Recent advances in CRISPR research

References

[1] Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A (2017) RNA targeting with CRISPR-Cas13. Nature 550:280–284

[2] Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ, Ladha A, Joung J, Kirchgatterer P, Cox DBT, Zhang F (2019) A cytosine deaminase for programmable single-base RNA editing. Science 365:382–386

[3] Allergan (2019) Single ascending dose study in participants with LCA10. ClinicalTrial.gov Identifier: NCT03872479. (clinicaltrials.-gov/ct2/show/NCT03872479)

[4] Amoasii L, Hildyard JCW, Li H, Sanchez-Ortiz E, Mireault A, Caballero D, Harron R, Stathopoulou TR, Massey C, Shelton JM (2018) Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy. Science 362:86–91

[5] Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149–157

[6] Cameron P, Coons MM, Klompe SE, Lied AM, Smith SC, Vidal B, Donohoue PD, Rotstein T, Kohrs BW, Nyer DB (2019) Harnessing type I CRISPR-Cas systems for genome engineering in human cells. Nat Biotechnol 37(12):1471–1477

[7] Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–1491

[8] Chen B, Guan J, Huang B (2016a) Imaging Specific genomic DNA in living cells. Annu Rev Biophys 45:1–23

[9] Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B (2016b) Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Res 44:e75

[10] Chen B, Zou W, Xu H, Liang Y, Huang B (2018) Efficient labeling and imaging of protein-coding genes in living cells using CRISPRTag. Nat Commun 9:5065

[11] Cheng AW, Jillette N, Lee P, Plaskon D, Fujiwara Y, Wang W, Taghbalout A, Wang H (2016) Casilio: a versatile CRISPR-Cas9Pumilio hybrid for gene regulation and genomic labeling. Cell Res 26:254–257

[12] Chinese PLA General Hospital (2018) Study of PD-1 gene-knocked out mesothelin-directed CAR-T cells with the conditioning of PC in mesothelin positive multiple solid tumors. Identifier: NCT03747965.

[13] Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y (2019) Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas. Mol Cell 74(5):936–950

[14] Dreissig S, Schiml S, Schindele P, Weiss O, Rutten T, Schubert V, Gladilin E, Mette MF, Puchta H, Houben A (2017) Live-cell CRISPR imaging in plants reveals dynamic telomere movements. Plant J 91:565–573

[15] Duan J, Lu G, Hong Y, Hu Q, Mai X, Guo J, Si X, Wang F, Zhang Y (2018) Live imaging and tracking of genome regions in CRISPR/ dCas9 knock-in mice. Genome Biol 19:192

[16] Edraki A, Mir A, Ibraheim R, Gainetdinov I, Yoon Y, Song CQ, Cao Y, Gallant J, Xue W, Rivera-Perez JA (2018) A compact, highaccuracy Cas9 with a dinucleotide PAM for in vivo genome editing. Mol Cell 73(4):714–726

[17] Fu Y, Rocha PP, Luo VM, Raviram R, Deng Y, Mazzoni EO, Skok JA (2016) CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat Commun 7:11707

[18] Gao X, Tao Y, Lamas V, Huang M, Yeh WH, Pan B, Hu YJ, Hu JH, Thompson DB, Shu Y (2018) Treatment of autosomal dominant hearing loss by in vivo delivery of genome editing agents. Nature 553:217–221

[19] Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551:464–471

[20] Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, Keith Joung J (2019) CRISPR adenine and cytosine base editors with reduced RNA off-target activities. bioRxiv.

[21] Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J (2018) Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 359:1050–1055

[22] Han D, Hong Y, Mai X, Hu Q, Lu G, Duan J, Xu J, Si X, Zhang Y (2019) Systematical study of the mechanistic factors regulating genome dynamics in vivo by CRISPRsie. J Mol Cell Biol 11:1018–1020

[23] Jin S, Zong Y, Gao Q, Zhu Z, Wang Y, Qin P, Liang C, Wang D, Qiu JL, Zhang F (2019) Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364:292–295

[24] Karvelis T, Bigelyte G, Young JK, Hou Z, Zedaveinyte R, Pociute K, Silanskas A, Venclovas Č, Siksnys V (2019) PAM recognition by miniature CRISPR-Cas14 triggers programmable doublestranded DNA cleavage. bioRxiv.

[25] Kelliher T, Starr D, Su X, Tang G, Chen Z, Carter J, Wittich PE, Dong S, Green J, Burch E (2019) One-step genome editing of elite crop germplasm during haploid induction. Nat Biotechnol 37:287–292

[26] Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V (2019) A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565:91–95

[27] Kim D, Lim K, Kim ST, Yoon SH, Kim K, Ryu SM, Kim JS (2017) Genome-wide target specificities of CRISPR RNA-guided programmable deaminases. Nat Biotechnol 35:475–480

[28] Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH (2019) Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature 571:219–225

[29] Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M (2015) Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 350:823–826

[30] Knight SC, Tjian R, Doudna JA (2018) Genomes in focus: development and applications of CRISPR-Cas9 imaging technologies. Angew Chem Int Ed Engl 57:4329–4337

[31] Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–424

[32] Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 37:67–78

[33] Kwon C-T, Heo J, Lemmon ZH, Capua Y, Hutton SF, Van Eck J, Park SJ, Lippman ZB (2019) Rapid customization of Solanaceae fruit crops for urban agriculture. Nat Biotechnol 38:182–188

[34] Liu Z, Cai Y, Wang Y, Nie Y, Zhang C, Xu Y, Zhang X, Lu Y, Wang Z, Poo M (2018) Cloning of macaque monkeys by somatic cell nuclear transfer. Cell 172(881–887):e887

[35] Liu C, Zhong Y, Qi X, Chen M, Liu Z, Chen C, Tian X, Li J, Jiao Y, Wang D (2019a) Extension of the in vivo haploid induction system from diploid maize to hexaploid wheat. Plant Biotechnol J 18:316–318

[36] Liu J-J, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB (2019b) CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566:218–223

[37] Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016a) CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol 214:529–537

[38] Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016b) Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34:528–530

[39] Ma H, Tu LC, Naseri A, Chung YC, Grunwald D, Zhang S, Pederson T (2018) CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods 15:928–931

[40] Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P (2019) Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 18:67–83

[41] Mao S, Ying Y, Wu X, Krueger CJ, Chen AK (2019) CRISPR/dualFRET molecular beacon for sensitive live-cell imaging of nonrepetitive genomic loci. Nucleic Acids Res 47:e131

[42] Merkle T, Merz S, Reautschnig P, Blaha A, Li Q, Vogel P, Wettengel J, Li JB, Stafforst T (2019) Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat Biotechnol 37:133–138

[43] Morisaka H, Yoshimi K, Okuzaki Y, Gee P, Kunihiro Y, Sonpho E, Xu H, Sasakawa N, Naito Y, Nakada S (2019) CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun 10:5302

[44] Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW (2016) Programmable RNA Tracking in live cells with CRISPR/Cas9. Cell 165:488–496

[45] Nelson CE, Wu Y, Gemberling MP, Oliver ML, Waller MA, Bohning JD, Robinson-Hamm JN, Bulaklak K, Castellanos Rivera RM, Collier JH (2019) Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nat Med 25:427–432

[46] Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M (2017) Live cell imaging of lowand non-repetitive chromosome loci using CRISPR-Cas9. Nat Commun 8:14725

[47] Qiu PY, Jiang J, Liu Z, Cai YJ, Huang T, Wang Y, Liu QM, Nie YH, Liu F, Cheng JM (2019) BMAL1 knockout macaque monkeys display reduced sleep and psychiatric disorders. Natl Sci Rev 6:87–100

[48] Qu L, Yi Z, Zhu S, Wang C, Cao Z, Zhou Z, Yuan P, Yu Y, Tian F, Liu Z (2019) Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs. Nat Biotechnol 37:1059–1069

[49] Rees HA, Liu DR (2018) Base editing: precision chemistry on the genome and transcriptome of living cells. Nat Rev Genet 19 (12):770–780

[50] Shao S, Zhang W, Hu H, Xue B, Qin J, Sun C, Sun Y, Wei W, Sun Y (2016) Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system. Nucleic Acids Res 44:e86

[51] Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F (2019a) Engineering of CRISPR-Cas12b for human genome editing. Nat Commun 10:1–8

[52] Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F (2019b) RNA-guided DNA insertion with CRISPR-associated transposases. Science 365:48–53

[53] Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:635–646

[54] Teng F, Li J, Cui T, Xu K, Guo L, Gao Q, Feng G, Chen C, Han D, Zhou Q (2019) Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds. Genome Biol 20:1–6

[55] Vertex (2018a) A safety and efficacy study evaluating CTX001 in subjects with severe sickle cell disease. ClinicalTrial.gov Identi fier: NCT03745287. (clinicaltrials.gov/ct2/show/NCT03745287)

[56] Vertex (2018b) A safety and efficacy study evaluating CTX001 in subjects with transfusion-dependent β-thalassemia. ClinicalTrial. gov Identifier: NCT03655678. (clinicaltrials.gov/ct2/show/ NCT03655678)

[57] Wang S, Su JH, Zhang F, Zhuang X (2016) An RNA-aptamer-based two-color CRISPR labeling system. Sci Rep 6:26857

[58] Wang B, Zhu L, Zhao B, Zhao Y, Xie Y, Zheng Z, Li Y, Sun J, Wang H (2019a) Development of a haploid-inducer mediated genome editing system for accelerating maize breeding. Mol Plant 12:597–602

[59] Wang C, Liu Q, Shen Y, Hua Y, Wang J, Lin J, Wu M, Sun T, Cheng Z, Mercier R (2019b) Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat Biotechnol 37:283–286

[60] Wang H, Nakamura M, Abbott TR, Zhao D, Luo K, Yu C, Nguyen CM, Lo A, Daley TP, La Russa M (2019c) CRISPR-mediated live imaging of genome editing and transcription. Science 365:1301–1305

[61] Wu X, Mao S, Ying Y, Krueger CJ, Chen AK (2019) Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR based Platforms. Genom Proteom Bioinform 17:119–128

[62] Xue Y, Acar M (2018) Live-cell imaging of chromatin condensation dynamics by CRISPR. iScience 4:216–235

[63] Yan S, Tu Z, Liu Z, Fan N, Yang H, Yang S, Yang W, Zhao Y, Ouyang Z, Lai C (2018) A Huntingtin Knockin PIG model recapitulates features of selective neurodegeneration in Huntington’s disease. Cell 173(989–1002):e1013

[64] Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV (2019) Functionally diverse type V CRISPR-Cas systems. Science 363:88–91

[65] Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL (2019) Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems. Mol Cell 76(981–997):e987

[66] Ye H, Rong Z, Lin Y (2017) Live cell imaging of genomic loci using dCas9-SunTag system and a bright fluorescent protein. Protein Cell 8:853–855

[67] Zhang F (2019) Development of CRISPR-Cas systems for genome editing and beyond. Q Rev Biophys 52:e6

[68] Zhang W, Wan H, Feng G, Qu J, Wang J, Jing Y, Ren R, Liu Z, Zhang L, Chen Z (2018) SIRT6 deficiency results in developmental retardation in cynomolgus monkeys. Nature 560:661–665

[69] Zhang R, Liu J, Chai Z, Chen S, Bai Y, Zong Y, Chen K, Li J, Jiang L, Gao C (2019) Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. Nat Plants 5:480–485

[70] Zhong Y, Liu C, Qi X, Jiao Y, Wang D, Wang Y, Liu Z, Chen C, Chen B, Tian X (2019) Mutation of ZmDMP enhances haploid induction in maize. Nat Plants 5:575–580

[71] Zhou Y, Wang P, Tian F, Gao G, Huang L, Wei W, Xie XS (2017) Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res 27:298–301

[72] Zhou C, Sun Y, Yan R, Liu Y, Zuo E, Gu C, Han L, Wei Y, Hu X, Zeng R (2019a) Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 571:275–278

[73] Zhou Y, Sharma J, Ke Q, Landman R, Yuan JL, Chen H, Hayden DS, Fisher JW, Jiang MQ, Menegas W (2019b) Atypical behaviour and connectivity in SHANK3-mutant macaques. Nature 570:326–331

[74] Zuo E, Sun Y, Wei W, Yuan T, Ying W, Sun H, Yuan L, Steinmetz LM, Li Y, Yang H (2019) Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364:289

RIGHTS & PERMISSIONS

The Author(s)