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Junjie CHEN

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Journal of Zhejiang University SCIENCE B 2021 Vol.22 No.1 P.1-20

http://doi.org/10.1631/jzus.B2000356


Mass spectrometry-based protein?protein interaction techniques and their applications in studies of DNA damage repair


Author(s):  Zhen CHEN, Junjie CHEN

Affiliation(s):  Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

Corresponding email(s):   jchen8@mdanderson.org

Key Words:  Protein?protein interaction, Interactome, Proteomics, Mass spectrometry, DNA repair, DNA damage response


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Zhen CHEN, Junjie CHEN. Mass spectrometry-based protein?protein interaction techniques and their applications in studies of DNA damage repair[J]. Journal of Zhejiang University Science B, 2021, 22(1): 1-20.

@article{title="Mass spectrometry-based protein?protein interaction techniques and their applications in studies of DNA damage repair",
author="Zhen CHEN, Junjie CHEN",
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pages="1-20",
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doi="10.1631/jzus.B2000356"
}

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%T Mass spectrometry-based protein?protein interaction techniques and their applications in studies of DNA damage repair
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%A Junjie CHEN
%J Journal of Zhejiang University SCIENCE B
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%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B2000356

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A1 - Zhen CHEN
A1 - Junjie CHEN
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B2000356


Abstract: 
Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein?protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein?protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein?protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein?protein interaction. In addition, we discuss the application of these tools in the investigation of protein?protein interaction networks involved in DNA damage response and DNA repair.

基于质谱技术的蛋白质互作研究方法进展及其在DNA损伤修复中的应用

摘要:蛋白质作为主要的生物功能分子往往通过相互作用形成复合体和动态的互作网络来行使其功能。这些互作网络使得细胞和器官能够正常行使功能,并有效地应对外界环境的刺激。在过去的几十年里,为了研究蛋白质相互作用网络,研究人员开发了许多生物化学方法来寻找目标蛋白质的相互作用蛋白。与此同时,蛋白质组和质谱技术的快速发展也使得鉴定相互作用蛋白并构建相关蛋白质互作网络成为了可能。利用这些蛋白质鉴定技术,蛋白质互作网络取得了很多重要进展,包括在DNA损伤修复研究领域。在近些年,通过蛋白质互作研究,大量的DNA损伤应答和修复相关蛋白被发现。而随着蛋白质富集和质谱技术的进一步发展,蛋白质互作研究进入了一个新的阶段。在这篇综述里,我们总结了蛋白质互作研究策略的最新进展,以及这些技术在DNA损伤应答及其修复研究中的应用。

关键词:蛋白质互作;相互作用组;蛋白质组;质谱;DNA损伤修复;DNA损伤应答

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1]AbbasiS, Schild-PoulterC, 2019. Mapping the Ku interactome using proximity-dependent biotin identification in human cells. J Proteome Res, 18(3):1064-1077.

[2]AliAM, PradhanA, SinghTR, et al., 2012. FAAP20: a novel ubiquitin-binding FA nuclear core-complex protein required for functional integrity of the FA-BRCA DNA repair pathway. Blood, 119(14):3285-3294.

[3]AndersenSL, BergstralhDT, KohlKP, et al., 2009. Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. Mol Cell, 35(1):128-135.

[4]AyyildizD, AntonialiG, D'AmbrosioC, et al., 2020. Architecture of the human APE1 interactome defines novel cancers signatures. Sci Rep, 10:28.

[5]BagciH, SriskandarajahN, RobertA, et al., 2020. Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms. Nat Cell Biol, 22(1):120-134.

[6]BassTE, LuzwickJW, KavanaughG, et al., 2016. ETAA1 acts at stalled replication forks to maintain genome integrity. Nat Cell Biol, 18(11):1185-1195.

[7]BatraJ, HultquistJF, LiuDD, et al., 2018. Protein interaction mapping identifies RBBP6 as a negative regulator of Ebola virus replication. Cell, 175(7):1917-1930.e13.

[8]BaymazHI, SpruijtCG, VermeulenM, 2014. Identifying nuclear protein鈥抪rotein interactions using GFP affinity purification and SILAC-based quantitative mass spectrometry. In: Warscheid B (Ed.), Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC): Methods and Protocols. Humana Press, New York, p.207-226.

[9]BotuyanMV, CuiGF, Dran茅P, et al., 2018. Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein. Nat Struct Mol Biol, 25(7):591-600.

[10]BrandsmaI, van GentDC, 2012. Pathway choice in DNA double strand break repair: observations of a balancing act. Genome Integr, 3:9.

[11]BranonTC, BoschJA, SanchezAD, et al., 2018. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol, 36(9):880-887.

[12]CannavoE, GerritsB, MarraG, et al., 2007. Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2. J Biol Chem, 282(5):2976-2986.

[13]CantorSB, BellDW, GanesanS, et al., 2001. BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell, 105(1):149-160.

[14]CastelloA, HorosR, StreinC, et al., 2016. Comprehensive identification of RNA-binding proteins by RNA interactome capture. In: Dassi E (Ed.), Post-Transcriptional Gene Regulation. Humana Press, New York, p.131-139.

[15]ChapmanJR, SossickAJ, BoultonSJ, et al., 2012. BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J Cell Sci, 125:3529- 3534.

[16]ChavezJD, SchweppeDK, EngJK, et al., 2016. In vivo conformational dynamics of Hsp90 and its interactors. Cell Chem Biol, 23(6):716-726.

[17]CheesemanIM, DesaiA, 2005. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci STKE, 2005( 266):pl1.

[18]CheesemanIM, NiessenS, AndersonS, et al., 2004. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev, 18(18):2255-2268.

[19]ChenJJ, SilverDP, WalpitaD, et al., 1998. Stable interaction between the products of the BRCA1 and BRCA2 tumor suppressor genes in mitotic and meiotic cells. Mol Cell, 2(3):317-328.

[20]ChenZ, TranM, TangMF, et al., 2016. Proteomic analysis reveals a novel mutator S (MutS) partner involved in mismatch repair pathway. Mol Cell Proteomics, 15(4):1299-1308.

[21]ChenZ, LeiCQ, WangC, et al., 2019. Global phosphoproteomic analysis reveals ARMC10 as an AMPK substrate that regulates mitochondrial dynamics. Nat Commun, 10:104.

[22]ChenZ, WangC, JainA, et al., 2020. AMPK interactome reveals new function in non-homologous end joining DNA repair. Mol Cell Proteomics, 19(3):467-477.

[23]ChoKF, BranonTC, RajeevS, et al., 2020. Split-TurboID enables contact-dependent proximity labeling in cells. Proc Natl Acad Sci USA, 117( 22):12143-12154.

[24]CortezD, WangY, QinJ, et al., 1999. Requirement of ATM-dependent phosphorylation of BRCA1 in the DNA damage response to double-strand breaks. Science, 286(5442):1162-1166.

[25]Cortez-RetamozoV, BackmannN, SenterPD, et al., 2004. Efficient cancer therapy with a nanobody-based conjugate. Cancer Res, 64(8):2853-2857.

[26]CoyaudE, RanadheeraC, ChengD, et al., 2018. Global interactomics uncovers extensive organellar targeting by Zika virus. Mol Cell Proteomics, 17(11):2242-2255.

[27]CraxtonA, MunnurD, Jukes-JonesR, et al., 2018. PAXX and its paralogs synergistically direct DNA polymerase 位 activity in DNA repair. Nat Commun, 9:3877.

[28]CristeaIM, WilliamsR, ChaitBT, et al., 2005. Fluorescent proteins as proteomic probes. Mol Cell Proteomics, 4(12):1933-1941.

[29]DavisZH, VerschuerenE, JangGM, et al., 2015. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell, 57(2):349-360.

[30]de MunterS, G枚rnemannJ, DeruaR, et al., 2017. Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions. FEBS Lett, 591(2):415-424.

[31]DiepJ, OoiYS, WilkinsonAW, et al., 2019. Enterovirus pathogenesis requires the host methyltransferase SETD3. Nat Microbiol, 4(12):2523-2537.

[32]DongYS, HakimiMA, ChenXW, et al., 2003. Regulation of BRCC, a holoenzyme complex containing BRCA1 and BRCA2, by a signalosome-like subunit and its role in DNA repair. Mol Cell, 12(5):1087-1099.

[33]Dran茅P, BraultME, CuiGF, et al., 2017. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. Nature, 543(7644):211-216.

[34]EckhardtM, ZhangW, GrossAM, et al., 2018. Multiple routes to oncogenesis are promoted by the human papillomavirus-host protein network. Cancer Discov, 8(11):1474-1489.

[35]FekairiS, ScaglioneS, ChahwanC, et al., 2009. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell, 138(1):78-89.

[36]FengW, LiuCZ, SpinozziS, et al., 2020. Identifying the cardiac dyad proteome in vivo by a BioID2 knock-in strategy. Circulation, 141(11):940-942.

[37]FengWJ, GuoYY, HuangJ, et al., 2016. TRAIP regulates replication fork recovery and progression via PCNA. Cell Discov, 2:16016.

[38]FleckO, NielsenO, 2004. DNA repair. J Cell Sci, 117(4):515-517.

[39]FriedbergEC, McDanielLD, SchultzRA, 2004. The role of endogenous and exogenous DNA damage and mutagenesis. Curr Opin Genet Dev, 14(1):5-10.

[40]GaoXD, TuLC, MirA, et al., 2018. C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nat Methods, 15(6):433-436.

[41]GavinAC, BoscheM, KrauseR, et al., 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415(6868):141-147.

[42]GavinAC, AloyP, GrandiP, et al., 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature, 440(7084):631-636.

[43]GheiratmandL, CoyaudE, GuptaGD, et al., 2019. Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites. EMBO J, 38(14):e101109.

[44]GhezraouiH, OliveiraC, BeckerJR, et al., 2018. 53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ. Nature, 560(7716):122-127.

[45]GhosalG, LeungJWC, NairBC, et al., 2012. Proliferating cell nuclear antigen (PCNA)-binding protein C1orf124 is a regulator of translesion synthesis. J Biol Chem, 287(41):34225-34233.

[46]GoCD, KnightJDR, RajasekharanA, et al., 2019. A proximity biotinylation map of a human cell. bioRxiv, preprint.

[47]Gonatopoulos-PournatzisT, WuMK, BraunschweigU, et al., 2018. Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons. Mol Cell, 72(3):510-524.e12.

[48]GongZH, ChenJJ, 2011. E3 ligase RFWD3 participates in replication checkpoint control. J Biol Chem, 286(25):22308-22313.

[49]GordonDE, JangGM, BouhaddouM, et al., 2020. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816):459-468.

[50]GuptaGD, 脡Coyaud, Gon莽alvesJ, et al., 2015. A dynamic protein interaction landscape of the human centrosome-cilium interface. Cell, 163(6):1484-1499.

[51]GuptaR, SomyajitK, NaritaT, et al., 2018. DNA repair network analysis reveals shieldin as a key regulator of NHEJ and PARP inhibitor sensitivity. Cell, 173(4):972-988.e23.

[52]HanJ, LiuT, HuenMS, et al., 2014. SIVA1 directs the E3 ubiquitin ligase RAD18 for PCNA monoubiquitination. J Cell Biol, 205(6):811-827.

[53]HanYS, BranonTC, MartellJD, et al., 2019. Directed evolution of split APEX2 peroxidase. ACS Chem Biol, 14(4):619-635.

[54]HavugimanaPC, HartGT, NepuszT, et al., 2012. A census of human soluble protein complexes. Cell, 150(5):1068-1081.

[55]HeinMY, HubnerNC, PoserI, et al., 2015. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell, 163(3):712-723.

[56]HoY, GruhlerA, HeilbutA, et al., 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415(6868):180-183.

[57]HoeijmakersJH, 2009. DNA damage, aging, and cancer. N Engl J Med, 361(15):1475-1485.

[58]HolthenrichA, DrexlerHCA, ChehabT, et al., 2019. Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von Willebrand factor secretion. Blood, 134(12):979-982.

[59]HungV, ZouP, RheeHW, et al., 2014. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell, 55(2):332-341.

[60]HungV, UdeshiND, LamSS, et al., 2016. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat Protoc, 11(3):456-475.

[61]HuttlinEL, TingL, BrucknerRJ, et al., 2015. The BioPlex network: a systematic exploration of the human interactome. Cell, 162(2):425-440.

[62]HuttlinEL, BrucknerRJ, PauloJA, et al., 2017. Architecture of the human interactome defines protein communities and disease networks. Nature, 545(7655):505-509.

[63]HuttlinEL, BrucknerRJ, Navarrete-PereaJ, et al., 2020. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. bioRxiv, preprint.

[64]IsabelleM, MoreelX, Gagn茅JP, et al., 2010. Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry. Proteome Sci, 8:22.

[65]J盲gerS, CimermancicP, GulbahceN, et al., 2012. Global landscape of HIV-human protein complexes. Nature, 481(7381):365-370.

[66]JiricnyJ, 2006. The multifaceted mismatch-repair system. Nat Rev Mol Cell Biol, 7(5):335-346.

[67]KadyrovFA, DzantievL, ConstantinN, et al., 2006. Endonucleolytic function of MutL伪 in human mismatch repair. Cell, 126(2):297-308.

[68]KaufmannT, GrishkovskayaI, PolyanskyAA, et al., 2017. A novel non-canonical PIP-box mediates PARG interaction with PCNA. Nucleic Acids Res, 45(16):9741-9759.

[69]KimDI, RouxKJ, 2016. Filling the void: proximity-based labeling of proteins in living cells. Trends Cell Biol, 26(11):804-817.

[70]KimDI, BirendraKC, ZhuWH, et al., 2014. Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proc Natl Acad Sci USA, 111(24):E2453-E2461.

[71]KimDI, JensenSC, NobleKA, et al., 2016. An improved smaller biotin ligase for BioID proximity labeling. Mol Biol Cell, 27(8):1188-1196.

[72]KimH, HuangJ, ChenJJ, 2007a. CCDC98 is a BRCA1-BRCT domain-binding protein involved in the DNA damage response. Nat Struct Mol Biol, 14(8):710-715.

[73]KimH, ChenJJ, YuXC, 2007b. Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response. Science, 316(5828):1202-1205.

[74]KristensenAR, GsponerJ, FosterLJ, 2012. A high-throughput approach for measuring temporal changes in the interactome. Nat Methods, 9(9):907-909.

[75]KroganNJ, CagneyG, YuHY, et al., 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440(7084):637-643.

[76]LamSS, MartellJD, KamerKJ, et al., 2015. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods, 12(1):51-54.

[77]LaranceM, KirkwoodKJ, TintiM, et al., 2016. Global membrane protein interactome analysis using in vivo crosslinking and mass spectrometry-based protein correlation profiling. Mol Cell Proteomics, 15(7):2476-2490.

[78]le Guerrou茅F, EckF, JungJ, et al., 2017. Autophagosomal content profiling reveals an LC3C-dependent piecemeal mitophagy pathway. Mol Cell, 68(4):786-796.e6.

[79]LeeYC, ZhouQ, ChenJJ, et al., 2016. RPA-binding protein ETAA1 is an ATR activator involved in DNA replication stress response. Curr Biol, 26(24):3257-3268.

[80]LeungJWC, WangYC, FongKW, et al., 2012. Fanconi anemia (FA) binding protein FAAP20 stabilizes FA complementation group A (FANCA) and participates in interstrand cross-link repair. Proc Natl Acad Sci USA, 109(12):4491-4496.

[81]LeungJWC, MakharashviliN, AgarwalP, et al., 2017. ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair. Genes Dev, 31(3):260-274.

[82]LiGM, 2008. Mechanisms and functions of DNA mismatch repair. Cell Res, 18(1):85-98.

[83]LiMH, JohnsonJR, TruongB, et al., 2019. Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. Nat Microbiol, 4(6):985-995.

[84]LiS, ChenPL, SubramanianT, et al., 1999. Binding of CtIP to the BRCT repeats of BRCA1 involved in the transcription regulation of p21 is disrupted upon DNA damage. J Biol Chem, 274(16):11334-11338.

[85]LiX, WangWQ, WangJD, et al., 2015. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Mol Syst Biol, 11(1):775.

[86]LiX, GaoM, ChoiJM, et al., 2017. Clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-coupled affinity purification/mass spectrometry analysis revealed a novel role of neurofibromin in mTOR signaling. Mol Cell Proteomics, 16(4):594-607.

[87]LingC, IshiaiM, AliAM, et al., 2007. FAAP100 is essential for activation of the Fanconi anemia-associated DNA damage response pathway. EMBO J, 26(8):2104-2114.

[88]LiuF, HeckAJR, 2015. Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry. Curr Opin Struct Biol, 35:100-108.

[89]LiuF, RijkersDTS, PostH, et al., 2015. Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nat Methods, 12(12):1179-1184.

[90]LiuF, L枚sslP, RabbittsBM, et al., 2018. The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes. Mol Cell Proteomics, 17(2):216-232.

[91]LiuT, GhosalG, YuanJS, et al., 2010. FAN1 acts with FANCI-FANCD2 to promote DNA interstrand cross-link repair. Science, 329(5992):693-696.

[92]LiuWS, SongHP, ChenQ, et al., 2018. Recent advances in the selection and identification of antigen-specific nanobodies. Mol Immunol, 96:37-47.

[93]LiuXN, SalokasK, TameneF, et al., 2018. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun, 9:1188.

[94]LiuZX, WuJX, YuXC, 2007. CCDC98 targets BRCA1 to DNA damage sites. Nat Struct Mol Biol, 14(8):716-720.

[95]LordCJ, AshworthA, 2012. The DNA damage response and cancer therapy. Nature, 481(7381):287-294.

[96]LossaintG, LarroqueM, RibeyreC, et al., 2013. FANCD2 binds MCM proteins and controls replisome function upon activation of S phase checkpoint signaling. Mol Cell, 51(5):678-690.

[97]LubinA, ZhangL, ChenH, et al., 2014. A human XPC protein interactome鈥攁 resource. Int J Mol Sci, 15(1):141-158.

[98]MackayC, D茅claisAC, LundinC, et al., 2010. Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2. Cell, 142(1):65-76.

[99]MalovannayaA, LanzRB, JungSY, et al., 2011. Analysis of the human endogenous coregulator complexome. Cell, 145(5):787-799.

[100]Mar茅chalA, ZouL, 2015. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res, 25(1):9-23.

[101]Mar茅chalA, LiJM, JiXY, et al., 2014. PRP19 transforms into a sensor of RPA-ssDNA after DNA damage and drives ATR activation via a ubiquitin-mediated circuitry. Mol Cell, 53(2):235-246.

[102]MartellJD, DeerinckTJ, SancakY, et al., 2012. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat Biotechnol, 30(11):1143-1148.

[103]MateusA, KurzawaN, BecherI, et al., 2020. Thermal proteome profiling for interrogating protein interactions. Mol Syst Biol, 16(3):e9232.

[104]MeeteiAR, de WinterJP, MedhurstAL, et al., 2003. A novel ubiquitin ligase is deficient in Fanconi anemia. Nat Genet, 35(2):165-170.

[105]MirmanZ, LottersbergerF, TakaiH, et al., 2018. 53BP1-RIF1-shieldin counteracts DSB resection through CST- and Pol伪-dependent fill-in. Nature, 560(7716):112-116.

[106]MirrashidiKM, ElwellCA, VerschuerenE, et al., 2015. Global mapping of the Inc-human interactome reveals that retromer restricts Chlamydia infection. Cell Host Microbe, 18(1):109-121.

[107]MohniKN, WesselSR, ZhaoRX, et al., 2019. HMCES maintains genome integrity by shielding abasic sites in single-strand DNA. Cell, 176(1-2):144-153.e13.

[108]MostofaAGM, PunganuruSR, MadalaHR, et al., 2018. S-phase specific downregulation of human O6-methylguanine DNA methyltransferase (MGMT) and its serendipitous interactions with PCNA and p21cip1 proteins in glioma cells. Neoplasia, 20(4):305-323.

[109]MuYH, LouJM, SrivastavaM, et al., 2016. SLFN11 inhibits checkpoint maintenance and homologous recombination repair. EMBO Rep, 17(1):94-109.

[110]Mu帽ozIM, HainK, D茅claisAC, et al., 2009. Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. Mol Cell, 35(1):116-127.

[111]MuyldermansS, 2013. Nanobodies: natural single-domain antibodies. Annu Rev Biochem, 82:775-797.

[112]MyersSA, WrightJ, PecknerR, et al., 2018. Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling. Nat Methods, 15(6):437-439.

[113]NegriniS, GorgoulisVG, HalazonetisTD, 2010. Genomic instability鈥攁n evolving hallmark of cancer. Nat Rev Mol Cell Biol, 11(3):220-228.

[114]NitureSK, DoneanuCE, VeluCS, et al., 2005. Proteomic analysis of human O6-methylguanine-DNA methyltransferase by affinity chromatography and tandem mass spectrometry. Biochem Biophys Res Commun, 337(4):1176-1184.

[115]NoordermeerSM, AdamS, SetiaputraD, et al., 2018. The shieldin complex mediates 53BP1-dependent DNA repair. Nature, 560(7716):117-121.

[116]OhtaS, ShiomiY, SugimotoK, et al., 2002. A proteomics approach to identify proliferating cell nuclear antigen (PCNA)-binding proteins in human cell lysates. Identification of the human CHL12/RFCs2鈥?article-title>5 complex as a novel PCNA-binding protein. J Biol Chem, 277(43):40362-40367.

[117]OlsonMG, WidnerRE, JorgensonLM, et al., 2019. Proximity labeling to map host-pathogen interactions at the membrane of a bacterium-containing vacuole in Chlamydia trachomatis-infected human cells. Infect Immun, 87(11):e0053719.

[118]O'ReillyFJ, RappsilberJ, 2018. Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology. Nat Struct Mol Biol, 25(11):1000-1008.

[119]PennBH, NetterZ, JohnsonJR, et al., 2018. An Mtb-human protein鈥抪rotein interaction map identifies a switch between host antiviral and antibacterial responses. Mol Cell, 71(4):637-648.e5.

[120]Pili茅PG, TangC, MillsGB, et al., 2019. State-of-the-art strategies for targeting the DNA damage response in cancer. Nat Rev Clin Oncol, 16(2):81-104.

[121]PrasadR, WilliamsJG, HouEW, et al., 2012. Pol 尾 associated complex and base excision repair factors in mouse fibroblasts. Nucleic Acids Res, 40(22):11571-11582.

[122]PrasadR, DyrkheevaN, WilliamsJ, et al., 2015. Mammalian base excision repair: functional partnership between PARP-1 and APE1 in AP-site repair. PLoS ONE, 10(5):e0124269.

[123]RamageHR, KumarGR, VerschuerenE, et al., 2015. A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Mol Cell, 57(2):329-340.

[124]RamanathanM, MajzoubK, RaoDS, et al., 2018. RNA鈥抪rotein interaction detection in living cells. Nat Methods, 15(3):207-212.

[125]RappoldI, IwabuchiK, DateT, et al., 2001. Tumor suppressor p53 binding protein 1 (53bp1) is involved in DNA damage鈥抯ignaling pathways. J Cell Biol, 153(3):613-620.

[126]ReardonJT, SancarA, 2006. Purification and characterization of Escherichia coli and human nucleotide excision repair enzyme systems. Methods Enzymol, 408:189-213.

[127]ReesJS, LiXW, PerrettS, et al., 2015. Protein neighbors and proximity proteomics. Mol Cell Proteomics, 14(11):2848-2856.

[128]RheeHW, ZouP, UdeshiND, et al., 2013. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science, 339(6125):1328-1331.

[129]RigautG, ShevchenkoA, RutzB, et al., 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol, 17(10):1030-1032.

[130]RobertsonAB, KlunglandA, RognesT, et al., 2009. DNA repair in mammalian cells. Cell Mol Life Sci, 66(6):981-993.

[131]RobuM, ShahRG, PurohitNK, et al., 2017. Poly(ADP-ribose) polymerase 1 escorts XPC to UV-induced DNA lesions during nucleotide excision repair. Proc Natl Acad Sci USA, 114(33):E6847-E6856.

[132]Rodr铆guezA, D'AndreaA, 2017. Fanconi anemia pathway. Curr Biol, 27(18):R986-R988.

[133]RouxKJ, KimDI, RaidaM, et al., 2012. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol, 196(6):801-810.

[134]RouxKJ, KimDI, BurkeB, 2013. BioID: a screen for protein鈥抪rotein interactions. Curr Protoc Protein Sci, 74(1):19.23.1-19.23.14. https://Vdoi.org/10.1002/0471140864.ps1923s74

[135]SavitskiMM, ReinhardFBM, FrankenH, et al., 2014. Tracking cancer drugs in living cells by thermal profiling of the proteome. Science, 346(6205):1255784.

[136]SchenstromSM, RebulaCA, TathamMH, et al., 2018. Expanded interactome of the intrinsically disordered protein Dss1. Cell Rep, 25(4):862-870.

[137]SchmidtTGM, SkerraA, 2007. The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins. Nat Protocols, 2(6):1528-1535.

[138]SchmidtmannE, AntonT, RombautP, et al., 2016. Determination of local chromatin composition by CasID. Nucleus, 7(5):476-484.

[139]SchoppIM, B茅thuneJ, 2018. Split-BioID鈥攑roteomic analysis of context-specific protein complexes in their native cellular environment. J Vis Exp, (134):e57479.

[140]SchoppIM, Amaya RamirezCC, DebeljakJ, et al., 2017. Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes. Nat Commun, 8:15690.

[141]SchweppeDK, HardingC, ChavezJD, et al., 2015. Host-microbe protein interactions during bacterial infection. Chem Biol, 22(11):1521-1530.

[142]SchweppeDK, ChavezJD, LeeCF, et al., 2017. Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proc Natl Acad Sci USA, 114(7):1732-1737.

[143]ScottDE, BaylyAR, AbellC, et al., 2016. Small molecules, big targets: drug discovery faces the protein鈥抪rotein interaction challenge. Nat Rev Drug Discov, 15(8):533-550.

[144]ScullyR, ChenJJ, PlugA, et al., 1997. Association of BRCA1 with Rad51 in mitotic and meiotic cells. Cell, 88(2):265-275.

[145]ScullyR, PandayA, ElangoR, et al., 2019. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat Rev Mol Cell Biol, 20(11):698-714.

[146]ShahPS, LinkN, JangGM, et al., 2018. Comparative flavivirus-host protein interaction mapping reveals mechanisms of dengue and Zika virus pathogenesis. Cell, 175(7):1931-1945.e18.

[147]SharanSK, MorimatsuM, AlbrechtU, et al., 1997. Embryonic lethality and radiation hypersensitivity mediated by RAD51 in mice lacking BRCA2. Nature, 386(6627):804-810.

[148]SobhianB, ShaoGZ, LilliDR, et al., 2007. RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science, 316(5828):1198-1202.

[149]SowaME, BennettEJ, GygiSP, et al., 2009. Defining the human deubiquitinating enzyme interaction landscape. Cell, 138(2):389-403.

[150]SrivastavaM, ChenZ, ZhangHM, et al., 2018. Replisome dynamics and their functional relevance upon DNA damage through the PCNA interactome. Cell Rep, 25(13):3869-3883.e4.

[151]SrivastavaM, SuD, ZhangHM, et al., 2020. HMCES safeguards replication from oxidative stress and ensures error-free repair. EMBO Rep, 21(6):e49123.

[152]StaceyRG, SkinniderMA, ScottNE, et al., 2017. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). BMC Bioinformatics, 18:457.

[153]St-DenisN, GuptaGD, LinZY, et al., 2016. Phenotypic and interaction profiling of the human phosphatases identifies diverse mitotic regulators. Cell Rep, 17(9):2488-2501.

[154]StukalovA, GiraultV, GrassV, et al., 2020. Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV. bioRxiv, preprint.

[155]SuDX, MaS, ShanL, et al., 2018. Ubiquitin-specific protease 7 sustains DNA damage response and promotes cervical carcinogenesis. J Clin Invest, 128(10):4280-4296.

[156]SungP, KleinH, 2006. Mechanism of homologous recombination: mediators and helicases take on regulatory functions. Nat Rev Mol Cell Biol, 7(10):739-750.

[157]SvendsenJM, SmogorzewskaA, SowaME, et al., 2009. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Cell, 138(1):63-77.

[158]SySMH, HuenMSY, ChenJJ, 2009. PALB2 is an integral component of the BRCA complex required for homologous recombination repair. Proc Natl Acad Sci USA, 106(17):7155-7160.

[159]TadiSK, Tellier-Leb猫gueC, NemozC, et al., 2016. PAXX is an accessory c-NHEJ factor that associates with Ku70 and has overlapping functions with XLF. Cell Rep, 17(2):541-555.

[160]TanCSH, GoKD, BisteauX, et al., 2018. Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells. Science, 359(6380):1170-1177.

[161]ThomashevskiA, HighAA, DrozdM, et al., 2004. The Fanconi anemia core complex forms four complexes of different sizes in different subcellular compartments. J Biol Chem, 279(25):26201-26209.

[162]Trinkle-MulcahyL, 2019. Recent advances in proximity-based labeling methods for interactome mapping. F1000Res, 8:135.

[163]UnnoJ, ItayaA, TaokaM, et al., 2014. FANCD2 binds CtIP and regulates DNA-end resection during DNA interstrand crosslink repair. Cell Rep, 7(4):1039-1047.

[164]WachiS, YonedaK, WuRE, 2005. Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics, 21(23):4205-4208.

[165]WanCH, BorgesonB, PhanseS, et al., 2015. Panorama of ancient metazoan macromolecular complexes. Nature, 525(7569):339-344.

[166]WanL, LouJM, XiaYS, et al., 2013. hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity. EMBO Rep, 14(12):1104-1112.

[167]WangB, MatsuokaS, BallifBA, et al., 2007. Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response. Science, 316(5828):1194-1198.

[168]WangJD, AroumougameA, LobrichM, et al., 2014. PTIP associates with Artemis to dictate DNA repair pathway choice. Genes Dev, 28(24):2693-2698.

[169]WangY, CortezD, YazdiP, et al., 2000. BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev, 14(8):927-939.

[170]WongAKC, OrmondePA, PeroR, et al., 1998. Characterization of a carboxy-terminal BRCA1 interacting protein. Oncogene, 17(18):2279-2285.

[171]WuLC, WangZW, TsanJT, et al., 1996. Identification of a ring protein that can interact in vivo with the BRCA1 gene product. Nat Genet, 14(4):430-440.

[172]WuWW, RokutandaN, TakeuchiJ, et al., 2018. HERC2 facilitates BLM and WRN helicase complex interaction with RPA to suppress G-quadruplex DNA. Cancer Res, 78(22):6371-6385.

[173]WuX, PetriniJH, HeineWF, et al., 2000. Independence of R/M/N focus formation and the presence of intact BRCA1. Science, 289(5476):11.

[174]WuX, ChavezJD, SchweppeDK, et al., 2016. In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Nat Commun, 7:13414.

[175]XiaB, ShengQ, NakanishiK, et al., 2006. Control of BRCA2 cellular and clinical functions by a nuclear partner, PALB2. Mol Cell, 22(6):719-729.

[176]XingMT, YangMR, HuoW, et al., 2015. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway. Nat Commun, 6:6233.

[177]XueMM, HouJJ, WangLL, et al., 2017. Optimizing the fragment complementation of APEX2 for detection of specific protein鈥抪rotein interactions in live cells. Sci Rep, 7:12039.

[178]YanZJ, DelannoyM, LingC, et al., 2010. A histone-fold complex and FANCM form a conserved DNA-remodeling complex to maintain genome stability. Mol Cell, 37(6):865-878.

[179]YanZJ, GuoR, ParamasivamM, et al., 2012. A ubiquitin-binding protein, FAAP20, links RNF8-mediated ubiquitination to the Fanconi anemia DNA repair network. Mol Cell, 47(1):61-75.

[180]YiCQ, HeC, 2013. DNA repair by reversal of DNA damage. Cold Spring Harb Perspect Biol, 5:a012575.

[181]YounJY, DunhamWH, HongSJ, et al., 2018. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies. Mol Cell, 69(3):517-532.e11.

[182]YuX, WuLC, BowcockAM, et al., 1998. The C-terminal (BRCT) domains of brca1 interact in vivo with CtIP, a protein implicated in the CtBP pathway of transcriptional repression. J Biol Chem, 273(39):25388--25392.

[183]ZhangAL, PengB, HuangP, et al., 2017. The p53-binding protein 1-Tudor-interacting repair regulator complex participates in the DNA damage response. J Biol Chem, 292(16):6461-6467.

[184]ZhangD, ZauggK, MakTW, et al., 2006. A role for the deubiquitinating enzyme USP28 in control of the DNA-damage response. Cell, 126(3):529-542.

[185]ZhangF, MaJL, WuJX, et al., 2009. PALB2 links BRCA1 and BRCA2 in the DNA-damage response. Curr Biol, 19(6):524-529.

[186]ZhangHM, ChenZ, YeY, et al., 2019. SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair. Nucleic Acids Res, 47(19):10181-10201.

[187]ZhongQ, ChenCF, LiS, et al., 1999. Association of BRCA1 with the hRad50-hMre11-p95 complex and the DNA damage response. Science, 285(5428):747-750.

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