S PhaseEdit
DNA replication during the S phase is a central and highly regulated part of the cell cycle, during which a complete copy of the genome is synthesized in preparation for cell division. In eukaryotic cells, the process is remarkable for its efficiency and fidelity, as thousands of replication origins fire in a controlled sequence to duplicate the genome once and only once per cycle. The S phase follows a growth-oriented G1 phase and precedes the structural changes of G2, setting the stage for mitosis. The integrity of DNA replication is essential for proper development and tissue maintenance, and disruptions in S-phase regulation are linked to genome instability and disease.
S phase overview and core machinery - Origins of replication and licensing: Before DNA synthesis begins, replication origins are licensed in a growth-permissive state during G1. This licensing involves the Origin Recognition Complex (Origin recognition complex), along with other factors such as Cdc6 and Cdt1, which load the helicase complex onto DNA. The loaded helicase is the MCM2-7 complex, which forms part of the active CMG helicase when replication starts. - Activation and progression: Entry into S phase activates the licensed origins through concerted kinase signaling, including the DDK (Cdc7-Dbf4) and CDK families. This activation leads to helicase activation and the unwinding of DNA. The core unwinding and progression of replication forks involve the CMG helicase complex in association with other factors such as Cdc45 and GINS. - Replisome and replication forks: At each active origin, the replisome coordinates leading- and lagging-strand synthesis. The leading strand is synthesized continuously by DNA polymerase epsilon (in cooperation with the sliding clamp PCNA), while the lagging strand is synthesized discontinuously as Okazaki fragments by DNA polymerase delta with help from primase DNA primase and ligation factors. Initiation of synthesis on the lagging strand requires RNA primer synthesis by the primase component, followed by extension by the DNA polymerases. - Copy number and fidelity: DNA polymerases operate with high fidelity, aided by proofreading domains and mismatch repair systems. DNA damage and replication stress are monitored by networked surveillance pathways that help prevent the propagation of errors to daughter cells.
Regulation of S-phase entry, duration, and checkpoints - Core regulators: The transition from G1 to S phase is governed by cyclin-dependent kinases (CDKs) in association with cyclins, particularly those that drive S-phase entry and progression. Proper timing ensures that replication occurs only after the genome is adequately prepared for duplication. - Checkpoints and genome surveillance: The cell employs checkpoints to monitor replication integrity. If DNA damage or replication stress is detected, signaling pathways involving ATM and ATR kinases, and downstream effectors such as CHK1 and CHK2, pause or slow S-phase progression to allow repair. Tumor suppressor proteins, including p53, influence the decision between arrest, repair, or apoptosis in cases of severe damage. - Nucleotide pools and replication stress: S-phase progression depends on the availability of nucleotides and proper chromatin structure. Cells can slow replication in response to insufficient nucleotide pools or structural obstacles, a mechanism that helps prevent fork stalling and genome instability.
Replication timing and chromatin context - Temporal organization: Replication does not occur uniformly across the genome; origins fire in a programmed sequence, creating early- and late-replicating domains. These timing programs are influenced by chromatin state and transcriptional activity, helping to coordinate replication with other nuclear processes. - Chromatin and origin activity: Euchromatin, which is generally more transcriptionally active, tends to host early replication origins, whereas heterochromatin and late-replicating regions often harbor origins that fire later in S phase. Histone modifications and higher-order chromatin organization help shape the accessibility of origins and the efficiency of fork progression.
Variation across organisms and developmental contexts - Model organisms: Although the core principles of S-phase replication are conserved, the details vary among organisms. In yeasts and other simpler eukaryotes, replication can be more rigidly linked to cell cycle cues, while in higher eukaryotes there is greater flexibility in origin usage and timing. - Early development and rapid cycles: In certain developmental contexts, such as early embryogenesis in some species, S phases can be extremely short and characterized by rapid, successive rounds of replication with limited gap phases. This rapid replication supports rapid cell proliferation during development. - Special cases and polyploidy: Some tissues exhibit endoreduplication or other changes in ploidy that alter S-phase dynamics, reflecting both developmental programs and tissue-specific needs.
Clinical and research relevance - Cancer and replication-targeted therapies: Abnormal S-phase regulation and replication stress are hallmarks of many cancers. Therapeutic strategies often exploit this vulnerability by using agents that disrupt DNA synthesis or the nucleotide supply, such as nucleoside analogs or inhibitors of ribonucleotide reductase. Understanding S-phase dynamics informs the development and optimization of these treatments. - Research tools: Techniques such as flow cytometry, DNA combing, and high-throughput sequencing approaches are used to study S-phase dynamics, replication origin usage, and replication timing. These studies illuminate how cells balance rapid genome duplication with the need to maintain sequence fidelity. - Genome stability and aging: Persistent replication stress and impaired DNA damage responses during S phase contribute to genome instability, a factor in aging and various diseases. Research in this area seeks to understand how replication machinery and checkpoint networks maintain genomic integrity over time.
See-through: historical and conceptual notes - The concept of a defined DNA synthesis phase emerged from work on the cell cycle that linked replication activity to discrete phases of growth and division. The molecular dissection of S-phase machinery has mapped a network of multiprotein complexes and signaling pathways that coordinate licensing, firing, elongation, and checkpoint responses.