The Helicase PIF1 Facilitates Resection over Sequences Prone to Forming G4 Structures

Jimeno, Sonia; Camarillo, Rosa; Mejías-Navarro, Fernando; Fernández-Ávila, María Jesús; Soria‐Bretones, Isabel; Prados-Carvajal, Rosario; Huertas, Pablo

doi:10.1016/j.celrep.2018.08.047

Cited by 38 publications

(27 citation statements)

References 50 publications

(76 reference statements)

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“…Human Pif1 is recruited to DNA double-strand breaks sites to promote homologous recombination (HR) at sequences predicted to form G4s. Treatment with G4 stabilising ligands can impair Pif1 functionality, which can be rescued by PIF1 overexpression [94]. G4s have also been suggested to function as potential sensor or trapping sites of oxidative DNA damage caused by reactive oxygen species.…”

Section: Biological Role Of G4smentioning

confidence: 99%

The Structure and Function of DNA G-Quadruplexes

Spiegel

Adhikari

Balasubramanian

2020

Trends in Chemistry

548

568

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Guanine-rich DNA sequences can fold into four-stranded, noncanonical secondary structures called G-quadruplexes (G4s). G4s were initially considered a structural curiosity, but recent evidence suggests their involvement in key genome functions such as transcription, replication, genome stability, and epigenetic regulation, together with numerous connections to cancer biology. Collectively, these advances have stimulated research probing G4 mechanisms and consequent opportunities for therapeutic intervention. Here, we provide a perspective on the structure and function of G4s with an emphasis on key molecules and methodological advances that enable the study of G4 structures in human cells. We also critically examine recent mechanistic insights into G4 biology and protein interaction partners and highlight opportunities for drug discovery. Beyond the DNA Double HelixA chemist's perspective on the function of a molecule, or a system of molecules, is typically led by a consideration of how molecular structure dictates function. The most widely recognised DNA structure is that of the classical DNA double helix [1], which defines a structural basis for the genetic code via defined base-pairing. Yet, it is evident that DNA is structurally dynamic and capable of adopting alternative secondary structures. One such class of DNA secondary structure is the four-stranded Gquadruplex (G4). Herein, we discuss some of the key scientific history that has shaped our understanding of this structural motif, its probable functions in biology, and major unanswered questions that remain to be solved.

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Section: Biological Role Of G4smentioning

confidence: 99%

The Structure and Function of DNA G-Quadruplexes

Spiegel

Adhikari

Balasubramanian

2020

Trends in Chemistry

548

568

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“…Topoisomerases TOP1 and TOP3B play a key role in maintaining the DNA tension in chromatin during transcription and their deficiency accumulates R-loops ( 8 , 9 ). Many RNA and DNA helicases have been identified to resolve persistent R-loops, including senataxin (SETX) ( 10 , 11 ), aquarius (AQR) ( 12 ), BLM ( 13 , 14 ), DDX1 ( 15 , 16 ), DDX5 ( 17 ), DDX21 ( 18 ), DDX23 ( 19 ), DHX9 ( 20 ) and PIF1 ( 21 ). Another class of enzyme that suppresses R-loops is the RNAse H1 and RNase H2 able to degrade the RNA component in the R-loop ( 22 ).…”

Section: Introductionmentioning

confidence: 99%

DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions

Mersaoui

Guitton-Sert

et al. 2020

NAR Cancer

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R-loops are three-stranded structures consisting of a DNA/RNA hybrid and a displaced DNA strand. The regulatory factors required to process this fundamental genetic structure near double-strand DNA breaks (DSBs) are not well understood. We previously reported that cellular depletion of the ATP-dependent DEAD box RNA helicase DDX5 increases R-loops genome-wide causing genomic instability. In this study, we define a pivotal role for DDX5 in clearing R-loops at or near DSBs enabling proper DNA repair to avoid aberrations such as chromosomal deletions. Remarkably, using the non-homologous end joining reporter gene (EJ5-GFP), we show that DDX5-deficient U2OS cells exhibited asymmetric end deletions on the side of the DSBs where there is overlap with a transcribed gene. Cross-linking and immunoprecipitation showed that DDX5 bound RNA transcripts near DSBs and required its helicase domain and the presence of DDX5 near DSBs was also shown by chromatin immunoprecipitation. DDX5 was excluded from DSBs in a transcription- and ATM activation-dependent manner. Using DNA/RNA immunoprecipitation, we show DDX5-deficient cells had increased R-loops near DSBs. Finally, DDX5 deficiency led to delayed exonuclease 1 and replication protein A recruitment to laser irradiation-induced DNA damage sites, resulting in homologous recombination repair defects. Our findings define a role for DDX5 in facilitating the clearance of RNA transcripts overlapping DSBs to ensure proper DNA repair.

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“…We demonstrated that FpG was able to repair the damages detected in the PhenDC3-treated cells, thus there is the possibility that accumulation of 8-oxo-7,8-dihydroguanine lesions in PhenDC3-treated samples might not have been repaired within the cells due to constraints induced by the stabilized G4 structures. In fact, DNA end resection during homologous recombination is impaired in pyridostatin-treated human cells, suggesting that stabilized G4 structures hinder the processing of DNA ends by the homologous recombination machinery ( 94 ).…”

Section: Discussionmentioning

confidence: 99%

“…Association and unwinding of 8-oxo-7,8-dihydroguanine-containing G4 structures by Pfh1 has not yet been studied, but one possibility can be that these G4 structures are not recognized and unwound by Pfh1, or that the rate of unwinding is too slow, which results in ssDNA breaks. The role of Pif1 helicases in cells might not only involve promoting G4 unwinding during DNA replication, but an additional conserved role of Pif1 helicases might be to suppress genomic rearrangements at G4 structures ( 21 ), perhaps by promoting resection at G4 structures that are induced by DNA double-strand breaks ( 21 , 94 ).…”

Section: Discussionmentioning

confidence: 99%

Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication

Obi

Rentoft

Singh

et al. 2020

Nucleic Acids Research

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G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.

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The Helicase PIF1 Facilitates Resection over Sequences Prone to Forming G4 Structures

Cited by 38 publications

References 50 publications

The Structure and Function of DNA G-Quadruplexes

The Structure and Function of DNA G-Quadruplexes

DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions

Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication

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