<i>Fan1</i> deficiency results in DNA interstrand cross-link repair defects, enhanced tissue karyomegaly, and organ dysfunction

Thongthip, Supawat; Bellani, Marina A.; Gregg, Siobhán Q.; Sridhar, Sunandini; Conti, Brooke A.; Chen, Yanglu; Seidman, Michael M.; Smogorzewska, Agata

doi:10.1101/gad.276261.115

Cited by 45 publications

(56 citation statements)

References 60 publications

(90 reference statements)

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“…Moreover, studies in fission yeast and more recently in mouse cells imply that FAN1 and SNM1A may play a redundant role in ICL repair, or contribute to different ICL repair sub‐pathways (Fontebasso et al , 2013; Thongthip et al , 2016). We have performed pilot studies to define the action of FAN1 on the ICL‐containing substrates utilised in this study.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, the FAN1 nuclease has also been demonstrated to act in an exo-like fashion and is able to degrade past and release DNA substrates containing ICLs (Wang et al, 2014;Zhao et al, 2014;Pizzolato et al, 2015). Moreover, studies in fission yeast and more recently in mouse cells imply that FAN1 and SNM1A may play a redundant role in ICL repair, or contribute to different ICL repair sub-pathways (Fontebasso et al, 2013;Thongthip et al, 2016). We have performed pilot studies to define the action of FAN1 on the ICL-containing substrates utilised in this study.…”

Section: Discussionmentioning

confidence: 99%

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RPA activates the XPF ‐ ERCC 1 endonuclease to initiate processing of DNA interstrand crosslinks

et al. 2017

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During replication‐coupled DNA interstrand crosslink (ICL) repair, the XPF‐ERCC1 endonuclease is required for the incisions that release, or “unhook”, ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL. Here, we report that while purified XPF‐ERCC1 incises simple ICL‐containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single‐stranded DNA (ssDNA)‐binding replication protein A (RPA) selectively restores XPF‐ERCC1 endonuclease activity on this structure. The 5′–3′ exonuclease SNM1A can load from the XPF‐ERCC1‐RPA‐induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF‐ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

RPA activates the XPF ‐ ERCC 1 endonuclease to initiate processing of DNA interstrand crosslinks

et al. 2017

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“…The nuclease activity of human and bacterial FAN1 proteins was examined according to published procedures [5,11]. Reaction mixtures were resolved in 15% denaturing polyacrylamide gels (with 8 M Urea) in 1X TBE buffer (89 mM Tris Borate, pH 8.4, and 2 mM EDTA) at 200 V for 40 min at room temperature.…”

Section: Nuclease Assaymentioning

confidence: 99%

“…The Fanconi-associated nuclease 1 (FAN1) is a DNA structure-specific nuclease involved in ICL repair via interaction with FANCI-FANCD2 complex [1][2][3][4]. FAN1 may also have a repair function that is independent of proteins in the Fanconi anemia (FA) pathway of DNA damage response [5]. Importantly, FAN1 mutations are thought to lead to the renal disease Karyomegalic Interstitial Nephritis (KIN) [6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Importance of homo-dimerization of Fanconi-associated nuclease 1 in DNA flap cleavage

et al. 2018

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Fanconi-associated nuclease 1 (FAN1) removes interstrand DNA crosslinks (ICLs) through its DNA flap endonuclease and exonuclease activities. Crystal structures of human and bacterial FAN1 bound to a DNA flap have been solved. The Pseudomonas aeruginosa bacterial FAN1 and human FAN1 (hFAN1) missing a flexible loop are monomeric, while intact hFAN1 is homo-dimeric in structure. Importantly, the monomeric and dimeric forms of FAN1 exhibit very different DNA binding modes. Here, we interrogate the functional differences between monomeric and dimeric forms of FAN1 and provide an explanation for the discrepancy in oligomeric state between the two hFAN1 structures. Specifically, we show that the flexible loop in question is needed for hFAN1 dimerization. While monomeric and dimeric bacterial or human FAN1 proteins cleave a short 5' flap strand with similar efficiency, optimal cleavage of a long 5' flap strand is contingent upon protein dimerization. Our study therefore furnishes biochemical evidence for a role of hFAN1 homodimerization in biological processes that involve 5' DNA Flap cleavage.

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“…However, a number of studies suggested that the cross-link repair function of FAN1 is not within the FA pathway as: (i) homologs of FAN1 have been found in bacteria, archaea, and unicellular eukaryotes which lack FA proteins (19,(21)(22)(23), (ii) mutations in FAN1 do not cause FA, but instead a kidney disorder called karyomegalic interstitial nephritis (KIN) (24), (iii) N-terminal UBZ domain is dispensable for ICL repair, but is required for genomic maintenance, suggesting that the interaction of FAN1 with ID serves a function outside of ICL repair (25)(26)(27). Nevertheless, the sensitivity of FAN1-deficient cells to ICL-forming agents implicates FAN1 in ICL resolution independently of the FA pathway.…”

Section: Dna Synthesis (Tls) and The Second Strand Is Repaired By Hommentioning

confidence: 99%

Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease

Jin

Roy

Lee

et al. 2018

Journal of Biological Chemistry

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The mechanism of ICL unhooking by bacterial FAN1 4 a "head to tail" dimer in the presence of DNA (34).The authors suggest that FAN1 dimer scans, latches, and unwinds DNA to pull the single-stranded DNA to the active site of a FAN1. Mutations of the residues at the dimeric interface abolished the nuclease activity of the HsFAN1, raising the possibility that the dimerization is important for its activity.Bacterial FAN1 homologs share a high similarity with HsFAN1 (Fig. 1A, 23,35). Second, PaFAN1 does not have a specific basic pocket that is critical for the proposed "3-nt exonuclease" mechanism (Fig. 1B, C, 33). Third, PaFAN1 lacks the basic motif in the SAP domain required for dimerization in one of the structures of the human nuclease (Fig. 1A, 34). These features raise the question if PaFAN1 can unhook ICLs, and if so, by which mechanism.To address these issues, we examined the ICL Based on these findings, we provide insights into how FAN1 might have evolved to have two basic regions to guide its nuclease activity and maintain genomic stability. RESULTS Substrate specificity of PaFAN1In previous study, we have used a DNA substrate with a four nucleotide 5' flap (23). (Fig. S1E-F). PaFAN1 efficiently incises ICL lesionTo examine whether the bacterial FAN1homolog shares the ICL resolving activity of mammalian FAN1, we examined the in vitro ICL unhooking activity of PaFAN1 using various DNA ICL substrates (Fig. 1D). We first analyzed ifPaFAN1 can unhook the ICL near the ss/ds junction.We used DNA substrates containing a nitrogen-like ICL, which is free of duplex distortion (15,36,37), The mechanism of ICL unhooking by bacterial FAN1 7 how PaFAN1 can catalyze multiple cleavage events.

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Fan1 deficiency results in DNA interstrand cross-link repair defects, enhanced tissue karyomegaly, and organ dysfunction

Cited by 45 publications

References 60 publications

RPA activates the XPF ‐ ERCC 1 endonuclease to initiate processing of DNA interstrand crosslinks

RPA activates the XPF ‐ ERCC 1 endonuclease to initiate processing of DNA interstrand crosslinks

Importance of homo-dimerization of Fanconi-associated nuclease 1 in DNA flap cleavage

Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease

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