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Abstract: The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms, and holds tremendous promise in clinical applications. The efficiency and accuracy of the technology are partly determined by the target binding affinity and residence time of Cas9-single-guide RNA (sgRNA) at a given site. However, little attention has been paid to the effect of target binding affinity and residence duration on the repair of Cas9-induced DNA double-strand breaks (DSBs). We propose that the choice of DSB repair pathway may be altered by variation in the binding affinity and residence duration of Cas9-sgRNA at the cleaved target, contributing to significantly heterogeneous mutations in CRISPR/Cas9 genome editing. Here, we discuss the effect of Cas9-sgRNA target binding and residence on the choice of DSB repair pathway in CRISPR/Cas9 genome editing, and the opportunity this presents to optimize Cas9-based technology.

CRISPR/Cas9靶点结合与滞留影响基因编辑中DNA双链断裂修复途径选择

[1]AbadiS, YanWX, AmarD, et al., 2017. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Comput Biol, 13(10):e1005807.

[2]AllenF, CrepaldiL, AlsinetC, et al., 2019. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotechnol, 37(1):64-72.

[3]AndersC, NiewoehnerO, DuerstA, et al., 2014. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature, 513(7519):569-573.

[4]BakkenistCJ, KastanMB, 2015. Chromatin perturbations during the DNA damage response in higher eukaryotes. DNA Repair, 36:8-12.

[5]BhargavaR, OnyangoDO, StarkJM, 2016. Regulation of single-strand annealing and its role in genome maintenance. Trends Genet, 32(9):566-575.

[6]BisariaN, JarmoskaiteI, HerschlagD, 2017. Lessons from enzyme kinetics reveal specificity principles for RNA-guided nucleases in RNA interference and CRISPR-based genome editing. Cell Syst, 4(1):21-29.

[7]BlackfordAN, JacksonSP, 2017. ATM, ATR, and DNA-PK: the trinity at the heart of the DNA damage response. Mol Cell, 66(6):801-817.

[8]BoboilaC, AltFW, SchwerB, 2012. Classical and alternative end-joining pathways for repair of lymphocyte-specific and general DNA double-strand breaks. Adv Immunol, 116:1-49.

[9]BolukbasiMF, GuptaA, OikemusS, et al., 2015. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat Methods, 12(12):1150-1156.

[10]BoyleEA, AndreassonJOL, ChircusLM, et al., 2017. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc Natl Acad Sci USA, 114(21):5461-5466.

[11]BustamanteC, BryantZ, SmithSB, 2003. Ten years of tension: single-molecule DNA mechanics. Nature, 421(6921):423-427.

[12]CasiniA, OlivieriM, PetrisG, et al., 2018. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat Biotechnol, 36(3):265-271.

[13]CeccaldiR, SarangiP, D'AndreaAD, 2016. The Fanconi anaemia pathway: new players and new functions. Nat Rev Mol Cell Biol, 17(6):337-349.

[14]ChakrabartiAM, Henser-BrownhillT, MonserratJ, et al., 2019. Target-specific precision of CRISPR-mediated genome editing. Mol Cell, 73(4):699-713.e6.

[15]ChangHHY, WatanabeG, GerodimosCA, et al., 2016. Different DNA end configurations dictate which NHEJ components are most important for joining efficiency. J Biol Chem, 291(47):24377-24389.

[16]ChenBH, GilbertLA, CiminiBA, et al., 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell, 155(7):1479-1491.

[17]ChenJS, DagdasYS, KleinstiverBP, et al., 2017. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature, 550(7676):407-410.

[18]ChuVT, WeberT, WefersB, et al., 2015. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol, 33(5):543-548.

[19]ChuaiGH, MaHH, YanJF, et al., 2018. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biol, 19:80.

[20]CicciaA, ElledgeSJ, 2010. The DNA damage response: making it safe to play with knives. Mol Cell, 40(2):179-204.

[21]ClarkeR, HelerR, MacDougallMS, et al., 2018. Enhanced bacterial immunity and mammalian genome editing via RNA-polymerase-mediated dislodging of Cas9 from double-strand DNA breaks. Mol Cell, 71(1):42-55.e8.

[22]CongL, RanFA, CoxD, et al., 2013. Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121):819-823.

[23]DoenchJG, FusiN, SullenderM, et al., 2016. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol, 34(2):184-191.

[24]FengYL, XiangJF, KongN, et al., 2016. Buried territories: heterochromatic response to DNA double-strand breaks. Acta Biochim Biophys Sin (Shanghai), 48(7):594-602.

[25]FengYL, XiangJF, LiuSC, et al., 2017. H2AX facilitates classical non-homologous end joining at the expense of limited nucleotide loss at repair junctions. Nucleic Acids Res, 45(18):10614-10633.

[26]FuYF, SanderJD, ReyonD, et al., 2014. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol, 32(3):279-284.

[27]GallagherDN, HaberJE, 2018. Repair of a site-specific DNA cleavage: old-school lessons for Cas9-mediated gene editing. ACS Chem Biol, 13(2):397-405.

[28]GarneauJE, DupuisM脠, VillionM, et al., 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 468(7320):67-71.

[29]GaudelliNM, KomorAC, ReesHA, et al., 2017. Programmable base editing of A鈥 to G鈥 in genomic DNA without DNA cleavage. Nature, 551(7681):464-471.

[30]GilbertLA, LarsonMH, MorsutL, et al., 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell, 154(2):442-451.

[31]GuoT, FengYL, XiaoJJ, et al., 2018. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol, 19:170.

[32]HegazyYA, FernandoCM, TranEJ, 2020. The balancing act of R-loop biology: the good, the bad, and the ugly. J Biol Chem, 295(4):905-913.

[33]HiltonIB, D'IppolitoAM, VockleyCM, et al., 2015. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol, 33(5):510-517.

[34]HinzJM, LaugheryMF, WyrickJJ, 2015. Nucleosomes inhibit Cas9 endonuclease activity in vitro. Biochemistry, 54(48):7063-7066.

[35]HorvathP, BarrangouR, 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science, 327(5962):167-170.

[36]HsuPD, LanderES, ZhangF, 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6):1262-1278.

[37]HuJH, MillerSM, GeurtsMH, et al., 2018. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, 556(7699):57-63.

[38]IsaacRS, JiangFG, DoudnaJA, et al., 2016. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. eLife, 5:e13450.

[39]IvanovIE, WrightAV, CofskyJC, et al., 2020. Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling. Proc Natl Acad Sci USA, 117(11):5853-5860.

[40]JasinM, RothsteinR, 2013. Repair of strand breaks by homologous recombination. Cold Spring Harb Perspect Biol, 5(11):a012740.

[41]JasinM, HaberJE, 2016. The democratization of gene editing: insights from site-specific cleavage and double-strand break repair. DNA Repair, 44:6-16.

[42]JeonY, ChoiYH, JangYS, et al., 2018. Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Nat Commun, 9:2777.

[43]JiangFG, DoudnaJA, 2017. CRISPR-Cas9 structures and mechanisms. Ann Rev Biophys, 46:505-529.

[44]JinekM, ChylinskiK, FonfaraI, et al., 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096):816-821.

[45]JonesDL, LeroyP, UnosonC, et al., 2017. Kinetics of dCas9 target search in Escherichia coli. Science, 357(6358):1420-1424.

[46]KearnsNA, PhamH, TabakB, et al., 2015. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods, 12(5):401-403.

[47]KimD, LukK, WolfeSA, et al., 2019. Evaluating and enhancing target specificity of gene-editing nucleases and deaminases. Annu Rev Biochem, 88:191-220.

[48]KimS, KimD, ChoSW, et al., 2014. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res, 24(6): 1012-1019.

[49]KleinstiverBP, PrewMS, TsaiSQ, et al., 2015a. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat Biotechnol, 33(12):1293-1298.

[50]KleinstiverBP, PrewMS, TsaiSQ, et al., 2015b. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature, 523(7561):481-485.

[51]KleinstiverBP, PattanayakV, PrewMS, et al., 2016. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature, 529(7587):490-495.

[52]KnightSC, XieLQ, DengWL, et al., 2015. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science, 350(6262):823-826.

[53]KomorAC, KimYB, PackerMS, et al., 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 533(7603):420-424.

[54]LemosBR, KaplanAC, BaeJE, et al., 2018. CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles. Proc Natl Acad Sci USA, 115(9):E2040-E2047.

[55]LieberMR, 2010. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem, 79:181-211.

[56]LinS, StaahlBT, AllaRK, et al., 2014. Enhanced homology- directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife, 3:e04766.

[57]MaHH, NaseriA, Reyes-GutierrezP, et al., 2015. Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci USA, 112(10):3002-3007.

[58]MaHH, TuLC, NaseriA, et al., 2016. CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol, 214(5):529-537.

[59]MaliP, YangLH, EsveltKM, et al., 2013. RNA-guided human genome engineering via Cas9. Science, 339(6121):823-826.

[60]MaruyamaT, DouganSK, TruttmannMC, et al., 2015. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol, 33(5):538-542.

[61]NewtonMD, TaylorBJ, DriessenRPC, et al., 2019. DNA stretching induces Cas9 off-target activity. Nat Struct Mol Biol, 26(3):185-192.

[62]NishimasuH, RanFA, HsuPD, et al., 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell, 156(5):935-949.

[63]OuyangJ, LanL, ZouL, 2017. Regulation of DNA break repair by transcription and RNA. Sci China Life Sci, 60(10): 1081-1086.

[64]PatelSS, PandeyM, NandakumarD, 2011. Dynamic coupling between the motors of DNA replication: hexameric helicase, DNA polymerase, and primase. Curr Opin Chem Biol, 15(5):595-605.

[65]Perez-PineraP, KocakDD, VockleyCM, et al., 2013. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods, 10(10):973-976.

[66]PugetN, MillerKM, LegubeG, 2019. Non-canonical DNA/RNA structures during transcription-coupled double-strand break repair: roadblocks or Bona fide repair intermediates? DNA Repair, 81:102661.

[67]QiLS, LarsonMH, GilbertLA, et al., 2013. Repurposing CRISPR as an RNA-guided platform for sequence- specific control of gene expression. Cell, 152(5):1173-1183.

[68]RanFA, HsuPD, LinCY, et al., 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154(6):1380-1389.

[69]ReesHA, LiuDR, 2018. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat Rev Genet, 19(12):770-788.

[70]RichardsonCD, RayGJ, DeWittMA, et al., 2016. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol, 34(3):339-344.

[71]RichardsonCD, KazaneKR, FengSJ, et al., 2018. CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nat Genet, 50(8):1132-1139.

[72]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.

[73]SeolJH, ShimEY, LeeSE, 2018. Microhomology-mediated end joining: good, bad and ugly. Mutat Res, 809:81-87.

[74]ShouJ, LiJH, LiuYB, et al., 2018. Precise and predictable CRISPR chromosomal rearrangements reveal principles of Cas9-mediated nucleotide insertion. Mol Cell, 71(4):498-509.e4.

[75]SinghD, MallonJ, PoddarA, et al., 2018. Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). Proc Natl Acad Sci USA, 115(21):5444-5449.

[76]SlaymakerIM, GaoLY, ZetscheB, et al., 2016. Rationally engineered Cas9 nucleases with improved specificity. Science, 351(6268):84-88.

[77]SternbergSH, ReddingS, JinekM, et al., 2014. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490):62-67.

[78]SternbergSH, LaFranceB, KaplanM, et al., 2015. Conformational control of DNA target cleavage by CRISPR-Cas9. Nature, 527(7576):110-113.

[79]StrohkendlI, SaifuddinFA, RybarskiJR, et al., 2018. Kinetic basis for DNA target specificity of CRISPR-Cas12a. Mol Cell, 71(5):816-824.e3.

[80]SymingtonLS, GautierJ, 2011. Double-strand break end resection and repair pathway choice. Annu Rev Genet, 45:247-271.

[81]SzczelkunMD, TikhomirovaMS, SinkunasT, et al., 2014. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci USA, 111(27):9798-9803.

[82]TanakaH, YaoMC, 2009. Palindromic gene amplification鈥攁n evolutionarily conserved role for DNA inverted repeats in the genome. Nat Rev Cancer, 9(3):216-224.

[83]VerkuijlSAN, RotsMG, 2019. The influence of eukaryotic chromatin state on CRISPR-Cas9 editing efficiencies. Curr Opin Biotechnol, 55:68-73.

[84]WangHF, la RussaM, QiLS, 2016. CRISPR/Cas9 in genome editing and beyond. Annu Rev Biochem, 85:227-264.

[85]YehCD, RichardsonCD, CornJE, 2019. Advances in genome editing through control of DNA repair pathways. Nat Cell Biol, 21(12):1468-1478.

[86]ZetscheB, GootenbergJS, AbudayyehOO, et al., 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell, 163(3):759-771.

[87]ZhangQ, WenFC, ZhangSQ, et al., 2019. The post-PAM interaction of RNA-guided spCas9 with DNA dictates its target binding and dissociation. Sci Adv, 5(11):eaaw9807.

[88]ZhangSQ, ZhangQ, HouXM, et al., 2020. Dynamics of Staphylococcus aureus Cas9 in DNA target association and dissociation. EMBO Rep, 21:e50184.

[89]ZhangXH, ChenL, ZhuBY, et al., 2020. Increasing the efficiency and targeting range of cytidine base editors through fusion of a single-stranded DNA-binding protein domain. Nat Cell Biol, 22(6):740-750.

[90]ZhangYX, PanWY, ChenJ, 2019. p53 and its isoforms in DNA double-stranded break repair. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 20(6):457-466.

[91]ZhuX, ClarkeR, PuppalaAK, et al., 2019. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Nat Struct Mol Biol, 26(8):679-685.