding in stable octamer formation.

Chromatin maintenance

Reestablishment of epigenetic marks

During the S phase of the cell cycle, DNA replication disrupts epigenetic marks on histones and DNA, necessitating their precise reestablishment to maintain gene expression patterns and cellular identity. Parental histones, carrying post-translational modifications (PTMs) such as methylation, are semi-conservatively recycled to daughter strands, resulting in a twofold dilution of these marks due to the incorporation of newly synthesized, unmodified histones.^[52] This dilution is counteracted by active restoration mechanisms, where enzymes recognize residual parental marks and apply PTMs to new histones, ensuring epigenetic fidelity across generations.^[53] Histone modification inheritance primarily occurs through the symmetric segregation of modified parental H3-H4 tetramers to both leading and lagging daughter strands, facilitated by components of the replisome like MCM2 and the POLE3/POLE4 subunits of DNA polymerase epsilon.^[52] For repressive marks like H3K9me3, which defines pericentric heterochromatin, parental histones are preferentially transferred to leading strands at certain loci, such as LINE retrotransposons, via interactions between the HUSH complex and polymerase epsilon.^[54] Active restoration involves methyltransferases like SETDB1, which, in complex with HP1α and chromatin assembly factor 1 (CAF1), monomethylates H3K9 (H3K9me1) on newly deposited histones during mid-S phase, providing a substrate for further trimethylation by SUV39H1/H2 to rebuild H3K9me3 domains.^[55] Similarly, H3K27me3 levels, associated with Polycomb-mediated silencing, drop during S phase but are restored post-replication through mechanisms including delayed accumulation on nascent DNA, which is essential for proper gene regulation, and facilitation by linker histone H1, which compacts chromatin to aid PRC2-mediated trimethylation, thereby preventing loss of silencing memory.^[56]^[57] These processes exhibit two propagation modes: rapid restoration for some PTMs within one cell cycle via continuous modification of both old and new histones, and slower, multi-generational establishment for marks like H3K9me3 and H3K27me3.^[53] DNA methylation patterns are reestablished post-replication through maintenance and de novo mechanisms. The primary maintenance methyltransferase DNMT1 preferentially methylates hemimethylated CpG sites generated during replication, ensuring propagation of parental methylation to daughter strands; this process is coordinated with S-phase progression via recruitment by UHRF1, which ubiquitylates histone H3 and the replication factor PAF15 to tether DNMT1 to replication foci.^[58] De novo methylation, primarily catalyzed by DNMT3A and DNMT3B, occurs at unmethylated CpGs and contributes to establishing new patterns, particularly at imprinted loci or during developmental reprogramming, though it overlaps with maintenance functions in replicating cells.^[59] DNMT1 also regulates the timing and targets of DNMT3 activity, linking maintenance to de novo events in an enzyme-dependent manner.^[60] Fidelity of epigenetic reestablishment relies on parental strand guidance, where recycled modified histones serve as templates for enzymes to restore patterns on new nucleosomes. An information-theoretic model describes this as a threshold-filling algorithm, where methyltransferases fill short gaps (3-6 unmodified nucleosomes) in daughter strands based on adjacent parental marks, minimizing inheritance errors to below 5% for marks like H3K27me3.^[61] Replication stress or disruptions in histone recycling, such as asymmetric segregation, compromise this guidance, leading to loss of silencing and increased genomic instability.^[52] Nucleosome assembly, occurring concurrently with replication, provides the scaffold prerequisite for these restoration events.^[62]

Higher-order chromatin domains

During S phase, replication timing is tightly correlated with chromatin domain types, with euchromatin regions typically replicating early and heterochromatin regions replicating late. This temporal program ensures that open, transcriptionally active euchromatic domains are duplicated first, while compact, repressive heterochromatic domains are replicated later, maintaining their distinct architectural identities.^[63]^[64] Following replication, higher-order chromatin loops are rapidly reformed through the reloading of CTCF and cohesin at anchor sites, which stabilize topologically associating domains (TADs). Cohesin extrudes DNA loops until encountering CTCF-bound boundaries, thereby reanchoring TAD structures; this process is essential for restoring intra-domain interactions disrupted by replication forks. Hi-C analyses reveal that TAD insulation, which weakens during S phase in a replication-timing-dependent manner (early for euchromatin-associated TADs, later for heterochromatin), but recovers in G1 phase, with insulation reaching a maximum as inter-TAD contacts are reestablished.^[65] A/B compartments, the large-scale spatial segregation of euchromatin (A) and heterochromatin (B), are also reestablished shortly after replication, guided in part by epigenetic cues. In heterochromatic B compartments, HP1 binding to H3K9me3-marked nucleosomes facilitates rapid compaction and phase separation behind the replisome, preventing dilution of repressive states during duplication.^[66]^[67] Insulator elements, primarily CTCF-bound sites, act as barriers to prevent the spreading of chromatin domains across TAD boundaries, ensuring faithful inheritance of architectural features. Recent studies indicate that promoter-proximal pausing of RNA polymerase II contributes to this barrier function by stabilizing local chromatin states and limiting ectopic interactions post-replication, thereby reinforcing domain insulation.^[68]^[69]

Checkpoints and responses

Intra-S phase checkpoint

The intra-S phase checkpoint serves as a critical surveillance mechanism that detects replication stress during S phase and modulates DNA replication to maintain genomic stability. Upon encountering replication obstacles, such as stalled replication forks, single-stranded DNA (ssDNA) regions become coated with replication protein A (RPA). This RPA-ssDNA complex recruits the ATR-ATRIP kinase complex, which senses the stress signal and initiates checkpoint activation.^[70] Subsequently, ATR recruits TopBP1, an activator that enhances ATR kinase activity, and the Rad17-RFC complex, which loads the 9-1-1 checkpoint clamp onto the DNA to further amplify the signal.^[71] This activation cascade ensures rapid response to fork stalling without immediately halting all cellular processes.^[72] Downstream of ATR activation, the checkpoint exerts multiple effects to mitigate replication stress. ATR phosphorylates the effector kinase Chk1, which in turn inhibits the firing of new replication origins by preventing the loading of additional replication factors, thereby conserving resources for ongoing forks. Additionally, Chk1 promotes the stabilization of stalled forks by counteracting nucleolytic degradation and excessive remodeling, reducing the risk of fork collapse into double-strand breaks.^[73] These actions collectively slow replication progression while allowing limited fork advancement under moderate stress.^[74] In physiological contexts, the intra-S phase checkpoint plays a vital role in preventing under-replication of the genome during conditions like hypoxia or nucleotide depletion, which impair fork progression and dNTP availability.^[75] The core signaling pathway involves ATR-mediated phosphorylation of Chk1, leading to the ubiquitination and degradation of Cdc25A phosphatase, which inhibits CDK2 activity and further restricts origin firing and cell cycle advancement.^[76] This mechanism ensures that replication completes faithfully even under resource-limited environments, coordinating with G2/M checkpoint activation to delay mitosis until S phase is resolved.^[77] Unlike the G1/S checkpoint, which primarily prevents entry into S phase in response to damage, the intra-S phase checkpoint permits partial replication progression while selectively suppressing late-origin firing and stabilizing existing forks, thereby integrating with broader cell cycle arrest in G2.^[74] This distinction allows cells to adapt dynamically to ongoing stress without fully aborting the replication program.^[78]

DNA damage detection and repair

During S phase, DNA replication forks encounter various lesions that threaten genomic integrity, including UV-induced pyrimidine dimers and double-strand breaks (DSBs) arising from replication fork collapse. UV-induced pyrimidine dimers, such as cyclobutane pyrimidine dimers, distort the DNA helix and block replicative polymerases, while fork collapse often generates one-ended DSBs due to encounters with unresolved structures or exogenous agents. These lesions are detected by specialized sensors: the Mre11-Rad50-Nbs1 (MRN) complex rapidly binds DSB ends at collapsed forks, initiating processing and signaling through its nuclease and ATPase activities, whereas poly(ADP-ribose) polymerases (PARPs), particularly PARP1, detect single-strand breaks and other lesions by binding directly to DNA ends and catalyzing PARylation to recruit repair factors. Repair of these lesions during S phase primarily involves nucleotide excision repair (NER) for bulky adducts like pyrimidine dimers and homologous recombination (HR) for DSBs. NER, which operates efficiently in S phase under ATR kinase regulation, excises oligonucleotides containing the lesion via dual incisions on either side, allowing gap filling by replicative polymerases; global genome NER predominates during replication to handle replication-blocking damage. HR predominates for DSB repair in S and G2 phases, utilizing the newly synthesized sister chromatid as a template to restore sequence fidelity through strand invasion and DNA synthesis, mediated by proteins like RAD51; this pathway is preferred over non-homologous end joining due to the availability of the homologous template. Checkpoint activation may transiently slow fork progression to facilitate these repairs. To coordinate repair with ongoing replication, cells employ translesion synthesis (TLS) polymerases, such as the Y-family Pol η and the B-family Pol ζ, which temporarily bypass lesions by incorporating nucleotides opposite damaged bases, allowing fork progression while leaving gaps for later resolution; TLS is tightly regulated by ubiquitination of PCNA to switch polymerases. Post-replicative mismatch repair (MMR) then addresses replication errors or small loops in the nascent strand, recognizing mismatches via MSH2-MSH6 and excising the error-prone segment using nicks in the daughter strand as entry points. Failure to repair these lesions can lead to persistent DSBs or gaps, triggering apoptosis through p53-dependent pathways or cellular senescence via sustained DNA damage response signaling. Recent studies using CRISPR-Cas9 to induce targeted damage have demonstrated enhanced HR efficiency specifically in S phase, with synchronization strategies boosting homology-directed repair rates up to twofold by optimizing sister chromatid availability.^[79]

References

[1]
An Overview of the Cell Cycle - Molecular Biology of the Cell - NCBI
DNA duplication occurs during S phase (S for synthesis), which requires 10–12 hours and occupies about half of the cell-cycle time in a typical mammalian cell.
[2]
The Eukaryotic Cell Cycle - NCBI - NIH
S phase is the period during which DNA replication occurs. The cell grows (more...) The duration of these cell cycle phases varies considerably in different ...
[3]
6.1 The Cell Cycle – Human Biology
During interphase, G1 involves cell growth and protein synthesis, the S phase involves DNA replication and the replication of the centrosome, and G2 involves ...
[4]
The cell cycle: a review of regulation, deregulation and therapeutic ...
S phase is preceded by a gap called G1 during which the cell is preparing for DNA synthesis and is followed by a gap called G2 during which the cell prepares ...
[5]
Preparation for DNA Replication: The Key to a Successful S phase
Both G1 and S phase progression are controlled by master cell cycle protein kinases and ubiquitin ligases that govern the activity and abundance of DNA ...
[6]
The Initiation and Completion of DNA Replication in Chromosomes
To replicate such a DNA molecule from end to end with a single replication fork moving at a rate of 50 nucleotides per second would require 0.02 × 150 × 106 = ...
[7]
The Human Genome - The Cell - NCBI Bookshelf - NIH
The ultimate goal of genome analysis is to determine the complete nucleotide sequence of the human genome: 3 × 109 base pairs of DNA.
[8]
Replication Fork Velocities at Adjacent Replication Origins Are ... - NIH
Our results show that replication forks moving from one origin, as well as from neighboring origins, tend to exhibit the same velocity.
[9]
S Phase Duration Is Determined by Local Rate and Global ... - NIH
May 7, 2022 · The fastest somatic mammalian cells which we have seen reported are activated CD8+ T cells who have S phases of under 5 h ex vivo [47] and in ...
[10]
DNA replication origins—where do we begin? - Genes & Development
Developmental and cell type-specific constraints on the DNA replication program dictate the number and distribution of origins throughout the genome. Extremes ...
[11]
A Precise Cdk Activity Threshold Determines Passage through the ...
Jan 18, 2018 · At the restriction point (R), mammalian cells irreversibly commit to divide. R has been viewed as a point in G1 that is passed when growth ...
[12]
Mitotic checkpoint genes in budding yeast and the dependence of ...
We conclude that the checkpoint in budding yeast consists of overlapping S-phase and G2-phase pathways that respond to incomplete DNA replication and/or DNA ...
[13]
A quantitative model for cyclin-dependent kinase control of the cell ...
Dec 27, 2011 · The oscillating activity of cyclin-dependent kinases (Cdks) acts as the master regulator for cell cycle progression.
[14]
Monitoring S phase progression globally and locally using BrdU ...
BrdU incorporation accurately measures S phase progression. Standard techniques to monitor cell cycle progression include flow cytometry ... thymidine. By ...
[15]
Regulation of the G1 phase of the mammalian cell cycle - Nature
Mar 1, 2000 · Cells that pass this restriction point are committed to complete the cycle. ... These mechanisms include: 1) activation by binding the ...
[16]
Integrating Old and New Paradigms of G1/S Control
Oct 15, 2020 · One possible outcome is that the location of the restriction point is developmentally regulated to take place in the prior cell cycle or in G1 ...
[17]
The structure of ORC–Cdc6 on an origin DNA reveals the ... - Nature
Jun 23, 2021 · In S. cerevisiae, origin licensing occurs by the assembly during G1 phase of a pre-replicative complex (pre-RC) at each potential origin. Pre-RC ...
[18]
ATPase-dependent quality control of DNA replication origin licensing
This is accomplished by first licensing origins during G1 phase with a pre-replicative complex containing an inactive double hexamer of the Mcm2–7 helicase, and ...
[19]
Structure of the Rb C-Terminal Domain Bound to E2F1-DP1
The retinoblastoma (Rb) protein negatively regulates the G1-S transition by binding to the E2F transcription factors, until cyclin-dependent kinases ...
[20]
Differentially Active Origins of DNA Replication in Tumor versus ...
May 16, 2006 · Each replicon contains one centrally placed functional origin (ori), where replication is initiated, with an estimated number of 104 to 106 ...
[21]
Core control principles of the eukaryotic cell cycle - Nature
Jun 8, 2022 · The core eukaryotic cell cycle control system is based on S phase and mitosis being controlled by cyclin-dependent kinases (CDKs) complexed with S phase ...
[22]
Cyclin‐dependent kinases: Masters of the eukaryotic universe - PMC
Cyclin‐dependent kinases (CDKs) are a conserved eukaryotic family of heterodimeric serine/threonine protein kinases, whose catalytic activity is entirely ...
[23]
Cyclin-dependent protein kinases and cell cycle regulation ... - Nature
Jan 13, 2025 · Cyclin E- CDK2 complex regulates beginning of DNA replication during S phase by phosphorylating CDC6, a key component of DNA pre-replication ...
[24]
Phosphorylation of mammalian CDC6 by Cyclin A/CDK2 regulates ...
... A/CDK2 is a negative regulatory event that could be implicated in preventing re‐replication during S phase and G2. Introduction. Progression through the ...
[25]
S-phase-promoting cyclin-dependent kinases prevent re-replication ...
We propose that S-phase-promoting cyclin B–Cdk complexes prevent re-replication during S, G2 and M phases by inhibiting the transition of replication origins ...
[26]
Cyclin E/CDK2: DNA Replication, Replication Stress and Genomic ...
Importantly, Cyclin E/CDK2 activity is negatively regulated by the KIP/CIP family of CDK inhibitors, p27KIP1 and p21CIP1, which prevent CDK2 activation by CAK ...
[27]
The NUCKS1-SKP2-p21/p27 axis controls S phase entry - Nature
Nov 29, 2021 · We propose that the NUCKS1-SKP2-p21/p27 axis integrates mitogenic and DNA damage signalling to control S phase entry.
[28]
Quaternary structure of the human Cdt1-Geminin complex regulates ...
Geminin tightly binds and sequesters Cdt1 in a complex that is unable to recruit MCM to origins. ... Geminin is reactivated before entry into S phase. Importantly ...
[29]
CLB5: a novel B cyclin from budding yeast with a role in S phase.
CLB5 is the only yeast cyclin whose deletion lengthens S phase. CLB5 may also have some role in promoting the G1/S transition, because cln1 cln2 strains require ...Missing: equivalents | Show results with:equivalents
[30]
Hierarchy of S-Phase-Promoting Factors: Yeast Dbf4-Cdc7 Kinase ...
Cells lacking CLB5, which rely on Clb6-Cdk1 for DNA replication, fail to activate late origins (17), suggesting that S-CDKs also act at the level of origins to ...
[31]
Origins of DNA Replication in Eukaryotes - PMC - NIH
This review focuses on the current understanding how the Origin Recognition Complex (ORC) contributes to determining the location of replication initiation.
[32]
From structure to mechanism—understanding initiation of DNA ...
Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative ...Missing: seminal | Show results with:seminal
[33]
Helicase Activation and Establishment of Replication Forks at ...
Two protein kinases, cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), work to complete the formation of the pre-IC. Each kinase is responsible for ...
[34]
The mechanism of eukaryotic CMG helicase activation - PMC
Nov 11, 2019 · We sought to understand how CMG is assembled and activated during the initiation of DNA replication, using purified budding yeast proteins. We ...
[35]
Mechanism of replication origin melting nucleated by CMG helicase ...
Jun 15, 2022 · Our results explain how ATP binding nucleates origin DNA melting by the CMG and maintains replisome stability at initiation.
[36]
Molecular choreography of primer synthesis by the eukaryotic Pol α ...
Jun 21, 2023 · The eukaryotic polymerase α (Pol α) synthesizes an RNA-DNA hybrid primer of 20–30 nucleotides. Pol α is composed of Pol1, Pol12, Primase 1 ...
[37]
Mechanism for priming DNA synthesis by yeast DNA Polymerase α
Apr 2, 2013 · The DNA Polymerase α (Pol α)/primase complex initiates DNA synthesis in eukaryotic replication. In the complex, Pol α and primase cooperate ...
[38]
Reconstitution of a eukaryotic replisome reveals suppression ... - eLife
Apr 14, 2015 · Hence, Pol ε is active with CMG on the leading strand, but it is unable to function on the lagging strand, even when Pol δ is not present.Pol α Primes And Extends... · Pol α Functions On Both... · Pol δ Functions On The 'pol...<|separator|>
[39]
Single molecule measurement of the “speed limit” of DNA polymerase
These data enabled the measurement of the intrinsic “speed limit” of DNA polymerase by separating the burst synthesis rate from pausing events.
[40]
Mechanisms of DNA replication termination - PMC - PubMed Central
Feb 22, 2019 · From bacteria to eukaryotic cells, replication initiation is regulated such that genome duplication is limited to a single round per cell cycle.
[41]
DNA polymerase ζ in DNA replication and repair - Oxford Academic
Aug 14, 2019 · If lesion bypass occurs in a gap left after replication, can pol ζ fill the gap on its own? Extensive DNA synthesis beyond a lesion by pol ζ.Dna Polymerase ζ In Dna... · Introduction · Pol ζ As A Major Extender...
[42]
Article The TRESLIN-MTBP complex couples completion of DNA ...
Sep 15, 2022 · We show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ATR/CHK1 kinases.Missing: deactivation decondensation
[43]
Chromatin decondensation in S-phase involves recruitment of Cdk2 ...
Cdk2 activity could be required during S-phase for initiation at late-firing origins, for replication fork progression, or for both. Although it has been ...Missing: deactivation | Show results with:deactivation
[44]
The fidelity of DNA synthesis by eukaryotic replicative and ... - NIH
This chapter reviews the fidelity with which undamaged and damaged DNA is copied, with a focus on the eukaryotic B and Y family DNA polymerases.
[45]
Replication-dependent histone biosynthesis is coupled to cell-cycle ...
Jul 29, 2021 · The nucleosome consists of four core histones, histone proteins H2A, H2B, H3, and H4, that come together as a 2:2:2:2 octamer, as well as one ...
[46]
A standardized nomenclature for mammalian histone genes
Oct 1, 2022 · There are multiple histone H3, H2A and H1 protein variants which replace the canonical histones at specific sites in the genome. Some of these ...
[47]
The histone gene activator HINFP is a nonredundant cyclin E/CDK2 ...
The human histone gene transcription factor HINFP is the final and essential link in the cyclin E/CDK2/p220NPAT/HINFP pathway that is required for cell cycle- ...
[48]
Degradation of histone mRNA requires oligouridylation followed by ...
Histone mRNAs are rapidly degraded at the end of S phase or when DNA replication is inhibited. Histone mRNAs end in a conserved stem–loop rather than a poly(A) ...
[49]
The histone chaperone NASP maintains H3-H4 reservoirs in the ...
Mar 17, 2023 · Histones are essential for chromatin packaging, and histone supply must be tightly regulated as excess histones are toxic.
[50]
Article Human Asf1 Regulates the Flow of S Phase Histones during ...
Asf1 (antisilencing function 1) is a histone chaperone that synergizes with CAF ... histones alone cannot be transferred to CAF-1 present in the nuclear extract.
[51]
Symmetric inheritance of parental histones governs epigenome ...
Sep 4, 2023 · Modified parental histones are segregated symmetrically to daughter DNA strands during replication and can be inherited through mitosis.
[52]
Two distinct modes for propagation of histone PTMs across the cell ...
We show that post-translational modifications (PTMs) are transmitted with parental histones to newly replicated DNA.
[53]
Asymmetric distribution of parental H3K9me3 in S phase silences L1 ...
Here, we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at Long Interspersed ...
[54]
The HP1α–CAF1–SetDB1‐containing complex provides H3K9me1 ...
Histone proteins are heavily modified post‐translationally, and patterns of these modifications mark specific functional nuclear domains. For example, ...
[55]
DNA replication–coupled histone modification maintains Polycomb ...
Aug 17, 2017 · In contrast, levels of H3K27me3 dropped during S phase, likely reflecting the incorporation of newly synthesized, unmodified histones.<|control11|><|separator|>
[56]
Two distinct modes of DNMT1 recruitment ensure stable ... - Nature
Mar 6, 2020 · In conclusion, we propose that maintenance of DNA methylation is coordinated with S-phase progression via UHRF1-dependent dual mono- ...Ubiquitylated Paf15... · Uhrf1 Recognizes The... · Paf15 Is Important For...
[57]
DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De ...
Here we demonstrate that two recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, are essential for de novo methylation and for mouse development.Missing: phase | Show results with:phase
[58]
DNMT1 regulates the timing of DNA methylation by DNMT3 in an ...
Jan 5, 2022 · DNMT1 actively regulates the timing and genomic targets of de novo methylation by DNMT3 in an enzymatic activity-dependent and independent manner, respectively.
[59]
Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes
### Summary of Bookmarking by FoxA1 Pioneer Factor During Mitosis and Its Relation to Epigenetic Retention
[60]
High fidelity epigenetic inheritance: Information theoretic model ...
The faithful inheritance of the histone marks from the parental to the daughter strands is a puzzle, given that each strand gets only half of the parental ...
[61]
How is epigenetic information maintained through DNA replication?
Oct 2, 2013 · As such, some histone modifications appear to be epigenetically inherited via a pre-replicative boost, which is subsequently diluted during DNA ...
[62]
Emergence of replication timing during early mammalian development
Dec 20, 2023 · During S phase the genome must replicate once and only once. Replication occurs through a coordinated programme whereby origins of replication ...
[63]
Early-replicating heterochromatin - Genes & Development
Euchromatin, which has an open structure and is frequently transcribed, tends to replicate in early S phase. Heterochromatin, which is more condensed and rarely ...
[64]
Roles for the 3D genome in the cell cycle, DNA replication, and ...
Hi-C methods now produce 3D genome maps of sufficient resolution to define nested subTADs within larger TADs. SubTADs are structurally akin to TADs but exhibit ...
[65]
Proteomic profiling reveals distinct phases to the restoration of ...
Jan 31, 2023 · Most chromatin proteins reassociate within minutes. Chromatin restoration is completed after mitosis, in the daughter cells. Heterochromatin is more propitious ...
[66]
HP1-driven phase separation recapitulates the thermodynamics and ...
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin ...<|control11|><|separator|>
[67]
RNA polymerase II promotes the organization of chromatin following DNA replication | EMBO reports
### Summary: Role of RNA Pol II Pausing in Preventing Domain Spreading or Insulator Function in Higher-Order Chromatin Domains Post-Replication
[68]
Insulator-based loops mediate the spreading of H3K27me3 over ...
Aug 3, 2020 · Our data highlight a new regulatory mode of H3K27me3 by insulator-based long-range interactions controlling distant euchromatic genes.
[69]
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02106-z
[70]
https://doi.org/10.1126/science.1083430
[71]
The essential kinase ATR: ensuring faithful duplication of a ... - NIH
One crucial function of the ATR pathway is to arrest the cell cycle following DNA damage in S phase. This arrest is initiated by the phosphorylation of CHK1 by ...
[72]
https://pmc.ncbi.nlm.nih.gov/articles/PMC5796526/
[73]
The Intra-S Checkpoint Responses to DNA Damage - PMC
Cells activate the intra-S checkpoint in response to damage during S phase to protect genomic integrity and ensure replication fidelity.
[74]
https://pmc.ncbi.nlm.nih.gov/articles/PMC5333063/
[75]
https://doi.org/10.1038/nrm.2017.67
[76]
the checkpoint kinases ATR, CHK1 and WEE1 restrain CDK activity ...
Sep 21, 2011 · Activation of mammalian Chk1 during DNA replication arrest: a role for Chk1 in the intra-S phase checkpoint monitoring replication origin firing.
[77]
https://academic.oup.com/nar/article/40/2/477/2409009