The replication-stress response enables the DNA replication machinery to overcome DNA lesions or intrinsic replication-fork obstacles, and it is essential to ensure faithful transmission of genetic information to daughter cells. Multiple replication stress–response pathways have been identified in recent years, thus raising questions about the specific and possibly redundant functions of these pathways. Here, we review the emerging mechanisms of the replication-stress response in mammalian cells and consider how they may influence the dynamics of the core DNA replication complex.
At a glance
- Causes and consequences of replication stress. Nat. Cell Biol. 16, 2–9 (2014). &
- Dormant origins licensed by excess Mcm2-7 are required for human cells to survive replicative stress. Genes Dev. 21, 3331–3341 (2007). , &
- Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 412, 553–557 (2001). &
- Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases. Mol. Cell 45, 696–704 (2012). et al.
- Replisome structure and conformational dynamics underlie fork progression past obstacles. Curr. Opin. Cell Biol. 21, 336–343 (2009). &
- Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. Mol. Cell 37, 247–258 (2010). , , &
- Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint. Genes Dev. 19, 1040–1052 (2005). , , , &
- Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol. Cell 21, 15–27 (2006). , &
- Uncoupling of leading- and lagging-strand DNA replication during lesion bypass in vivo. Science 300, 1300–1303 (2003). &
- Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells. J. Cell Biol. 208, 563–579 (2015).
This paper shows that replication-fork reversal is a general response to a wide range of genotoxic treatments in human cells and that Rad51 is required for this process.
- FANCM regulates DNA chain elongation and is stabilized by S-phase checkpoint signalling. EMBO J. 29, 795–805 (2010). , , &
- WRN helicase regulates the ATR-CHK1-induced S-phase checkpoint pathway in response to topoisomerase-I-DNA covalent complexes. J. Cell Sci. 124, 3967–3979 (2011). , , &
- ATR signalling: more than meeting at the fork. Biochem. J. 436, 527–536 (2011). &
- Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science 300, 1542–1548 (2003). &
- Surviving chromosome replication: the many roles of the S-phase checkpoint pathway. Phil. Trans. R. Soc. Lond. B 366, 3554–3561 (2011). &
- ATR phosphorylates SMARCAL1 to prevent replication fork collapse. Genes Dev. 27, 1610–1623 (2013). et al.
- FANCD2 binds MCM proteins and controls replisome function upon activation of s phase checkpoint signaling. Mol. Cell 51, 678–690 (2013). et al.
- Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories. J. Cell Biol. 191, 1285–1297 (2010). &
- The effect of the intra-S-phase checkpoint on origins of replication in human cells. Genes Dev. 25, 621–633 (2011). &
- ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 155, 1088–1103 (2013). et al.
- ATR-mediated phosphorylation of FANCI regulates dormant origin firing in response to replication stress. Mol. Cell 58, 323–338 (2015). et al.
- Rescuing stalled or damaged replication forks. Cold Spring Harb. Perspect. Biol. 5, a012815 (2013). , , &
- Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat. Rev. Mol. Cell Biol. 13, 141–152 (2012). , &
- Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439, 557–562 (2006). &
- The Escherichia coli replisome is inherently DNA damage tolerant. Science 334, 235–238 (2011). &
- UV stalled replication forks restart by re-priming in human fibroblasts. Nucleic Acids Res. 39, 7049–7057 (2011). , , , &
- Repriming of DNA synthesis at stalled replication forks by human PrimPol. Nat. Struct. Mol. Biol. 20, 1383–1389 (2013). et al.
- PrimPol bypasses UV photoproducts during eukaryotic chromosomal DNA replication. Mol. Cell 52, 566–573 (2013). et al.
- PrimPol, an archaic primase/polymerase operating in human cells. Mol. Cell 52, 541–553 (2013).
Refs. 27–29 show that PrimPol uses its primase activity to bypass UV photoproducts.
- DNA damage tolerance: a double-edged sword guarding the genome. Transl. Cancer Res. 2, 107–129 (2013). &
- The RAD6 DNA damage tolerance pathway operates uncoupled from the replication fork and is functional beyond S phase. Cell 141, 255–267 (2010). &
- Ubiquitin-dependent DNA damage bypass is separable from genome replication. Nature 465, 951–955 (2010). , &
- Regulation of PCNA-protein interactions for genome stability. Nat. Rev. Mol. Cell Biol. 14, 269–282 (2013). , &
- BLM is required for faithful chromosome segregation and its localization defines a class of ultrafine anaphase bridges. EMBO J. 26, 3397–3409 (2007). , &
- Replication stress induces 53BP1-containing OPT domains in G1 cells. J. Cell Biol. 193, 97–108 (2011). et al.
- Replication fork reversal and the maintenance of genome stability. Nucleic Acids Res. 37, 3475–3492 (2009). &
- Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nat. Struct. Mol. Biol. 20, 347–354 (2013).
This paper defines the mechanism by which RECQ1 and PAPR1 regulate fork reversal and restart.
- Replication fork reversal in eukaryotes: from dead end to dynamic response. Nat. Rev. Mol. Cell Biol. 16, 207–220 (2015). &
- Topoisomerase I poisoning results in PARP-mediated replication fork reversal. Nat. Struct. Mol. Biol. 19, 417–423 (2012). et al.
- A model for replication repair in mammalian cells. J. Mol. Biol. 101, 417–425 (1976). , &
- Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297, 599–602 (2002). , &
- Cooperation of RAD51 and RAD54 in regression of a model replication fork. Nucleic Acids Res. 39, 2153–2164 (2011). , &
- SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication. Genes Dev. 26, 151–162 (2012). et al.
- Remodeling of DNA replication structures by the branch point translocase FANCM. Proc. Natl. Acad. Sci. USA 105, 16107–16112 (2008). , , , &
- The HARP-like domain-containing protein AH2/ZRANB3 binds to PCNA and participates in cellular response to replication stress. Mol. Cell 47, 410–421 (2012). , &
- Polyubiquitinated PCNA recruits the ZRANB3 translocase to maintain genomic integrity after replication stress. Mol. Cell 47, 396–409 (2012). et al.
- Yeast Rad5 protein required for postreplication repair has a DNA helicase activity specific for replication fork regression. Mol. Cell 28, 167–175 (2007). et al.
- Role of double-stranded DNA translocase activity of human HLTF in replication of damaged DNA. Mol. Cell. Biol. 30, 684–693 (2010). , , &
- HLTF's Ancient HIRAN domain binds 3′ DNA ends to drive replication fork reversal. Mol. Cell 58, 1090–1100 (2015). et al.
- FBH1 catalyzes regression of stalled replication forks. Cell Reports 10, 1749–1757 (2015). et al.
- The Werner and Bloom syndrome proteins catalyze regression of a model replication fork. Biochemistry 45, 13939–13946 (2006). , , &
- Hydroxyurea-stalled replication forks become progressively inactivated and require two different RAD51-mediated pathways for restart and repair. Mol. Cell 37, 492–502 (2010). , , , &
- Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell 145, 529–542 (2011). et al.
- A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2. Cancer Cell 22, 106–116 (2012).
Refs. 53 and 54 provide the first demonstration of a DSB-independent role of HDR and FA factors in protecting stalled replication forks from MRE11-dependent degradation, thus extending knowledge of the causes of the high genomic instability associated with mutations in these HDR and FA genes.
- DNA2 drives processing and restart of reversed replication forks in human cells. J. Cell Biol. 208, 545–562 (2015). et al.
- The intra-S phase checkpoint targets Dna2 to prevent stalled replication forks from reversing. Cell 149, 1221–1232 (2012). et al.
- Substrate-selective repair and restart of replication forks by DNA translocases. Cell Reports 3, 1958–1969 (2013). et al.
- The dissolution of double Holliday junctions. Cold Spring Harb. Perspect. Biol. 6, a016477 (2014). &
- Error-free DNA damage tolerance and sister chromatid proximity during DNA replication rely on the Polα/Primase/Ctf4 complex. Mol. Cell 57, 812–823 (2015). , , , &
- Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. Proc. Natl. Acad. Sci. USA 105, 12411–12416 (2008). et al.
- Human SHPRH is a ubiquitin ligase for Mms2-Ubc13-dependent polyubiquitylation of proliferating cell nuclear antigen. Proc. Natl. Acad. Sci. USA 103, 18107–18112 (2006). et al.
- SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis. Mol. Cell 42, 237–249 (2011). , , , &
- A novel role for non-ubiquitinated FANCD2 in response to hydroxyurea-induced DNA damage. Oncogene doi:10.1038/onc.2015.68 (20 April 2015). , , &
- RecA acts as a switch to regulate polymerase occupancy in a moving replication fork. Proc. Natl. Acad. Sci. USA 110, 5410–5415 (2013). , , &
- Mre11-dependent degradation of stalled DNA replication forks is prevented by BRCA2 and PARP1. Cancer Res. 72, 2814–2821 (2012). , &
- FANCD2-controlled chromatin access of the Fanconi-associated nuclease FAN1 is crucial for the recovery of stalled replication forks. Mol. Cell. Biol. 34, 3939–3954 (2014). , &
- Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat. Struct. Mol. Biol. 17, 1305–1311 (2010). , , &
- Nonenzymatic role for WRN in preserving nascent DNA strands after replication stress. Cell Reports 9, 1387–1401 (2014). et al.
- Mre11 protein complex prevents double-strand break accumulation during chromosomal DNA replication. Mol. Cell 8, 137–147 (2001). et al.
- Brca2, Rad51 and Mre11: performing balancing acts on replication forks. DNA Repair (Amst.) 10, 1060–1065 (2011).
- Exo1 processes stalled replication forks and counteracts fork reversal in checkpoint-defective cells. Mol. Cell 17, 153–159 (2005). et al.
- CtIP mediates replication fork recovery in a FANCD2-regulated manner. Hum. Mol. Genet. 23, 3695–3705 (2014). , , &
- Break-induced replication: functions and molecular mechanism. Curr. Opin. Genet. Dev. 23, 271–279 (2013). &
- Break-induced replication occurs by conservative DNA synthesis. Proc. Natl. Acad. Sci. USA 110, 13475–13480 (2013). &
- Migrating bubble during break-induced replication drives conservative DNA synthesis. Nature 502, 389–392 (2013).
Refs. 74 and 75 provide new insight into the mechanism by which break-induced replication drives conservative DNA synthesis.
- Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration. Nature 502, 393–396 (2013). et al.
- Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science 343, 88–91 (2014). et al.
- Template switching during break-induced replication. Nature 447, 102–105 (2007). , &
- Chromosome rearrangements via template switching between diverged repeated sequences. Genes Dev. 28, 2394–2406 (2014). et al.
- Break-induced replication is highly inaccurate. PLoS Biol. 9, e1000594 (2011). et al.
- The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks. Nat. Struct. Mol. Biol. 14, 1096–1104 (2007). et al.
- Oncogenes induce genotoxic stress by mitotic processing of unusual replication intermediates. J. Cell Biol. 200, 699–708 (2013). , , &
- Holliday junction resolution: regulation in space and time. DNA Repair (Amst.) 19, 176–181 (2014). &
- MUS81 promotes common fragile site expression. Nat. Cell Biol. 15, 1001–1007 (2013). et al.
- The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage. Nat. Commun. 6, 6746 (2015). et al.
- Substrate specificity of the MUS81-EME2 structure selective endonuclease. Nucleic Acids Res. 42, 3833–3845 (2014). &
- Switch on the engine: how the eukaryotic replicative helicase MCM2-7 becomes activated. Chromosoma 124, 13–26 (2015). , &
- DNA replication: making two forks from one prereplication complex. Mol. Cell 40, 860–861 (2010). &
- Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. Cell 139, 719–730 (2009). et al.
- Regulated eukaryotic DNA replication origin firing with purified proteins. Nature 519, 431–435 (2015). , , , &
- The structural basis for MCM2–7 helicase activation by GINS and Cdc45. Nat. Struct. Mol. Biol. 18, 471–477 (2011).
This study reports important structural information on the architecture of the CMG complex and provides a groundwork for future studies on the conformational changes of CMG during both normal and perturbed replication.
- Cdc45 (cell division cycle protein 45) guards the gate of the eukaryote replisome helicase stabilizing leading strand engagement. Proc. Natl. Acad. Sci. USA 112, E249–E258 (2015). et al.
- Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase. Cell 146, 931–941 (2011). et al.
- Cdc45 protein-single-stranded DNA interaction is important for stalling the helicase during replication stress. J. Biol. Chem. 288, 7550–7563 (2013). &
- RAD51- and MRE11-dependent reassembly of uncoupled CMG helicase complex at collapsed replication forks. Nat. Struct. Mol. Biol. 19, 17–24 (2012). , &
- The DNA translocase FANCM/MHF promotes replication traverse of DNA interstrand crosslinks. Mol. Cell 52, 434–446 (2013).
This paper shows that the moving replisome traverses ICLs in a FANCM-dependent manner.
- DNA polymerase stabilization at stalled replication forks requires Mec1 and the RecQ helicase Sgs1. EMBO J. 22, 4325–4336 (2003). , , , &
- Checkpoint-mediated control of replisome-fork association and signalling in response to replication pausing. Oncogene 23, 1206–1213 (2004). et al.
- Checkpoint kinase 2 (Chk2) inhibits the activity of the Cdc45/MCM2-7/GINS (CMG) replicative helicase complex. Proc. Natl. Acad. Sci. USA 109, 13163–13170 (2012). , &
- Direct observation of stalled fork restart via fork regression in the T4 replication system. Science 338, 1217–1220 (2012). , , &