Phosphorylation of Nucleotide Excision Repair Factor Xeroderma Pigmentosum Group A by Ataxia Telangiectasia Mutated and Rad3-Related–Dependent Checkpoint Pathway Promotes Cell Survival in Response to UV Irradiation

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Haploinsufficiency of checkpoint factors ATM or Rad9 changes double-strand break repair dynamics, implying that checkpoint pathways may control DNA repair quantitatively.

“Strikingly, even haploinsufficiency of checkpoint factors (ATM/Rad9) leads to different double-strand break repair dynamics, implying that checkpoint pathways may control DNA repair activity quantitatively (28).”

• cites [28] Smilenov LB, Lieberman HB, Mitchell SA, Baker RA, Hopkins KM, Hall EJ. Combined haploinsufficiency for ATM and RAD9 as a factor in cell transformation, apoptosis, and DNA lesion repair dynamics. Cancer Res 2005; 65: 933–8. sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

The S/TQ sequence is the minimal requirement for phosphorylation by all three PIKK family kinases.

“Recent analyses using an oriented peptide library have revealed that the S/TQ sequence is a minimal requirement for phosphorylation by all three PIKK family kinases (21,22).”

• cites [21] Kim ST, Lim DS, Canman CE, Kastan MB. Substrate specificities and identification of putative substrates of ATM kinase family members. J Biol Chem 1999; 274: 37538–43. sourceSupported
• cites [22] O'Neill T, Dwyer AJ, Ziv Y, et al. Utilization of oriented peptide libraries to identify substrate motifs selected by ATM. J Biol Chem 2000; 275: 22719–27. sourcePartly supported

  The peptide-library comparison reports that SQ was the most highly phosphorylated library for ATM and DNA-PK. But the Discussion describes other substrate motifs for these kinases, so SQ is not established as a strict minimal requirement. ATR is mentioned only as potentially sharing their substrate preferences; the paper does not demonstrate the requirement for all three kinases or for TQ. (LLM, conf=0.87)

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim.

NER processing of UV damage is necessary for checkpoint activation in nonreplicating cells.

“Several studies have suggested that NER may function in the upstream of cellular checkpoint response to UV irradiation as NER processing of UV damage was necessary for checkpoint activation in nonreplicating cells (31)(32)(33).”

• cites [31] Giannattasio M, Lazzaro F, Longhese MP, Plevani P, Muzi-Falconi M. Physical and functional interactions between nucleotide excision repair and DNA damage checkpoint. EMBO J 2004; 23: 429–38. sourceSupported
• cites [32] Neecke H, Lucchini G, Longhese MP. Cell cycle progression in the presence of irreparable DNA damage is controlled by a Mec1- and Rad53-dependent checkpoint in budding yeast. EMBO J 1999; 18: 4485–97. sourceNot checked — no full text of the source
• cites [33] O'Driscoll M, Ruiz-Perez VL, Woods CG, Jeggo PA, Goodship JA. A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome. Nat Genet 2003; 33: 497–501. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Both homologous recombination and nonhomologous end-joining double-strand break repair are modulated by the ATM- and Chk2-dependent checkpoint.

“Both homologous recombination and nonhomologous end-joining pathways of double-strand break repair have been shown to be modulated by the ATM-and Chk2-dependent checkpoint (23)(24)(25).”

• cites [23] Chen G, Yuan SS, Liu W, et al. Radiation-induced assembly of Rad51 and Rad52 recombination complex requires ATM and c-Abl. J Biol Chem 1999; 274: 12748–52. sourcePartly supported

  The Discussion (page unavailable) reports that ATM-mediated signaling is required for Rad51 phosphorylation and assembly of recombination complexes, supporting modulation of homologous-recombination machinery. The paper mentions nonhomologous end-joining as another DSB-repair pathway, but does not show its modulation by this signaling pathway; it discusses c-Abl rather than Chk2. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [24] Morrison C, Sonoda E, Takao N, Shinohara A, Yamamoto K, Takeda S. The controlling role of ATM in homologous recombinational repair of DNA damage. EMBO J 2000; 19: 463–71. sourcePartly supported

  The Discussion (page unavailable) says ATM controls homologous recombinational repair. It describes a link between ATM and nonhomologous end-joining as suggested by yeast data, not as a finding established by this paper. The Introduction (page unavailable) identifies Chk2 as an ATM target, but does not show that a Chk2-dependent checkpoint modulates both repair pathways. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [25] Zhang J, Willers H, Feng Z, et al. Chk2 phosphorylation of BRCA1 regulates DNA double-strand break repair. Mol Cell Biol 2004; 24: 708–18. sourceNot checked — no full text of the source

Classified as probably not a substantial claim. May combine two claims.

ATM is activated mainly by double-strand breaks, whereas ATR is critical for checkpoint responses to stalled replication forks and to DNA damage such as UV and cisplatin.

“ATM kinase seems to be activated primarily in response to the induction of double-strand breaks whereas ATR is critical for cellular checkpoint responses to stalled replication forks and to many types of DNA damage, such as those induced by UV light and cisplatin (16,17).”

• cites [16] Abraham RT. Cell cycle checkpoint signaling through the ATM and ATR kinases. Genes Dev 2001; 15: 2177–96. sourcePartly supported

  The Conclusions describe ATM as responding primarily to DNA double-strand breaks and ATR as central to responses involving impeded replication forks and UV-induced lesions. The G1 checkpoint section likewise identifies ATR as a front-line responder to UV light and replication-interfering agents. Our copy does not mention cisplatin, so that example is not supported by this source. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [17] Siddik ZH. Cisplatin: mode of cytotoxic action and molecular basis of resistance. Oncogene 2003; 22: 7265–79. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

In ATM/ATR-deficient cells, the radiosensitive phenotype has been attributed to double-strand break repair defects.

“Moreover, in ATM/ATR-deficient cells, the radiosensitive phenotype has been ascribed to the double-strand break repair defects (26,27).”

• cites [26] Kuhne M, Riballo E, Rief N, Rothkamm K, Jeggo PA, Lobrich M. A double-strand break repair defect in ATM-deficient cells contributes to radiosensitivity. Cancer Res 2004; 64: 500–8. sourcePartly supported

  The Abstract and Discussion attribute a significant component of radiosensitivity in ATM-deficient cells to failure to repair a subset of double-strand breaks. The paper studies ATM deficiency, not ATR deficiency, so it does not support the ATR part of the citing sentence. (LLM, conf=0.90)

  Experimental — accuracy not yet measured
• cites [27] Wang H, Wang H, Powell SN, Iliakis G, Wang Y. ATR affecting cell radiosensitivity is dependent on homologous recombination repair but independent of nonhomologous end joining. Cancer Res 2004; 64: 7139–43. sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

In yeast, deletion of MEC1 and Rad53 checkpoint kinases or downstream effector kinases dramatically decreases double-strand break repair efficiency.

“Similarly, such a checkpoint-dependent regulation of double-strand break repair has been observed in yeast where deletion of the MEC1 and Rad53 checkpoint kinases or downstream effector kinases led to a dramatic decrease in double-strand break repair efficiency (29,30).”

• cites [29] DeMase D, Zeng L, Cera C, Fasullo M. The Saccharomyces cerevisiae PDS1 and RAD9 checkpoint genes control different DNA double-strand break repair pathways. DNA Repair (Amst) 2005; 4: 59–69. sourceNot checked — no full text of the source
• cites [30] Haghnazari E, Heyer WD. The DNA damage checkpoint pathways exert multiple controls on the efficiency and outcome of the repair of a double-stranded DNA gap. Nucleic Acids Res 2004; 32: 4257–68. sourcePartly supported

  In “Mec1 and Rad53 kinases are required for efficient gap repair” (page not provided), the paper reports a fivefold reduction in double-strand gap repair in mec1 and rad53 mutants. But it also reports that the downstream kinase mutants dun1 and chk1 did not differ significantly from wild type in repair frequency, so the claim overextends that finding to downstream effector kinases. (LLM, conf=0.90)

  Experimental — accuracy not yet measured

May combine two claims.

A high-salt wash disrupts protein-protein and protein-DNA interactions, removing XPA from the ATR complex.

“After immunoprecipitation with anti-ATR antibodies, the immunoprecipitates were washed with buffer of high salt concentration (0.6 mol/L NaCl) to disrupt protein-protein and protein-DNA interactions (Fig. 4C, lane 2, shows the loss of XPA from the complex following the high salt wash).”

• cites [13] Wu X, Yang Z, Liu Y, Zou Y. Preferential localization of hyperphosphorylated replication protein A to double-strand break repair and checkpoint complexes upon DNA damage. Biochem J 2005; 391: 473–80. sourcePartly supported

  The Figure 5F caption (indexed under Discussion; page unavailable) describes a 600 mM NaCl wash used to remove proteins bound to Rad51 or Rad52 immunoprecipitates. It does not show a high-salt wash of an ATR complex or loss of XPA; the Figure 4 caption instead describes ATR immunoprecipitation followed by detection of RPA32. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [15] Wu X, Shell SM, Zou Y. Interaction and colocalization of Rad9/Rad1/Hus1 checkpoint complex with replication protein A in human cells. Oncogene 2005; 24: 4728–35. sourceNot checked — no full text of the source

May combine two claims.

Without UV, ATR shows a few bright nuclear spots and XPA is homogeneously distributed in the nucleus.

“In the cells without UV irradiation, immunostaining with ATR antibody revealed a few bright nuclear spots [Fig.4D (B)], probably reflecting the proposed role of ATR in monitoring genome integrity during normal cell cycle progression (43).In contrast, XPA seemed to be homogeneously distributed throughout the nucleus without formation of apparent bright foci [Fig.4D (C)].”

• cites [43] Dart DA, Adams KE, Akerman I, Lakin ND. Recruitment of the cell cycle checkpoint kinase ATR to chromatin during S-phase. J Biol Chem 2004; 279: 16433–40. sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

The radiosensitive phenotype of ATR kinase-dead cells has been attributed to defects in double-strand break repair.

“The radiosensitive phenotype of ATR kinase-dead cells has been ascribed to the double-strand break repair defects (27).”

• cites [27] Wang H, Wang H, Powell SN, Iliakis G, Wang Y. ATR affecting cell radiosensitivity is dependent on homologous recombination repair but independent of nonhomologous end joining. Cancer Res 2004; 64: 7139–43. sourceSupported
  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Overexpression of protein kinase C or activation of ERK1/2 signaling stimulated NER activity.

“overexpression of protein kinase C or activation of extracellular signal-regulated kinase 1/2 signaling stimulated NER activity (45,46).”

• cites [45] Lin YW, Chuang SM, Yang JL. Persistent activation of ERK1/2 by lead acetate increases nucleotide excision repair synthesis and confers anti-cytotoxicity and anti-mutagenicity. Carcinogenesis 2003; 24: 53–61. sourceSupported
• cites [46] Louat T, Canitrot Y, Jousseaume S, et al. Atypical protein kinase C stimulates nucleotide excision repair activity. FEBS Lett 2004; 574: 121–5. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

XPA migrates as two distinct SDS-PAGE bands at about 38 and 40 kDa, probably because of different reduction status related to disulfide bond formation.

“The NER factor XPA is a zinc-finger protein with a molecular weight of 32 kDa but migrates as two distinct bands in SDS-PAGE at the positions of f38 and 40 kDa, probably due to the different reduction status of XPA related to the formation of disulfide bonds within the protein (12,38,39).”

• cites [12] Liu Y, Liu Y, Yang Z, et al. Cooperative interaction of human XPA stabilizes and enhances specific binding of XPA to DNA damage. Biochemistry 2005; 44: 7361–8. sourcePartly supported

  The Results (Purification of XPA; page not provided) report two XPA bands on SDS-PAGE under one purification condition and suggest that different reduction states related to disulfide bonds probably explain the heterogeneity. Our copy does not give the claimed band positions of about 38 and 40 kDa or establish the sentence’s stated 32-kDa molecular weight. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [38] Iakoucheva LM, Kimzey AL, Masselon CD, Smith RD, Dunker AK, Ackerman EJ. Aberrant mobility phenomena of the DNA repair protein XPA. Protein Sci 2001; 10: 1353–62. sourceCould not verify

  The closest passage in the paper’s body (section labeled “X. Tan”; page unavailable) concerns zinc and cysteine oxidation in carboxypeptidase A, not XPA. Searches for XPA, SDS-PAGE, the 38/40 kDa bands, and disulfide-related reduction status found no passage addressing the claim. (LLM, conf=0.78)

  Experimental — accuracy not yet measured
• cites [39] Miura N, Miyamoto I, Asahina H, Satokata I, Tanaka K, Okada Y. Identification and characterization of xpac protein, the gene product of the human XPAC (xeroderma pigmentosum group A complementing) gene. J Biol Chem 1991; 266: 19786–9. sourceNot checked — no full text of the source

May combine two claims.

ATR kinase-dead cells and ATR-deficient cells both show a UV-sensitive phenotype.

“such cells and the ATR-deficient cells both displayed an UV-sensitive phenotype (33,49).”

• cites [33] O'Driscoll M, Ruiz-Perez VL, Woods CG, Jeggo PA, Goodship JA. A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome. Nat Genet 2003; 33: 497–501. sourceNot checked — no full text of the source
• cites [49] Wright JA, Keegan KS, Herendeen DR, et al. Protein kinase mutants of human ATR increase sensitivity to UV and ionizing radiation and abrogate cell cycle checkpoint control. Proc Natl Acad Sci U S A 1998; 95: 7445–50. sourcePartly supported

  The Discussion reports that cells expressing kinase-dead ATR had increased UV sensitivity. It does not report the same phenotype in ATR-deficient cells; instead, it says ATR-null cells would be needed to clarify ATR’s role. The deficient cells studied here were ATM-deficient, not ATR-deficient. (LLM, conf=0.89)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Phosphorylation of xeroderma pigmentosum group B helicase by casein kinase II has been suggested to impair the NER function of transcription factor IIH.

“phosphorylation of xeroderma pigmentosum group B helicase by casein kinase II has been suggested to impair the NER function of transcription factor IIH (44)”

• cites [44] Coin F, Auriol J, Tapias A, Clivio P, Vermeulen W, Egly JM. Phosphorylation of XPB helicase regulates TFIIH nucleotide excision repair activity. EMBO J 2004; 23: 4835–46. sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

XPA, probably as a dimer, participates in DNA damage recognition and recruits other NER factors such as RPA, XPAG, and XPF/ERCC1 to the damage site to form dual incision complexes.

“XPA, likely in dimer (36), is involved in DNA damage recognition and also in the recruitment of other NER factors, such as RPA, XPAG, and XPF/ ERCC1, to the DNA damage site to form dual incision complexes through protein-protein interactions (8,10).”

• cites [36] Yang ZG, Liu Y, Mao LY, Zhang JT, Zou Y. Dimerization of human XPA and formation of XPA2-RPA protein complex. Biochemistry 2002; 41: 13012–20. sourceSupported
• cites [8] Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 2004; 73: 39–85. sourceNot checked — no full text of the source
• cites [10] Wood RD. DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie 1999; 81: 39–44. sourceNot checked — no full text of the source

May combine two claims.

Ser196 of XPA is a biologically significant residue that is phosphorylated in vivo.

“The Ser196 of XPA was identified as a biologically significant residue to be phosphorylated in vivo.”

May combine two claims.

In cells, XPA phosphorylation depends on ATR and is stimulated by UV irradiation.

“whereas in cells XPA was phosphorylated in an ATR-dependent manner and stimulated by UV irradiation.”

May combine two claims.

After UV irradiation, XPA and ATR interact and colocalize in cells.

“We observed the apparent interaction and colocalization of XPA with ATR in response to UV irradiation.”

• Also stated in: § Introduction · hedged

  “We also showed that ATR and XPA could physically interact and apparently colocalize to form nuclear foci on UV irradiation.”

May combine two claims.

XPA-S173A, XPA-S196A, and wild-type XPA were all efficiently phosphorylated by DNA-PK in vitro, showing that both residues can be phosphorylated in vitro.

“we found that XPA-S173A, XPA-S196A, and XPA-WT all could be phosphorylated efficiently by DNA-PK in vitro, confirming that both residues are phosphorylable in vitro (Fig. 5A, top, lane 1-3).”

May combine two claims. The quote only partly states this claim.

XPA phosphorylation is UV-inducible, with a marginal amount also present without UV, and phosphorylated XPA predominantly resides in nuclei.

“Such phosphorylation was UV-inducible and the phosphorylated XPA predominantly resided in the nuclei.”

• Also stated in: § Results · hedged

  “The XPA phosphorylation seems to be UV-inducible (Fig. 1A (a), lanes 1 and 2) although a marginal amount of the phosphorylated XPA band was also observed in the absence of UV irradiation.”

May combine two claims.

XPA antibody immunoprecipitates ATR, and recombinant His-XPA pulls down endogenous ATR.

“In the reciprocal experiments, XPA antibody was able to immunoprecipitate ATR (Fig. 4B, top) and, when recombinant His-XPA was added into cell lysates, endogenous ATR also was pulled down by the exogenous protein (Fig. 4B, bottom).”

May combine two claims.

After UV exposure, XPA-S196D cells formed colonies more readily than wild-type XPA cells, a difference significant by t test (P = 0.011 at 5 J/m2).

“the XPA-S196D cells were more likely to form cell colonies than XPA-WT although the aspartic acid could not completely mimic the phosphoryl group in cells.This enhancement in cellular resistance to UV due to the S196D mutation was significant as determined by the t test (P = 0.011 <0.05 at 5 J/m 2 ).”

• AssumptionRests on an assumption: Substituting aspartic acid at Ser196 of XPA adequately mimics the phosphorylated state of XPA for the purpose of assessing its effect on cell survival.

May combine two claims.

XPA-S173A and wild-type XPA cells formed colonies with similar efficiency, whereas XPA-S196A and XPA-S196.173A cells showed significantly fewer colonies after the same UV dose.

“the XPA-S173A and XPA-WT cells showed the similar efficiency in forming colonies whereas, for both XPA-S196A and XPA-S196.173Acells, the number of colonies was significantly reduced after the same dose of UV treatment.”

May combine two claims.

Phosphorylated XPA is overwhelmingly nuclear, likely chromatin-bound, with little if any in the cytoplasm.

“As shown in Fig. 1C, phosphorylated XPA was overwhelmingly located in the nucleus, likely as the chromatin-bound protein, whereas the cytoplasmic fraction contained little, if any, phosphorylated XPA.”

May combine two claims.

UV treatment causes cytoplasm-to-nucleus translocation of XPA, increasing total nuclear XPA.

“The significant increase of total XPA in the nuclear extracts following UV treatment was due to an UV-induced cytoplasm-to-nucleus translocation of XPA (data not shown).”

May combine two claims.

ATR antibody immunoprecipitates XPA from cell lysates, whereas rabbit IgG does not.

“As shown in Fig. 4A, the ATR antibody could efficiently immunoprecipitate XPA from cell lysates whereas rabbit immunoglobulin G could not, indicating that the coimmunoprecipitation of ATR with XPA was not the result of nonspecific antibody binding.”

May combine two claims.

Phosphorylation of XPA at Ser173 was absent in cells, and the Ser173-to-alanine mutation did not change cellular UV resistance.

“phosphorylation of Ser173 of XPA was absent in cells, and thus the mutation of Ser173 to alanine did not alter the cellular UV resistance (Fig. 6A and C).”

May combine two claims.

ATM knockdown only marginally affects XPA phosphorylation, whereas ATR knockdown almost completely eliminates UV-induced XPA phosphorylation.

“As shown in Fig. 3C, XPA phosphorylation was only marginally affected by ATM knockdown whereas ATR siRNA transfection almost completely eliminated the UV-induced phosphorylation of XPA.”

May combine two claims.

After UV, XPA phosphorylation is limited at 2 hours, more apparent at 4 hours and later, increases gradually, peaks at 16 hours, and persists until 24 hours.

“In time-course experiments, it was found that whereas limited fraction of phosphorylated XPA was observed at 2 hours after UV exposure (20 J/m 2 ), phosphorylation of XPA was much more apparent at 4 hours and after (Fig. 1D (b)).The phosphorylation increased gradually and then reached a maximum after 16 hours and persisted until the 24th hours.”

May combine two claims.

UV irradiation causes ATR redistribution to nuclei and brighter nuclear foci, and induces XPA nuclear focus formation.

“On exposure to UV, a clear redistribution of ATR to nuclei occurred and brighter nuclear foci were formed [Fig.4D (F)].In the case of XPA, UV irradiation induced significant nuclear focus formation [Fig.4D (G)].”

May combine two claims.

Replacing Ser196 of XPA with alanine increased cellular UV sensitivity, while the Ser173A mutation had little effect on cell viability.

“replacement of Ser196 of XPA with alanine increased the UV sensitivity of the cells whereas Ser173A mutation resulted in little effects on cell viability (Fig. 6A).”

May combine two claims.

ATR and XPA interact and colocalize following UV irradiation.

“The apparent interaction and colocalization of ATR with XPA following UV irradiation (Fig. 4)”

May combine two claims.

DNA-PK phosphorylates XPA in vitro, with lower efficiency than RPA32.

“As shown in Fig. 2A, DNA-PK did phosphorylate XPA in the presence of [g-32 P]ATP under in vitro experimental conditions (lanes 2-4), albeit the phosphorylation efficiency was relatively low in comparison with that of RPA32, which contains multiple S/TQ motifs and undergoes hyperphosphorylation in response to DNA damage (Fig. 2A, lane 1; ref. 40).”

• cites [40] Binz SK, Sheehan AM, Wold MS. Replication protein A phosphorylation and the cellular response to DNA damage. DNA Repair (Amst) 2004; 3: 1015–24. sourceNot checked — no full text of the source

May combine two claims.

The third XPA band is susceptible to CIAP, and its mobility shift is preserved by the CIAP inhibitor glycerophosphate.

“Interestingly, this band was susceptible to treatment with calf intestinal alkaline phosphatase (CIAP; Fig. 1A (a), lanes 3 and 4) whereas addition of a CIAP inhibitor, glycerophosphate, preserved the mobility shift of this band (Fig. 1A (a), lanes 5 and 6).”

Probably not a substantial claim: may not pass S3 (load-bearing).

A third XPA band is consistently observed when gels are run for an unusually long time.

“During our studies of cellular XPA function with A549 cells, we consistently observed a third band of XPA when the gel was run for an unusually long time (Fig. 1A, top, band 3).”

May combine two claims.

In ATR-deficient cells, XPA is not phosphorylated after UV, whereas in ATM-deficient cells XPA is phosphorylated as in normal cells.

“As revealed in Fig. 3D, the XPA was phosphorylated in UV-irradiated ATM cells as in normal cells but no phosphorylation was observed for XPA in ATR cells after UV exposure.”

• AssumptionRests on an assumption: The GM18366 and GM09607 cell lines are deficient in ATR and ATM, respectively.

May combine two claims.

Mutating Ser196 alone was enough to eliminate the UV-induced radioactive band and the up-shifted band of XPA.

“mutation of Ser196 alone was sufficient to cause the loss of the radioactive band (top) and the up-shifted band (bottom) of XPA induced by UV irradiation.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

XPA participates in DNA damage recognition and recruits other NER factors to damage sites through protein-protein interactions.

“It is generally believed that XPA is involved in DNA damage recognition and also in the recruitment of other NER factors to the DNA damage site to form dual incision complexes through protein-protein interactions (8,(10)(11)(12).”

• cites [8] Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 2004; 73: 39–85. sourceNot checked — no full text of the source
• cites [10] Wood RD. DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie 1999; 81: 39–44. sourceNot checked — no full text of the source
• cites [11] Patrick SM, Turchi JJ. Xeroderma pigmentosum complementation group A protein (XPA) modulates RPA-DNA interactions via enhanced complex stability and inhibition of strand separation activity. J Biol Chem 2002; 277: 16096–101. sourceNot checked — no full text of the source

Classified as probably not a substantial claim. May combine two claims.

Checkpoint activation is important for optimal DNA repair activity, transcription activation, and in some cases apoptosis.

“Recent evidence, however, indicated that in addition to controlling cell cycle transitions, checkpoint activation is also important for optimal DNA repair activity, activation of transcription, and, in some instances, induction of apoptosis (4).”

• cites [4] Zhou BB, Elledge SJ. The DNA damage response: putting checkpoints in perspective. Nature 2000; 408: 433–9. sourceNot checked — no full text of the source

Classified as probably not a substantial claim. May combine two claims.

XPA is indispensable for NER and is required for both global genome repair and transcription-coupled repair.

“xeroderma pigmentosum group A (XPA) plays an indispensable role and is required for both global genome repair and transcription-coupled repair (6)(7)(8)(9).”

• cites [6] Costa RM, Chigancas V, Galhardo Rda S, Carvalho H, Menck CF. The eukaryotic nucleotide excision repair pathway. Biochimie 2003; 85: 1083–99. sourceNot checked — no full text of the source
• cites [7] Thoma BS, Vasquez KM. Critical DNA damage recognition functions of XPC-hHR23B and XPA-RPA in nucleotide excision repair. Mol Carcinog 2003; 38: 1–13. sourceNot checked — no full text of the source
• cites [8] Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 2004; 73: 39–85. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

ATR and ATM are members of the phosphatidylinositol-3-kinase-related kinase family.

“ATR and ATM belong to the phosphatidylinositol-3-kinase-related kinase (PIKK) family of proteins.”

May combine two claims.

Phosphorylation of XPA may facilitate NER in the late stage for removal of persistent DNA lesions, which is critical for cell survival.

“we propose that phosphorylation of XPA may play a role in facilitating the cellular function of NER in the late stage for removal of persistent DNA lesions (6), which is critical for cell survival.”

• cites [6] Costa RM, Chigancas V, Galhardo Rda S, Carvalho H, Menck CF. The eukaryotic nucleotide excision repair pathway. Biochimie 2003; 85: 1083–99. sourceNot checked — no full text of the source

May combine two claims.

In cells, XPA is phosphorylated mainly at Ser196, even though both Ser173 and Ser196 can be phosphorylated in vitro.

“we concluded that phosphorylation of XPA primarily occurred at Ser196 residue in vivo although both Ser173 and Ser196 could be phosphorylated in vitro.”

May combine two claims.

Unphosphorylated XPA is a unique NER factor and is indispensable for both NER subpathways, global genome repair and transcription-coupled repair.

“The unphosphorylated form of XPA is a unique factor in NER and is indispensable for both subpathways (global genome repair and transcription-coupled repair) of NER in cells (6)(7)(8).”

• cites [6] Costa RM, Chigancas V, Galhardo Rda S, Carvalho H, Menck CF. The eukaryotic nucleotide excision repair pathway. Biochimie 2003; 85: 1083–99. sourceNot checked — no full text of the source
• cites [7] Thoma BS, Vasquez KM. Critical DNA damage recognition functions of XPC-hHR23B and XPA-RPA in nucleotide excision repair. Mol Carcinog 2003; 38: 1–13. sourceNot checked — no full text of the source
• cites [8] Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 2004; 73: 39–85. sourceNot checked — no full text of the source

May combine two claims.

Phosphorylation of XPA by the ATR checkpoint may positively regulate NER activity and help cells recover from NER-related DNA damage.

“we propose that the phosphorylation of XPA by ATR checkpoint may positively regulate NER activity and thus may facilitate the cells to recover from NER-related DNA damages.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The budding yeast checkpoint genes Rad9 and Rad24 are required for inducible NER.

“On the other hand, two checkpoint genes in budding yeast (Rad9 and Rad24, the human homologues of BRCA1 and Rad17, respectively) have been shown to be required for the inducible NER (34).”

• cites [34] Yu S, Teng Y, Lowndes NF, Waters R. RAD9, RAD24, RAD16 and RAD26 are required for the inducible nucleotide excision repair of UV-induced cyclobutane pyrimidine dimers from the transcribed and non-transcribed regions of the Saccharomyces cerevisiae MFA2 gene. Mutat Res 2001; 485: 229–36. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

In mammalian systems, the checkpoint abrogator UCN-01 inhibits NER activity against cisplatin.

“And in mammalian system, the checkpoint abrogator UCN-01 inhibited the NER activity against cisplatin (35).”

• cites [35] Jiang H, Yang LY. Cell cycle checkpoint abrogator UCN-01 inhibits DNA repair: association with attenuation of the interaction of XPA and ERCC1 nucleotide excision repair proteins. Cancer Res 1999; 59: 4529–34.Not checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

The difference in XPA phosphorylation with ATR and ATM siRNAs could be affected by different knockdown efficacy.

“However, it should be noted that the difference in XPA phosphorylation with siRNAs for ATR and ATM could be affected by the different knockdown efficacy of the siRNAs.”

May combine two claims.

ATR-dependent phosphorylation of XPA at Ser196 is important for cell survival after UV damage, probably by fine-tuning NER activity.

“these results suggest that the ATR-dependent phosphorylation of XPA at Ser196 is important for cell survival in response to UV damage, probably by fine-tuning the NER activity in cells.”

May combine two claims.

The checkpoint kinase ATR can interact with XPA and regulate its phosphorylation in response to DNA damage, which appears important for cell viability after UV irradiation.

“the checkpoint kinase ATR was able to interact with XPA and to actively regulate the phosphorylation of XPA in response to DNA damage, which seemed to be important for cell viability following UV irradiation.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Modulating XPA function may affect only cellular NER activity.

“it is conceivable that modulation of XPA function may exclusively affect the cellular NER activity.”

May combine two claims.

In cells, XPA is phosphorylated by the checkpoint kinase ATR after UV irradiation, though phosphorylation by ATR downstream kinases such as Chk1 cannot be fully excluded.

“Here we show that XPA was phosphorylated by checkpoint kinase ATR in cells after UV irradiation although the possibility cannot be completely excluded that XPA could be phosphorylated by the downstream kinase(s) of ATR (e.g., Chk1).”