Table S1. Abbreviations. Abbreviation Definition Cas - - PDF document

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table s1 abbreviations abbreviation definition cas crispr

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Table S1. Abbreviations. Abbreviation Definition Cas CRISPR-associated proteins Cas9 Native Cas9 nuclease Cas9n Cas9 nickase CRISPR Clustered, regularly interspaced short palindromic repeats CRISPRi CRISPR interference crRNA CRISPR RNA

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Table S1. Abbreviations. Abbreviation Definition Cas CRISPR-associated proteins Cas9 Native Cas9 nuclease Cas9n Cas9 nickase CRISPR Clustered, regularly interspaced short palindromic repeats CRISPRi CRISPR interference crRNA CRISPR RNA dCas9 Inactivated or ‘dead’ Cas9 DSB dsDNA break dsDNA Double-stranded DNA gRNA Guide RNA HDR Homology-directed repair indels Small insertions and deletions NHEJ Non-homologous end joining NLS Nuclear location signal PAM Protospacer adjacent motif RNAi RNA interference ssDNA Single-stranded DNA TAL Transcription activator-like repeat TALEN Transcription activator-like effector nuclease tracrRNA trans-acting CRISPR RNA ZF Zinc finger motif ZFN Zinc-finger nuclease

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Table S2. Application of Cas9-based tool in genome editing and transcriptional control.

Application Strategies Mutation types Organisms/cell types Target loci Efficiency Referen ces Genome editing Cas9 and tracrRNA:crRNA duplex NHEJ-induced indels Mouse Th 4.8-27% 1 Human HEK 293FT cells EMX1, PVALB 1.5-21% 1 Rice callus cells CAO1 2 DNA insertion Streptococcus pneumoniae srtA, bgaA, ermAM 100% 3 Escherichia coli rpsL 96% 3 DNA deletion Human HEK 293FT cells EMX1, PVALB 1.6% 1 Cas9 and gRNA NHEJ-induced indels Human K562, HEK 293FT and iPS cells AAVS1, DNMT3a/b, CLTA, CCR5, C4BPB 2-33% 4-7 Zebrafish embryos fh, apoea, th1, rgs4, tph1a, gsk3b, gata4/5, drd3, tia1l, etsrp 24.1-59.4% 7, 8 Drosophila preblastoderm embryos Yellow, rosy 7.7-75% 9 Caenorhabditis elegans germ line unc-119, dpy-11, dpy-13, klp-12, Y61A9LA.1, EGFP, lin-5, rol-1 0.5-80.3% 10, 11 Xenopus tropicalis embryos tyr, six3 100% 12 Saccharomyces cerevisiae CAN1 0.01-0.07% 13 Arabidopsis protoplast and seedlings AtPDS3,AtFLS2, AtRACK1b, AtRACK1c, GFP 1.1-5.6% in protoplast; 2.7% in leaf agroinfiltration 14, 15 Rice protoplast and callus cells OsMPK2/5, GFP, OsPDS, LAZY1, CAO1, Os02g23823, OsBADH2 3-38% in protoplast 2, 15- 17 Wheat protoplast TaMLO 28.5% 17 Tobacco protoplast and leaf NbPDS, GFP 37.7-38.5% in protoplast; 2.1- 4.8% in leaf agroinfiltration 14, 15, 18 Sorghum immature embryos GFP 28% 15 DNA insertion Human HEK293T and iPS cells AAVS1, eGFP 2.51% 4, 7 Zebrafish embryos etsrp 33.3% 7 Drosophila preblastoderm embryos Yellow 81.3% 9

C. elegansgerm line

F14E5,nmy-2, his-72, lin-31 9-32% 19

S. cerevisiae

CAN1 100% 13 Mouse Tet1/2, Sox2, Nanog, Oct4, 3’UTR, Mecp2 10-58% 20, 21 Arabidopsis protoplast CYCD3, YF-FP reporter 10.7-42% 14, 22, 23 Tobacco protoplast and leaf NbPDS 9% 14 Rice protoplast OsPDS 6.9% 17 DNA deletion Drosophila preblastoderm embryos Yellow 81.3% 9 Human K562 cells AAVS1 16.9% 4 Xenopus tropicalise mbryos six3 proximal promoter 50% 12 Cas9n and tracrRNA:crRNA duplex DNA insertion Human HEK 293FT cells EMX1 0.46% 1

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3 Double nicking by Cas9n-gRNA complex NHEJ-induced indels Human HEK293FT cells EMX1, DYRK1A, GRIN2B Up to 40% 24 Mouse zygotes Mecp2 24 NHEJ-mediated ligation Human HEK293FT EMX1 24 DNA insertion Human HUES62, HEK293FT cells EMX1 0.4-9.9% 24 DNA deletion Human HEK293FT cells DYRK1A 24 Transcriptional control dCas9 and tracrRNA:crRNA duplex Transcription repression

E. coli

gfp-mut2 and its promoter 100-fold repression 25

S. pneumoniae

bgaA 14- fold repression 25 dCas9 and gRNA Transcription repression

E. coli

mRFP, sfGFP, lacZ, lacI, crp, cya 300-fold repression individually*; 1,000-fold repression synergistically** 26 Human HEK293 cells EGFP 63% repression 26

S. cerevisiae

rTA-binding site of TetON-Venus reporter, CD71, CXCR4, AP1 enhancer, SP1 enhancer 115-fold repression 27 dCas9-effector and tracrRNA:crRNA duplex dCas9-ormega chimera-mediated activation

E. coli

lacZ, gfp-mut2 23-fold activation 25 dCas9-effector and gRNA dCas9-VP64 chimera-mediated activation Human HEK293 cells REX1, OCT4, SOX2, NANOG, tdTomato promoter, Gal4 UAS-GFP reporter 23-fold activation individually*; 30-fold activation synergistically** 27, 28 dCas9-KRAB chimera-mediated repression Human HEK293 cells EGFP, CD71, CXCR4, AP1 enhancer and SP1 enhancer 15-fold repression 27 dCas9-Mxi1 chimera-mediated repression

S. cerevisiae

TEF1-GFP 53-fold repression 27 dCas9 and gRNA-aptamer gRNA-MS2 chimera- mediated activation Human HEK 293T cells REX1 Up to 10-fold activation synergistically** 28 Individually*: the efficiency was produced by an individual gRNA. Synergistically**: the efficiency was produced by cooperative works of multiple gRNAs.

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