Yangbin Gao and Yunde Zhao

Section of Cell and Developmental Biology,University of California San Diego,9500 Gilman Drive,La Jolla,CA 92093-0116,USA.＊Correspondence:yundezhao@ucsd.edu

INTRODUCTION

The CRISPR/Cas9 system(Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated endonuclease Cas9)has been shown to mediate efficient genome editing in human cells(Cong et al.2013;Mali et al.2013),mice(Li et al.2013a),rat(Li et al.2013b),zebrafish(Chang et al.2013;Hwang et al.2013),Caenorhabditis elegans(Chen et al.2013),Drosophila(Ren et al.2013),yeast(Cong et al.2013;DiCarlo et al.2013),Arabidopsis(Feng et al.2013),and crop plants(Feng et al.2013;Miao et al.2013;Shan et al.2013).CRISPR/Cas9 relies on RNA-guided DNA cleavage to generate double-stranded breaks(Haurwitz et al.2010).CRISPR provides a very simple approach for targeted gene disruption and targeted gene insertion.To disrupt a gene by CRISPR,only two components are needed:(1)the Cas9 protein that contains the nuclease domains,and(2)the guide RNA(gRNA)that provides sequence specificity to the target DNA.The first 20-nucleotide sequence at the 5′-end of the gRNA is complementary to the target sequence and it provides the specificity for the CRISPR/Cas9 system(Haurwitz et al.2010).The 3′portion of the gRNA forms certain secondary structures and is required for Cas9 activities.The gRNA brings the Cas9 nuclease to the specific target and subsequently Cas9 generates double-stranded breaks in the target DNA at the protospacer-adjacent motif(PAM)site.Non-homologous end-joining repair of the doublestranded breaks often leads to deletions or small insertions that disrupt the target DNA.

There are two major challenges in using CRISPR for targeted mutagenesis:(1)production of the gRNAs,and(2)analysis of the CRISPR-generated mutations.The first 20-nucleotide sequence of the gRNA is used to guide targeted DNA cleavage.Additional bases at the 5′-end of gRNA or other modifications may abolish the gRNA’s ability to guide DNA cleavage by Cas9(Haurwitz et al.2010).RNAs transcribed by RNA polymerase II(pol II),which is the polymerase responsible for the production of the majority of mRNAs,cannot be used as gRNAs because they undergo extensive processing and modification at both ends.Additionally,most mRNAs are actively transported from the nucleus into the cytoplasm after transcription,while the Cas9/gRNA only has access to the genomic DNA inside the nucleus.Most of the well-characterized promoters are transcribed by pol II and have not been used to produce gRNA for CRISPR.Therefore,promoters such as U3 and U6,which are transcribed by the RNA polymerase III(pol III)were previously chosen to produce gRNA in various organisms.There are many limitations to U6-or U3-based gRNA production.First,U6 snRNA and U3 snRNA are housekeeping genes and they are ubiquitously expressed.Therefore,they cannot be used to generate gRNAs with cell or tissue specificity.Second,the U6 and U3 promoters in many organisms have not been characterized,making it difficult to choose the correct U6/U3 promoters for CRISPR.Third,the U6 and U3 promoters are not suitable for routine in vitro production of gRNAs because RNA pol III is not commercially available.Furthermore,the U6 and U3 promoters limit the CRISPR target sequences to G(N)20GG and A(N)20GG,respectively.Improved methods for producing gRNAs in vivo are needed in order to conduct targeted mutagenesis with spatial and temporal control in a wide range of organisms.

The second challenge in using CRISPR for genome editing is detecting and analyzing the mutations generated.Mutations are often detected by enzyme digestion of a PCR product that contains the target region,followed by DNA sequencing.Restriction digestion can only work when a restriction site is altered and many useful mutations may not be detected by restriction digestion.CEL I-based enzyme digestion can also be used to detect mutations(Oleykowski et al.1998).However,CRISPR often generates many different mutations in a tissue or an organism,making a CEL I-based method less effective.We believe that the best way to detect mutations caused by CRISPR is to use the specific gRNA and Cas9 protein to digest the PCR products that contain the target sequence(Haurwitz et al.2010).However,such a method requires an easy and efficient way to produce gRNAs in vitro.

In this paper,we present a method that successfully overcomes the aforementioned challenges in using CRISPR for genome editing.We take advantage of the nuclease activity of ribozymes(Scott et al.1996;Nakano et al.2000)to design an artificial gene RGR(Ribozyme-gRNA-Ribozyme).We hypothesize that the primary transcripts of RGR undergo self-catalyzed cleavage to precisely release the designed gRNA.We show that gRNA is specifically released from the primary transcripts of RGR by self-processing in vitro.The produced gRNA efficiently guides Cas9-mediated cleavage of target DNA in vitro.Furthermore,we introduce the RGR gene into yeast under the control of the alcohol dehydrogenase 1(ADH1)promoter,which is transcribed by pol II,and we observe the targeted DNA cleavage in yeast.Our results demonstrate that production of gRNAs is no longer limited to a specialty promoter such as the U6 promoter,thereby enabling us to conduct genome editing with spatial and temporal precision if proper promoters are chosen.In addition,we demonstrate that the target sequences are no longer limited to G(N)20GG or A(N)20GG because our method does not require the specific G or A for transcription initiation for gRNA production as is the case for U6 and U3 promoters.We also show that the efficient production of gRNAs by in vitro transcription from a commonly used promoter such as SP6 makes it very easy to use gRNA and Cas9 to detect mutations caused by CRISPR/Cas9.

RESULTS

Design an RNA molecule with self-processing capacity for gRNA production

We took advantage of the nuclease activities of ribozymes that catalyze the cleavage at a specific site within an RNA molecule.We designed an RNA molecule(pre-gRNA)that was predicted to undergo self-catalyzed processing(Figure 1A).The RNA molecule we designed contained a Hammerhead(HH)type ribozyme(Pley et al.1994)at the 5′-end,a gRNA that targets a green fluorescent protein(GFP)gene in the middle,and a hepatitis delta virus(HDV)ribozyme(Ferre-D’Amare et al.1998)at the 3′-end(Figure 1A).After the self-cleavage at the predicated sites,the mature gRNA was released(Figure 1A).The gRNA was predicted to guide Cas9 to cut DNA at the targeted sites(Figure 1B).By altering only the first six nucleotides of the HH ribozyme,our design can be employed to generate gRNAs that target any DNA sequence with a PAM site(NGG).Previous CRISPR targets were limited to either G(N)20GG or A(N)20GG.

Production of a gRNA by in vitro transcription and self-processing

The designed pre-gRNA molecule can be generated by in vitro transcription of the corresponding DNA sequence,which we named the Ribozyme-gRNA-Ribozyme(RGR)gene(Figure 2A).We placed the RGR gene under the control of the SP6 promoter and conducted in vitro transcription using the commercially available SP6 RNA polymerase.As shown in Figure 2B,the primary transcripts of the RGR were selfprocessed into several RNA bands.The smallest RNA band was the predicted gRNA(Figure 2B).We introduced mutations in the HH ribozyme and in the HDV ribozyme individually to disrupt their self-processing ability.We also mutated the two ribozymes simultaneously.We then tested the self-processing ability of the mutated pre-gRNAs(Figure 2B,Lanes 2,3,and 4,respectively).Disruption of the two ribozymes simultaneously led to a complete failure to self-process the transcripts(Figure 2B,Lane 4).Inactivation of the HH ribozyme(5′-end)blocked the separation of the 5′-end ribozyme from the rest of the RNA molecule,but did not affect the processing of the 3′-end HDV ribozyme(Figure 2B,Lane 2).On the other hand,mutations in the HDV ribozyme only disrupted the removal of the 3′-end portion of the pre-gRNA molecule(Figure 2B,Lane 3).We noticed that the processing ability of the HDV ribozyme was not as strong as that of the HH ribozyme because partial cleavage directed by the HDV ribozyme was observed(Figure 2B,Lanes 1 and 2).

Guide RNA molecules produced in vitro guided-specific cleavage of the target DNA

We next investigated whether the gRNA molecules produced from in vitro transcription and self-processing have the ability to guide Cas9 to perform sequence-specific cleavage of the target DNA in vitro.When the gRNA,Cas9,and the PCR fragment containing the target sequence were mixed and incubated for 60 min,we observed efficient and complete cleavage of the target DNA(Figure 2C,Lane 1).The cleavage appeared to be specific because the sizes of the resulting DNA fragments were the same as predicted.We discovered that unprocessed pre-gRNA molecules generated from the in vitro transcription of the mutated RGR gene failed to guide the cleavage of the targeted sequences(Figure 2C,Lane 4).Removal of the HDV ribozyme alone was also insufficient to support Cas9 digestion(Figure 2C,Lane 2).However,gRNA with the HDV ribozyme at the 3′-end still retained sufficient activity to guide Cas9 to cut target DNA(Figure 2C,Lane 3).The gRNAs used in the assays were not purified,suggesting that the free ribozymes and other components from the in vitro transcription did not interfere with the Cas9/gRNA-mediated cleavage.These results bode well for using this method in vivo,where many other RNAs and proteins exist.

Figure 1.The schematic design of a self-processing RNA molecule for gRNA production(A)The modular structure of the pre-gRNA,which contains a Hammerhead ribozyme at the 5′-end,the sequence-specific gRNA portion in the middle(shaded yellow),and a HDV ribozyme at the 3′-end.The predicted secondary structures of both ribozymes are shown.The hairpin(stem)regions in the Hammerhead ribozyme are labeled H1,H2,and H3.P1,P2,P3,and P4 refer to the hairpin regions in the HDV ribozyme.The pre-gRNA undergoes self-catalyzed processing to release the mature gRNA.The 5′-end(in red)of the mature gRNA is complementary to the target sequences and the 3′-end(in green)is universal for all gRNAs in this work.(B)Schematic representation of gRNA and Cas9-mediated cleavage of target DNA.Note that the target sequence contains the NGG PAM site,which is not in the gRNA.

Figure 2.gRNA production and gRNA-mediated specific cleavage of a DNA target in vitro(A)DNA sequence of the artificial gene RGR that encodes the pre-gRNA.The first six nucleotides(in red)of the Hammerhead(HH)ribozyme must be complementary to the first six nucleotides of the target sequence(in red).The entire mature gRNA sequence is in bold and is underlined.The HDV ribozyme is in green.The two arrows mark the cleavage sites for the ribozyme-catalyzed reactions.(B)Analysis of the self-processing capacity of transcripts generated by in vitro transcription.The primary transcripts are 416 bp long(extra bases are added to both ends of the pre-gRNA during in vitro transcription).The predicted size of mature gRNA is 100 bp,the length from the transcription initiation site to the Hammerhead cleavage site is 131 bp,and the length from the HDV cleavage site to the end is 185 bp.Lane 1:gRNA is released from the pre-gRNA with both functional ribozymes.Note that the cleavage of the HDV ribozyme is incomplete.Lane 2:the Hammerhead ribozyme is mutated,which does not prevent the processing of the 3′-end of HDV ribozyme.However,the processing of HDV ribozyme is incomplete.Lane 3:the HDV ribozyme is mutated and only the Hammerhead ribozyme is released.The self-processing of the 5′-end of the pre-gRNA is complete,but no mature gRNA is released.Lane 4:both Hammerhead and HDV ribozymes are mutated and no self-processing is observed.(C)The gRNA-mediated cleavage of target DNA in vitro.The PCR fragment of the GFP gene is used as a substrate for gRNA/Cas9 digestion.gRNA released from wild-type pre-gRNA leads to a complete digestion of the target DNA(Lane 1).However,RNAs from pre-gRNAs with mutations in the Hammerhead ribozyme fail to guide the target cleavage(Lanes 2 and 4).Interestingly,the gRNA with the 3′-end HDV ribozyme mutated is still partially active(Lane 3).

Guide RNAs produced from the ADH1 promoter guidespecific DNA cleavage in yeast

We next tested whether our method for producing a selfprocessing RNA molecule to generate a gRNA could succeed in vivo.We placed the RGR gene under the control of the ADH1 promoter,which is transcribed by pol II(Figure 3A).The transcripts of the RGR gene contained the gRNA portion that was designed to target the GFP gene(Figure 3A).We introduced the plasmid along with another Cas9-expressing plasmid to a yeast strain that harbors a GFP gene in its chromosomes and that is brightly fluorescent(Figure 3B).We first analyzed whether our constructs disrupted the fluorescence displayed in the yeast cells.The yeast cells that harbored the plasmids failed to produce any fluorescence,indicating that the GFP gene had likely been disrupted in the cells(Figure 3B).Interestingly,partially processed pre-gRNA with the HDV remaining at the 3′-end displayed significant activity in vitro(Figure 2C,Lane 3).However,such an RNA molecule did not function in yeast as we did not observe any silencing of the GFP signal when the HDV was mutated in the pre-gRNA(data not shown).

We extracted the genomic DNA from the yeast cells and amplified the GFP gene by PCR.The PCR fragments were resistant to Cas9/gRNA digestion(Figure 3C).By sequencing,we found that deletion mutations were generated in the GFP gene as was expected for CRISPR-mediated mutations(Figure 3D).

Figure 3.ADH1 promoter-driven expression of the pre-gRNA is sufficient to guide Cas9-mediated disruption of a target gene in yeast(A)Schematic representation of the constructs that express Cas9 and the pre-gRNA.(B)Yeast cells that harbor the GFP gene display bright green fluorescence(left).The DIC image of the control is also shown.Expression of the Cas9 and the gRNA silences the fluorescence of GFP(right two panels).(C)PCR fragments of the GFP gene amplified from the genomic DNA of different yeast clones expressing Cas9 and RGR.The GFP fragments are resistant to Cas9/gRNA in vitro cleavage,indicating that the target sites in the GFP gene have likely been mutated.Lanes 1–5:PCR fragments amplified from different yeast colonies.Lane 6:wild-type GFP fragment as a positive control.Lane 7:no gRNA was added.(D)DNA sequencing confirms that the GFP gene is mutated by expressing Cas9 and the pre-gRNA in yeast.The target sequence and the 1 bp deletion are indicated(red).The PAM site(blue)is also marked.

DISCUSSION

We demonstrate that gRNAs can be efficiently produced in vitro and in vivo from essentially any promoters when the primary transcripts are flanked by self-cleaving ribozymes.The produced gRNAs can guide Cas9-mediated specific cleavage of DNA targets both in vitro and in vivo.This work opens the door to conducting more sophisticated CRISPR-mediated genome editing in many organisms.Because gRNAs can now be produced using tissue-specific promoters,hormone-responsive promoters,environmental signalregulated promoters,and other well-characterized promoters;this work lays the foundation for studying the roles of specific genes in various developmental and pathological processes.For example,temporal control of gRNA production is necessary when sequential disruption of different genes is preferred,which cannot be achieved by modulating the Cas9 expression alone.Additionally,when multiplex gene targeting is desired,different RGR genes can be expressed as a single transcript under one single promoter.Furthermore,gRNA and Cas9 together enable us to cut specific DNA in vitro,thus greatly enhancing our ability to manipulate DNA in vitro.

There are two main structural differences between the gRNAs produced in this work and the gRNAs generated using U6 and U3 promoters.First,gRNAs transcribed from U6 and U3 promoters have a triphosphate group at the 5′-end whereas gRNAs generated from self-processing of the pre-gRNAs have a hydroxyl group at the 5′-end.Second,the 3′-end of the gRNAs reported in this work is 2′,3′-cyclic phosphate while transcripts from U6 or U3 often end with hydroxyl groups at both 2′and 3′positions.Although both types of gRNAs possess the ability to guide the cleavage of target DNA in vivo,the structural features in the ends of our gRNAs may have advantages.For example,our gRNAs may be more stable because some nucleases require the 5′-terminal phosphate group for specific cleavage(Park et al.2011).

We have shown that we can effectively use Cas9 as a restriction enzyme in vitro to cut specific DNA sequences that complement the 20 nucleotides of the 5′-end of the gRNA.Because we have shown that the specific gRNAs can be easily produced from in vitro transcription(Figure 2),we can now generate specific Cas9 sites in DNA molecules to facilitate routine molecular cloning.This application is especially useful when no other restriction enzyme sites are available in the region.Another application we have successfully demonstrated in this work is using Cas9/gRNA to detect the mutations generated by CRISPR(Figure 3C).

Our system has the potential for automation and highthroughput production of gRNAs,thus laying the foundation for systematically knocking out every single gene in an organism using CRISPR technology.Because the RGR genes we designed mainly differ in the 20-nucleotide sequence encoding for the specific portion of the gRNA,every RGR gene can potentially be amplified by PCR with a pair of universal primers.If the SP6 or T7 promoter sequences are included in the primers,we can easily transcribe all of the RGR genes and produce the corresponding gRNAs using commercially available RNA polymerases(Figure 2).Amplification and in vitro transcription can be programmed for automation if thousands of different gRNAs are needed.

Only one construct is needed for generating a specific gRNA in vitro and in vivo.The construct can be transformed into a cell/organism to generate targeted modifications in the genome.The same construct also serves as the DNA template for amplifying the RGR gene using universal primers.The PCR fragments can be used for in vitro transcription to produce gRNAs,which along with Cas9 can be used for detecting mutations generated by the same gRNA.

MATERIALS AND METHODS

Design ribozyme-flanked gRNAs

The gRNA sequence except for the target sequence was adapted from(Mali et al.2013).The sequence in the GFP gene targeted by the Cas9/gRNA in this study was 5′-CGTGCTGAAGTCAAGTTTGAAGG-3′,with the first 20 bp as the beginning of the gRNA.At the 5′-end of the gRNA was a HH ribozyme,and at the 3′-end of the gRNA was a HDV ribozyme.The design of both ribozymes was based on the work of Avis et al.(2012).The mutated HH ribozyme(mHH)had a 13 bp deletion at its 5′-end,which affected the H1 and H2 stem-loop region as well as the conserved CUGANGA domain of the HH ribozyme(Figure 1).The mutated HDV ribozyme(mHDV)had a 15 bp deletion at its 3′-end,which affected the P2 and P4 region(Figure 1).Four different ribozymeflanked gRNAs(pre-gRNA)were generated by overlapping PCR reactions:HH-gRNA-HDV(referred as “Full”),mHH-gRNA-HDV(referred as “mHH”),HH-gRNA-mHDV(referred as “mHDV”),and mHH-gRNA-mHDV(referred as“mm”).

Cloning,expression,and purification of Cas9

The human-codon-optimized Cas9c gene template was a generous gift from Luhan Yang(G.Church Laboratory,Harvard University).The Cas9 gene was cloned into pET28a plasmid in order to express the N-terminally His-tagged Cas9 protein.The pET28a-Cas9 plasmid was transformed into BL21(DE3)(Invitrogen,Carlsbad,CA,United States).One single colony harboring pET28a-Cas9 was inoculated into 5 mL of Luria–Bertani(LB)media and grown at 250 rpm,37°C for 7 h.All of the 5 mL culture was transferred into 50 mL of LB and then grown overnight at 250 rpm,17°C.Of the overnight culture,50 mL was transferred into pre-chilled 1 000 mL of terrific broth(TB)media,and the resulting culture was grown at 250 rpm,17°C for 24 h.When the OD600reached to 1,the cells were chilled on ice for 30 min.Isopropylthio-β-galactoside was then added to the final concentration of 1 mmol/L,and MgCl2was added to the final concentration of 10 mmol/L.The cells were then grown at 250 rpm,17°C for 48 h before harvesting.

Cells were collected by centrifugation at 5,000 rpm for 10 min.Cells were then frozen at-80°C for 30 min,followed by thawing on ice for 15 min.Cells were re-suspended in 18 mL lysis buffer(50 mmol/L HEPES,pH 7.5,300 mmol/L NaCl,10 mmol/L imidazole).Lysozyme was added to the final concentration of 1 mg/mL.Cells were incubated on ice for 30 min and DTT was added to the final concentration of 2 mmol/L.Cells were then lysed by sonication on ice for 80 s.

His-tagged Cas9 protein was purified from the cell lysate using Ni-NTA Agarose from Qiagen,Hilden,Germany following the manufacturer’s instructions.The wash buffer contained 50 mmol/L HEPES,pH 7.5,300 mmol/L NaCl,20 mmol/L imidazole and the elution buffer contained 50 mmol/L HEPES,pH 7.5,300 mmol/L NaCl,250 mmol/L imidazole.The buffer was then exchanged to Cas9 storage buffer(20 mmol/L HEPES,pH 7.5,150 mmol/L KCl,and 1 mmol/L TCEP)using the PD-10 Desalting Columns(GE Healthcare Life Sciences,Waltham,MA,United States).The purified protein was kept at 4°C.

Yeast strains and constructs

The yeast strain LPY16936 expressing GFP as a C-terminal fusion protein of the GDH1 gene was used for the Cas9/gRNA in vivo assay.The yeast strain LPY142 was used as a negative control for GFP fluorescence imaging.Both yeast strains were gifts from Bessie Xue Su(L.Pillus Laboratory,UCSD).

To express Cas9 in yeast cells,the Cas9 gene with SV40 NLS signal at its C-terminal was cloned into the HindIII sites in the pACT2 vector(Leu selection marker)between the ADH1 promoter and ADH1 terminator.The sequence between the HindIII sites,including the region for the GAL4 activation domain,was removed.To express ribozyme-flanked gRNAs,the DNA fragment corresponding to the designed pre-gRNA molecules was cloned into pRS316(Ura selection marker)between the BamHI and EcoRI sites by overlapping PCR.The pACT2-Cas9 and pRS316-pre-gRNA constructs were sequentially transformed into LPY16936.

In vitro transcription for gRNA production

The templates for in vitro transcription were amplified by PCR from pRS316-pre-gRNA constructs using common primers 5′-GTCACTATTTAGGTGACACTATAGAAGCGCCTCGTCATTGTTCTCGTTCC-3′and 5′-ACGTATCTACCAACGATTTGACC-3′.In vitro transcription was carried out at 40 °C for 3 h in a total volume of 50 μL with 700 ng purified DNA template,2 μL of SP6 RNA polymerase(19U/μL,Promega,Madison,WI,United States),0.5 mmol/L rNTPs,1×Transcription Optimized Buffer(Promega),10 mmol/L DTT and 1μL of RNasin Ribonuclease Inhibitor(Promega).Of 500 mmol/L EDTA,1 μL was added to each tube to terminate the reactions.The RNA transcripts were not further purified.Of the in vitro transcription products,4μL were analyzed by electrophoresis in 12%denaturing urea polyacrylamide gels.The RNA bands were stained with ethidium bromide and visualized using a UV transilluminator.

In vitro cleavage assay using Cas9 protein and gRNA

For each in vitro cleavage assay,approximately 100 ng of purified PCR products were digested with 0.2 μL of the purified Cas9 and 0.8 μL of the gRNA from the in vitro transcription reaction in 1×cleavage buffer(20 mmol/L HEPES pH 7.5,150 mmol/L KCl,1 mmol/L TCEP,and 10 mmol/L MgCl2)in a total volume of 20 μL,at 37 °C for 60 min.The reaction was stopped by adding 2 μL of 10%SDS,and was then chilled on ice for 2 min,and centrifuged at 13,000 rpm for 2 min.The supernatant was analyzed by 1%–1.5%agarose gel electrophoresis.The DNA bands were stained with ethidium bromide and visualized using a UV transilluminator.

Green Fluorescent Protein fluorescent imaging of yeast

To observe the collective GFP fluorescence of yeast cells in different constructs,each yeast strain harboring the corresponding plasmids(if any)were grown in SD-Ura-Leu media overnight.The OD600of each strain was measured(around 1.0)and concentrated to the OD600of 20 in 50%glycerol.The 0.15 μL concentrated culture of each strain was carefully spotted onto ProbeOn Precleaned slides(Fisher Biotech,Waltham,MA,United States),covered and photographed under a DIC or fluorescent microscope(10×objective lens).

ACKNOWLEDGEMENTS

We would like to thank Luhan Yang(G.Church Laboratory,Harvard University)and Bessie Xue Su(L.Pillus Laboratory,UCSD)for materials and reagents.This work was supported by NIH R01GM068631 to Y.Z.

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