In vitro and in vivo CRISPR gene editing with MAD7€¦ · Genomic DNA from untreated cells were used as control (lane 5). We compared gene editing efficiency of MAD7:guide RNA plasmids

Conclusions• Comparison of MAD7 and Cas9 editing efficiencies shows that:

• MAD7 editing occurs with most tested guide RNAs.• MAD7 editing efficiency is similar to the range observed for Cas9.• MAD7 editing efficiencies vary depending on the target sequence and additional work is

required to determine the criteria for best target sequence selection.• MAD7 editing efficiencies vary depending on the nuclease source (expression plasmid or

purified protein).• Although, the results with ssODN repair templates suggest MAD7 can be used for gene

knock-in for targeted gene repair, the precision of these repairs have not been assessed by DNA sequencing.

• MAD7 was very effective in generating deletions in mouse embryos, producing both heterozygous and homozygous embryos at the ROSA 26 locus.

• Both mRNA or protein formats of MAD7 were efficient in generating indels in mouse embryos when delivered by micro-injections.

• MAD7 can be an alternative endonuclease for gene knockout in mammalian systems and can be a good option for editing in targets that lack an NGG PAM.

AbstractMAD7 is a Class 2 Type V-A CRISPR-Cas system isolated from Eubacterium rectale and re-engineered by Inscripta (Boulder, CO). Analogous to Cas9, it is an RNA-guided nuclease with a diverse protein structure, mechanism of action, and has demonstrated gene editing activity in E. coli and yeast cells. Similar to Acidaminococcus sp. Cas12a, MAD7 does not require a tracrRNA and prefers T-rich PAMs (TTTV and CTTV). To investigate the utility of MAD7 as another tool in the arsenal for genome engineering, we evaluated MAD7 nuclease activity for gene knockout and precise knock-in in mammalian cells and embryos. Overall, MAD7 shows efficient gene editing activity in cell lines by transient transfection with MAD7 and guide RNA as plasmid DNA, as well as ribonucleoprotein complex (RNP) delivery with MAD7 protein and synthetic guide RNAs. Data from gene knock-in with single-strand oligonucleotide donors (ssODN) in cell lines and in mouse embryos will also be presented.

MAD7 enzyme

Evaluation of MAD7 editing activity with expressed guide RNAs

Evaluation of MAD7 editing activity with ribonucleoprotein complex

MAD7 efficiently created deletions at the ROSA 26 locus in C57BL/6J mouse embryos

MAD7-mediated gene knock-in using single strand DNA

MAD7 shows nuclease activity in mammalian cells with synthetic guide RNAs

MAD7 shows nuclease activity similar to SpyCas9 in in vitro assay

In vitro and in vivo CRISPR gene editing with MAD7Elena Maksimova1, John A. Schiel1, Guojun Zhao2, Hidevaldo B. Machado1, Emily M. Anderson1, Michael D’Angelo3, Philippe Collin3, Kevin Forbes2, Annaleen Vermeulen1, Zaklina Strezoska1, Anja van Brabant Smith1

1Dharmacon, a Horizon Discovery Company, Lafayette, CO, USA 2Horizon Discovery, St. Louis, MO, USA

3Horizon Discovery, Cambridge, UK

©2019 Horizon Discovery Group Company—All rights reserved. First published February 2019. UK Registered Head Office: Building 8100, Cambridge Research Park, Cambridge, CB25 9TL, United Kingdom. UK Registration No. 05363294 | UK VAT No. GB 189 1993 44

horizondiscovery.com

MAD7 is an RNA-guided nuclease isolated from Eubacterium rectale (WP_055225123.1) and classified as type V-A (Cpf1-like) Cas nuclease. MAD7 requires only a CRISPR RNA (crRNA) as the guide to create a staggered cut on the target DNA sequence. MAD7 guide RNA (gRNA) comprises a 35 nucleotide 5’ repeat (in black) sequence and a 21 nucleotide target specific spacer (N, in blue) directly adjacent to the 3’ end of the TTTV or CTTV PAM.

In vitro assays were carried out in cell-free extracts of HEK293T transiently transfected with MAD7, SpyCas9 (Cas9) or AsCpf1 (Cpf1) expression plasmids. (A) Guide RNA target sites were selected within PPIB or DNMT3B PCR amplicon substrates. (B) Guide RNA was added to cell-extracts and cleavage activity was evaluated by agarose gel electrophoresis. Most of the MAD7 guide RNA target sites tested show cutting activity similar to that observed with Cas9 control.

When MAD7 protein was complexed with synthetic guide RNAs (RNPs) and transfected into in HCT116 cells, gene editing efficiencies were similar to those observed with Cas9 RNPs. Again, we observed no difference in activity when using 42- or 56-nt guide RNAs with MAD7.

Editing activity was detected in co-transfections of MAD7, Cas9 or Cpf1-expressing plasmid with their respective synthetic guide RNAs. (A) PPIB and (B) DNMT3B gene editing activities (estimated percentage of indels) of were determined by a DNA mismatch detection assay with T7EI. MAD7 showed activity similar to AsCpf1 in U2OS cells. No significant difference in activity was observed with guide RNAs of 42- or 56-nt in length.

Knock-in by homology directed repair was evaluated by co-transfection of MAD7-expressing plasmid, synthetic guide RNA and oligonucleotide donors (ODN) in HEK293T cells. We tested ODNs with symmetric homology arms (HA) of 30- or 70-nt in length matching the coding (C) and non-coding (NC) sequences. Alternatively, we annealed both complementary ODNs to create a double-strand ODN (DS). ODN strands were modified on both ends with two phosphorothioates linkages to improve nuclease resistance. Insertion of the ODN introduces a NheI restriction site to the repaired target sequence which was detected by restriction fragment length polymorphism (RFLP) assay.

(A) Mouse Neuro2A cells were transfected with synthetic guide RNAs (targets #1-4, lanes 1-4) and MAD7 mRNA. Seventy-two hours post-transfection, genomic DNA was extracted and analyzed for indels by a DNA mismatch detection assay with Cel-I nuclease. Genomic DNA from untreated cells were used as control (lane 5).

We compared gene editing efficiency of MAD7:guide RNA plasmids to Cas9:sgRNA plasmids by co-transfection in HCT116 cells. We compared MAD7 target sites that were (A) distinct from the Cas9 target site, (B) fully overlapping or (C) seed overlapping with the Cas9 target site based on the work of Wang et al. 2018 (Genome Biol. 19:62). In general MAD7 activity was slightly less that Cas9 editing activity and no clear pattern could be discerned to generate rules for distinct or overlapping sites.

We repeated the micro-injection of the synthetic guide RNA #1 with (B) MAD7 mRNA or (C) complexed with MAD7 protein in additional mouse C57BL/6J embryos, respectively. These embryos were transferred to pseudo-pregnant females and collected between 13-14 days after implantation (E13-E14). The ROSA 26 target site in each embryo was again analyzed by DNA mismatch detection assay followed by Sanger sequencing (asterisk marks indicate the expected fragment sizes: 302, 201 and 101 bp).

Analyses of the E13-E14 embryos edited with MAD7 RNP showed efficient editing with at least 70% of the embryos carrying deletions of 1 to 26 bp. From embryos treated with MAD7 mRNA and synthetic guide RNA, only one carried deletions in both alleles (1/10) while from those treated with MAD7 RNP, two of four embryos carried deletions in both alleles.

5’-GUCAAAAGACCUUU UUAAUUUCUACUCUUGUAGAU NNNNNNNNNNNNNNNNNNNNN-3’

5'-GUCAAAAGACCUUU UUAAUUUCUACUCUUGUAGAU NNNNNNNNNNNNNNNNNNNNN-3'

PPIB F primer PPIB R primer

DNMT3B F primer DNMT3B R primer

PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr

MAD7 + 42-nt gRNA MAD7 + 56-nt gRNA Cpf1 PPIB gRNA No gRNA

Target amplicon MW bp

400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15

MAD7 + 42-nt gRNA No gRNA

MAD7 MW DNMT3B

Target amplicon

Cleaved fragments

MAD7 + 56-nt gRNA Cas9 DNMT3B cr/tracr

NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)

g4 g10 g17 56-nt gRNA

g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2

PPIB non-overlapping targets

UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2

Cas9 MAD7 UN NF1 fully overlapping target

Cas9 MAD7 UN

28 ± 2 23 ± 2

STAG2 fully overlapping target

Indels (%)

(B)

29 ± 1 14 ± 2

Cas9 MAD7 UN CACNA1D overlapping seed

Cas9 MAD7 UN

15 ± 1 6 ± 1

PPP1R12C overlapping seed

Indels (%)

(C)

Cas9 MAD7 42-nt MAD7 56-nt NTC

NF1 fully overlapping target

5 ± 1 6 ± 0 3 ± 0

Cas9 MAD7 42-nt MAD7 56-nt NTC STAG2 fully overlapping target

29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1

CACNA1D overlapping seed Cas9 MAD7 42-nt MAD7 56-nt NTC


<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1

gRNA 4 control gRNA NTC


gRNA 10 gRNA 21

MAD7 42-nt gRNA

gRNA 4 gRNA 10 gRNA 21

Cas9 MAD7 56-nt gRNA

6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)

DNA mismatch detection assay (T7EI)

UT 0%

Cas9 Nontargeting Ctrl #1 0%

PPIB MAD7 gRNA 1 6%

PPIB MAD7 gRNA 2 23%


PPIB Cas9 crRNA:tracrRNA 28%

nd nd nd nd nd nd nd nd nd

MAD7 gRNA 1 gRNA 2 gRNA 3 30-nt HA 30-nt HA 30-nt HA

C NC DS C NC DS C NC DS

UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd

gRNA 1 gRNA 2 70-nt HA 70-nt HA

C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4

Target # PAM Target sequence

1 TTTC TGGGAGTTCTCTGCTGCCTCC

2 TTTC TAGAAGATGGGCGGGAGTCTT

3 CTTC TAGAAAGACTGGAGTTGCAGA

4 TTTA AGCCTGCCCAGAAGACTCCCG

(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5

Embryo # Genotype Deletion (bp) sequence

MAD7 mRNA + guide RNA #1 1 wt - 2 wt - 3 het 4 4 het 26 5 het 7 6 het 9 7 hom 2, 4 8 wt - 9 het 11

10 het 1

MAD7 protein + guide RNA #1 1 hom 7, 6 2 het 11 3 hom 10, 15 4 wt -

Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA5'-GUCAAAAGACCUUU UUAAUUUCUACUCUUGUAGAU NNNNNNNNNNNNNNNNNNNNN-3'



PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA

50

100

150

200 300

1 2 3 4 5 MW MW




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

(A)

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

(B)

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

(C)



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

(A)

(B)

(C)


UT 0%


PPIB MAD7 gRNA 1 6%







UT 30-nt HA

40% nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

(B)

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW (C)

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






(A)

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA




PCR amplicon

504 bp

544 bp

(A)

g4

Cas9 PPIB

cr/tracr NTC

cr/tracr



400

200

50

Cleaved fragments

PPIB g8 g10 g14 g15


MAD7 MW DNMT3B

Target amplicon

Cleaved fragments


NTC cr/tracr

bp

400

200

50

(B)

% cutting

g17 g21 g24 g25 g26

100 93 77 100 100 85 99 99 21 98 99 83 46 100 100 85 100 99 19 100 97 8

% cutting 100 92 0 96 89 88 46 92 53 47 100 92 0 96 87 81 34 92 71 46 97

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

- -

- - -

- DNMT3B cr/tracr

g4 g8 g10 g14 g15 g17 g21 g24 g25 g26

g1 g2 g4 g6 g8 g9 g10 g13 g14 g15

DNMT3B

- cr/tr cr/tr

200

400

MW bp

MAD7 Cas9

200

400

- - UT MW bp

MAD7 Cpf1

11 2 5 17 16

11 3 4 9 12

NTC

DNMT3B

cr/tr cr/tr

(B)

g1 g6 g8 56-nt gRNA

g1 g6 g8 42-nt gRNA

g1 g1 56-nt 42-nt

Indels (%)

Indels (%)

6

PPIB

- g4

Indels (%)

cr/tr cr/tr

NTC MAD7 Cas9

Indels (%)

- UT UT

MAD7 Cpf1

10 0 18 19

13 16 0 20 25

cr/tr cr/tr

PPIB

g10 g17 42-nt gRNA

(A)


g4 g4 56-nt 42-nt

20 ± 0 20 ± 1 7 ± 1 26 ± 2


UN g4 Cas9 MAD7

g10 g17 sgRNA

Indels (%)

A

20 ± 2 15 ± 2


Cas9 MAD7 UN

28 ± 2 23 ± 2


Indels (%)

B

29 ± 1 14 ± 2


Cas9 MAD7 UN

15 ± 1 6 ± 1


Indels (%)

C



5 ± 1 6 ± 0 3 ± 0


29 ± 1 30 ± 0 30 ± 1 Indels (%)


8 ± 0 10 ± 1 5 ± 1



<1 <1 <1 Indels (%)

9 ± 2 25 ± 3 10 ± 1 30 ± 2 25 ± 1



gRNA 10 gRNA 21

MAD7 42-nt gRNA



6 ± 0 5 ± 2 Indels (%)

A

B

C

DNA mismatch detection assay (T7)EI

UT 0%


PPIB MAD7 gRNA 1 6%




Cells edited by MAD7 were able to use ssODN with 70 nt homology arms with sequences matching either strand. Knock-in efficiency with MAD7 was about half the observed Cas9 efficiency. While SpyCas9 may show higher efficiency depending on the strand sequence used, no preference was observed for MAD7. While knock-in efficiency is shown, the samples have not been sequenced to determine at this time.




UT 30-nt HA

nd nd nd

Cas9 crRNA:tracrRNA

C NC DS

19% 21% nd nd nd nd


C NC DS C NC DS

18% 20% nd

70-nt HA C NC DS

gRNA 3

MAD7

nd, not detected

B

50

100

150

200 250 300

*

*

*

MW 1 2 3 4 5 6 7 8 9 10 MW C

*

50

100

150 200 250 300

*

*

MW 1 2 3 4






A

*

50

100

150

200 250 300 *

*

MW MW 1 2 3 4 5



10 het 1


Genomic DNA

MAD7 Nuclease5'3'

5'

3'

5'3'

TTTVor

CTTV

crRNA

(A)

Documents

In vitro and in vivo CRISPR gene editing with MAD7€¦ · Genomic DNA from untreated cells were used as control (lane 5). We compared gene editing efficiency of MAD7:guide RNA plasmids