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Control of structure-specific endonucleases to maintain genome stability

Key Points

  • Structure-specific endonucleases (SSEs) process various types of DNA secondary structures that arise during DNA replication, repair, recombination and transcription, and are important for the maintenance of genome stability.

  • Elaborate regulatory mechanisms ensure that SSEs act in an efficient, specific and timely manner so that they do not themselves become a source of genome instability.

  • The control of SSEs relies on a combination of catalytic regulation; modulation of their cellular localization, which regulates their targeting to the appropriate substrate or instead ensures their sequestration to reduce the risk of uncontrolled DNA processing; and protein turnover.

  • SSEs can function genome-wide, such as during the repair of DNA adducts by nucleotide excision repair, or their function can be specific to genomic loci that are prone to the formation of DNA secondary structures that need to be processed during replication and/or transcription. Such loci include, for example, the ribosomal DNA or telomeres, which contain DNA repeats, or regions that replicate late in S phase and therefore might not be replicated on time before the onset of mitosis, such as common fragile sites.

  • The control of SSEs is critical during DNA replication, during which inappropriate SSE activity, especially of MUS81 nucleases, can have dire consequences for genome stability.

  • Nuclease scaffolds are particularly important for the regulation of SSEs, by helping in their efficient recruitment to DNA and coordination with other factors. Nuclease scaffolds can directly modulate the catalytic activity of SSEs and change their substrate specificity. Some scaffolds are dedicated to the control of a single SSE, whereas others control several SSEs, either independently or by coordinating their activity within the same pathway.

Abstract

Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families — including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes — during processes such as DNA adduct repair, Holliday junction processing and replication stress. We also discuss newly characterized connections between SSEs and other classes of DNA-remodelling enzymes and cell cycle control machineries, which reveal the importance of SSE scaffolds such as the synthetic lethal of unknown function 4 (SLX4) tumour suppressor for the maintenance of genome stability.

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Figure 1: DNA secondary structures processed by structure-specific endonucleases.
Figure 2: Control of structure-specific endonucleases during nucleotide excision repair.
Figure 3: Controlling the processing of Holliday junctions by structure-specific endonucleases.
Figure 4: Function of FEN1 in Okazaki fragment maturation.
Figure 5: Function of structure-specific endonucleases during replication stress.
Figure 6: Scaffold protein control of structure-specific endonucleases.

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Acknowledgements

The authors apologize for the many studies that were not cited owing to space limitations. The authors thank all members of their laboratory for stimulating discussions, especially S. Scaglione, J.-H. Guervilly and B. LLorente. The authors thank S. Scaglione and J.-H. Guervilly for their critical and careful reading of the manuscript. The authors also thank R. Wood, P. Russell, N. Boddy, P. McHugh and J. Matos for enlightening and enthusiastic discussions, with special thanks to R. Wood, P. Russell and N. Boddy for their feedback on the manuscript. Finally, the authors thank the referees for their thorough reviewing, which has undoubtedly helped improve the manuscript. This work was supported by grants from the Institut National du Cancer (PLBIO 2012–111), Agence Nationale de la Recherche (ANR Blanc EME1PHOSUMO) and the Siric-Cancéropôle PACA (AAP Projets émergents 2015).

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Correspondence to Pierre-Henri L. Gaillard.

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Supplementary information

Supplementary information S1

Conserved families of structure-specific endonucleases (PDF 519 kb)

Supplementary information S2

Positive and negative regulation of SSEs (PDF 207 kb)

Supplementary information S3

Controlling the resolution of joint molecules by SSEs in meiosis. (PDF 783 kb)

Supplementary information S4

Structure-specific endonuclease scaffolds. (PDF 238 kb)

PowerPoint slides

Glossary

Single-stranded flaps

Single-stranded DNA protrusions from duplex DNA with either 5′ phosphate or 3′ hydroxyl ends.

Stem–loops

DNA structures that comprise two adjacent complementary sequences that form duplex DNA (the stem) with an intervening single-stranded closed loop.

Displacement loops

(D-loops). DNA structures that form early during homologous recombination by the invasion of duplex DNA by complementary single-stranded DNA.

Holliday junctions

Four-way DNA junction structures that form after complementary strand exchange between homologous sequences during DNA double-strand break repair by homologous recombination or during replication. Holliday junctions constitute covalent links between chromosomes.

DNA adducts

Chemical compounds or proteins that are covalently linked to DNA.

R-loops

Three-stranded nucleic acid structures that contain an RNA–DNA hybrid that results from the pairing of a nascent RNA with the DNA template during transcription.

Fanconi anaemia core complex

A multiprotein complex that resolves blocks to DNA replication such as DNA interstrand crosslinks. Mutations in the complex cause Fanconi anaemia, which is characterized mainly by haematological problems and cancer predisposition.

Trans-lesion DNA synthesis

Low-fidelity (and thereby mutagenic) DNA replication over damaged bases by specialized trans-lesion polymerases.

Ubiquitin-binding motif

A modular protein domain that mediates the non-covalent binding to monoubiquitin and/or polyubiquitin chains.

Double Holliday junctions

Structures that comprise two proximal Holliday junctions, which represent an intermediate stage of homologous recombination.

Holliday junction dissolution

A process by which double Holliday junctions are merged into a hemicatenane structure, in which one of the strands of one duplex passes between the strands of the other duplex. This structure is processed by a single-strand cut that releases the two duplexes from one another.

Bloom syndrome

A hereditary disorder that arises from mutations in the gene encoding the RecQ DNA helicase Bloom syndrome protein (BLM). It is characterized by growth deficiencies, sun sensitivity, immunodeficiency and predisposition to cancer.

Okazaki fragments

DNA fragments that are synthesized during replication of the lagging strand by DNA polymerase-α (Polα) and Polδ; the fragments are joined together by DNA ligase I to form the continuous lagging strand.

Common fragile sites

(CFSs). Chromosomal regions that are prone to replication stress. CFSs are a potential source of genome instability and are associated with chromosomal rearrangements in cancer.

NPL4 zinc finger domain

(NZF domain). A domain that mediates binding to monoubiquitin and polyubiquitin.

Winged-helix domain

A subclass of the helix-turn-helix DNA-binding domain that is found in DNA-processing enzymes and many transcription factors.

S phase checkpoint

A signalling pathway that is triggered by replication stress and that delays cell cycle progression and protects the integrity of replication forks.

Forkhead-associated domain

(FHA domain). A domain that mediates recognition of phosphopeptides.

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Dehé, PM., Gaillard, PH. Control of structure-specific endonucleases to maintain genome stability. Nat Rev Mol Cell Biol 18, 315–330 (2017). https://doi.org/10.1038/nrm.2016.177

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