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https://doi.org/10.1038/s41477-019-0461-5
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolution-
ized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea,
and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process,
various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing,
epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appre-
ciated and solutions explored. This Review intends to provide an informative summary of the latest developments and break-
throughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not
only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to
improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural,
environmental and ecological challenges.
G
enerating targeted genetic changes in living cells and organ- engineering will likely head. We hope this Review provides a com-
isms has historically been a great challenge in many species. prehensive guide on the current status and some future directions of
The basic strategy to introduce genetic changes is to gen- CRISPR technology in plants.
erate double-strand breaks (DSBs) by a sequence-specific nucle-
ase (SSN) at the targeted genomic site. Repair of DSBs in somatic The diverse and expanding CRISPR toolbox
cells of higher eukaryotes is predominantly done through the non- CRISPR arrays exist in bacteria and archaea DNA sequences,
homologous end joining (NHEJ) pathway, which results in inser- consisting of short repeats separated by unique spacer sequences.
tions/deletions (indels). Homology-directed repair (HDR), as a Small clusters of genes encoding Cas proteins can be found around
minor pathway, helps achieve precise genomic changes. Early SSNs, CRISPR arrays. Cas proteins are used to classify diverse CRISPR
including zinc finger nucleases (ZFNs)1 and transcription activator- systems based on their phylogenetic, structural and functional
like effector nucleases (TALENs)2, rely on protein–DNA interac- characteristics. During CRISPR antiviral defence, if the pre-
tions to determine specificity, which are difficult to engineer and CRISPR RNA (pre-crRNA) processing and interference stages are
multiplex. In 2012, the clustered regularly interspaced short palin- accomplished by one single multifunctional protein, the CRISPR
dromic repeat (CRISPR)–CRISPR-associated (Cas) system was first system is grouped as class 2; otherwise, it is grouped as a class 1
used for programmable RNA-guided genome editing in vitro3. The system17. Each class can be divided into multiple types according
following year, genome editing using CRISPR was successfully dem- to their signature proteins: type I, III and IV belong to class 1, with
onstrated in a mammalian system4,5. CRISPR, as a versatile, simple Cas3, Cas10 and Csf1 as their respective signature proteins17; while
and inexpensive system for genetic manipulation, has since domi- type II (Cas9), type V (Cas12a–e (Cas12d and Cas12e are also
nated the genome editing field. known as CasY and CasX, respectively), Cas12g–i and Cas14a–c)
Since the first demonstration of CRISPR in plant genome edit- and type VI (Cas13a–d) belong to class 2 (refs. 18–23). Each type of
ing in 2013 (refs. 6–8) there has been much progress in basic plant CRISPR system can be further grouped into subtypes based on
science and crop improvement9,10. Numerous molecular tools and operon organization and Cas proteins at the CRISPR loci. Although
platforms have been developed to achieve plant genetic engineering, the classification of CRISPR systems is constantly under develop-
including targeted mutagenesis11–13, base editing14, precise editing by ment, the current established classification method will facilitate
HDR15 and transcriptional regulation16. In this Review, we describe our understanding of CRISPR systems and the discovery of new
the state-of-the-art development of CRISPR technologies that have Cas proteins.
been applied in plants or remain to be fully explored, which are
partly illustrated in Fig. 1. We cover available CRISPR nucleases and CRISPR–SpCas9 genome editing system. Cas9 is a class 2, type
their variants, expression systems for multiplexing, diverse ways II CRISPR system and has been adapted for genome editing in the
to achieve precise genome editing, epigenome editing and tran- vast majority of organisms. Targeted genome cleavage requires Cas9
scriptome regulation. We address specific considerations in plant to assemble with a single-guide RNA (sgRNA; a fusion of crRNA
genome editing, such as temperature sensitivity, transgene-free and trans-activating crRNA (tracrRNA)), then recognize and bind
editing, polyploid genome editing and germline editing through to desired DNA sequences followed by a protospacer adjacent motif
floral dip. Recent breakthroughs that combine CRISPR with other (PAM). Streptococcus pyogenes Cas9 (SpCas9) recognizes a very sim-
cutting-edge technologies in plant breeding are also presented. We ple PAM (NGG), making it the most commonly used CRISPR–Cas9
envision some new frontiers where CRISPR-based plant genome system. SpCas9 has been codon-optimized for different species,
Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA. 2Institute for Bioscience and Biotechnology
1
RNA editing
ºC Temperature sensitivity
Organelle genome editing
90
High activity 80
70
RNA base editing 60
50
40
Low activity 30
20
C
as
C
10
as
Mitochondria
12
C
12
b
as
Plastid
a
9
Cyto
plas
m
Introduce Nuc
leus
stop codon
Gene knockout
D
Regulatory elements Promoter 5′ UTR Exon1 Intron Exon2 3′ UTR Terminator
LHA RHA
Transcriptional regulation
D Edit splicing sites
Regulatory elements Promoter 5′ UTR Exon1 Intron Exon2 3′ UTR Terminator
D R
Fig. 1 | Applications of CRISPR technology in plant cells. Outside the cell, CRISPR reagents can be delivered as plasmids, dsDNA, RNA and RNPs
through PEG-mediated transformation, particle bombardment or nanoparticles. Plasmids can also be delivered by Agrobacterium and viral vectors. In the
cytoplasm, CRISPR can cleave and edit RNA molecules through RNA-targeting Cas proteins, such as FnCas9 and Cas13, and the ADAR-derived RNA base
editor, respectively. CRISPR may also be introduced into organelles to edit organelle genomes. Commonly used Cas systems (Cas9, Cas12a and Cas12b)
are temperature sensitive, requiring higher temperatures for optimal activities. In the nucleus, CRISPR technology is applied to achieve gene knockout,
precise genome editing through base editing, HDR and transcriptional regulation. To knock out genes, CRISPR–Cas nucleases can be used to target coding
regions or regulatory elements. Base editors can be used to target coding regions (for example, to introduce stop codons) or regulatory elements. When
the DNA repair donor with the left homology arm (LHA) and the right homology arm (RHA) are introduced along CRISPR–Cas, precise genome editing
can be achieved through HDR. To regulate transcription, CRISPR–Cas nucleases and base editors can be used to edit regulatory elements or splicing sites.
Transcriptional regulation can also be achieved by using dead Cas proteins to recruit regulators to the promoter region, including activators, repressors,
DNA methyltransferase, demethylase and so on.
including human (Homo sapiens; hCas9)5, plant (pcoCas9 and (nCas9) is generated that only cleaves the targeting or non-targeting
Cas9p)6,24, Arabidopsis thaliana (AteCas9)25, maize (Zea mays; strand, respectively4,29,30. When both mutations are introduced, the
zCas9)26,27 and soybean (Glycine max; GmCas9)28, to improve the nuclease activity is abolished, resulting in a catalytically inactive or
expression level in vivo. By introducing the point mutations D10A dead Cas9 (dCas9)31. Cas9 nuclease, nCas9 and dCas9 can all be
in the RuvCI domain or H840A in the HNH domain, a Cas9 nickase applied to develop many versatile genome engineering tools.
Expanding target ranges with Cas9 variants and orthologues. and Nicotiana tabacum)68,73,74, tomato (Solanum lycopersicum)73,
The PAM requirement of SpCas9 limits its targeting scope in a soybean74, cotton (Gossypium hirsutum)75 and citrus76.
genome. The PAM-interacting (PI) domain can be engineered Similar to Cas9, Cas12a also contains a recognition (REC) lobe
through rationale design and directed evolution to obtain mutated and a nuclease (NUC) lobe63. However, the introduction of muta-
versions with altered PAM requirements (Table 1). The SpCas9 tions at the catalytic residues in the RuvC domain of Cas12a abol-
VQR, EQR and VRER variants can robustly recognize NGA, ishes the cleavage of both DNA strands at target sites62,63. Therefore,
NGAG and NGCG PAMs, respectively32. Similarly, the QQR1 there is no Cas12a nickase currently available. Multiple versions
variant was engineered with highly specific binding to the NAAG of catalytically dead Cas12a (dCas12a) have been engineered and
PAM33. Using phage-assisted continuous evolution, xCas9 has been repurposed for different applications, including dAsCas12a, dLb-
developed, recognizing NG, GAA and GAT PAM sites34. In addi- Cas12a and DNase-dead Cas12a (namely ddCas12a)62,63,66,77. To
tion, a rationally engineered SpCas9-NG recognizes relaxed NG broaden the target ranges of Cas12a, mutations have been intro-
PAMs and outperforms xCas9 at sites with NGH PAMs35. Many of duced to the wedge and PI domains to generate RR and RVR vari-
these SpCas9 variants have been demonstrated in plants, such as ants78,79 (Table 1). Similar mutations have been further introduced
the VQR variant36,37 and the VRER variant36 in rice (Oryza sativa), into rice-codon-optimized LbCas12a and FnCas12a for genome
as well as xCas9 and SpCas9-NG in rice and Arabidopsis38–46. Both editing in plants; only LbCas12a variants successfully edit sites with
xCas9 and SpCas9-NG have shown lower editing activity than wild- altered PAMs in plants67,80. Recently, an enhanced AsCas12a variant
type SpCas9 at NGG PAMs while exhibiting higher activity at non- (enAsCas12a) has been engineered to recognize a broader range of
canonical NG PAMs39,40,46. Specifically, SpCas9-NG is superior to PAM sites and also exhibits enhanced activity at low temperatures81.
xCas9 at most target sites with NG PAMs, as well as AT-rich PAM To further expand the utility of Cas12a in genome editing, ortho-
sites such as GAT, GAA and CAA39,40. Although the performance of logues from diverse bacteria species have been surveyed62,82 (Table 1).
some Cas9 variants may be suboptimal in plants, further optimiza- Cas12a orthologues with editing activity at loosened or shorter
tion could help restore editing activity in a plant cellular environ- PAM sites include Moraxella bovoculi 237 Cas12a (MbCas12a),
ment to achieve efficient genome editing. M. bovoculi AAX08_00205 Cas12a (Mb2Cas12a), M. bovoculi
Alternative PAM recognition can also be achieved by harnessing AAX11_00205 Cas12a (Mb3Cas12a), Thiomicrospira sp. XS5 Cas12a
Cas9 orthologues from other bacterial and archaeal species (Table 1). (TsCas12a), Btyrivibrio sp. NC3005 Cas12a (BsCas12a), Helcococcus
Staphylococcus aureus Cas9 (SaCas9) recognizes an NNGRRT kunzii ATCC 51366 Cas12a (HkCas12a), Lachnospira pectinoschiza
PAM and is smaller in size compared to SpCas9, making it pre- strain 2789STDY5834886 Cas12a (LpCas12a), Pseudobutyrivibrio
ferred for virus-based delivery47. SaCas9 nickase48, dead SaCas9 ruminis CF1b Cas12a (PrCas12a) and Pseudobutyrivibrio xylaniv-
(ref. 47) and a KKH variant49 with a loosened PAM requirement orans strain DSM 10317 Cas12a (PxCas12a)62,79,82,83, which could
have been developed to expand the application of this system. potentially be useful for plant genome editing.
SaCas9 has been demonstrated in multiple plant species, including
Nicotiana benthamiana50, rice50, Arabidopsis51 and citrus52. Other Emerging DNA-targeting CRISPR nucleases. Cas12b, formerly
Cas9 orthologues that have been used for genome editing in mam- known as C2c1, is a class 2 type V-B endonuclease. Cas12b recog-
malian systems include Streptococcus thermophilus Cas9 (St1Cas9) nizes target sequences with a distal 5′-T-rich PAM sequence and
and St3Cas9 (ref. 53); Neisseria meningitidis Cas9 (NmCas9)54; generates staggered DSBs with 7-nt 5′-overhangs21,84. Like Cas9,
Francisella novicida Cas9 (FnCas9) and its RHA variant55, Cas12b requires both crRNA and tracrRNA for target recogni-
Treponema denticola Cas9 (TdCas9)56; Campylobacter jejuni Cas9 tion, which can be engineered as a sgRNA21. Like Cas12a, Cas12b
(CjCas9)57 and Streptococcus canis Cas9 (ScCas9)58, of which contains a REC lobe and a NUC lobe without a HNH domain85.
only St1Cas9 has been demonstrated to edit plant genomes Two Cas12b nucleases, Alicyclobacillus acidoterrestris Cas12b
(Arabidopsis)51. Brevibacillus laterosporus Cas9 (BlatCas9) has also (AacCas12b) and Bacillus thermoamylovorans Cas12b (BthCas12b),
been characterized and is used for maize genome editing59. Notably, have initially shown editing activity in vitro with a preference for
Cas9s from class 2 type II-A and II-C have shown RNA-guided sin- higher temperatures (48–50 ℃)21, which is not ideal for mamma-
gle-stranded RNA cleavage activity60. Moreover, by grafting the PI lian and plant genome editing. By exploring diverse Cas12b ortho-
domain of a Streptococcus macacae Cas9 (SmacCas9) to SpCas9, logues, Alicyclobacillus acidiphilus Cas12b (AaCas12b) has been
iSpy-macCas9 has been developed to recognize NAA PAM61. In discovered and shows efficient editing activity at a broader range
general, the availability of Cas9 orthologues increases the accessible of temperatures86. Later, Bacillus hisashii Cas12b (BhCas12b) was
target sites for genome editing. Cas9 orthologues can be used for screened from multiple Cas12b orthologues and further engineered
orthogonal genome engineering, benefiting from their distinctive to increase activity at lower temperatures87. The Cas12b orthologues
sgRNA structures. that possess nuclease activity at lower temperatures may be applied
for plant genome editing.
Cas12a is a distinct CRISPR system. Cas12a (formerly known as CasX (also known as Cas12e), which was discovered from pre-
Cpf1, CRISPR from Prevotella and Francisella 1), a class 2 type V viously uncultivated environmental microbial communities, is a
endonuclease, is a genome editing system that is distinct from Cas9 group of dual-RNA-guided Cas proteins targeting double-stranded
(ref. 62). First, the PAM requirement allows Cas12a to target T-rich DNA (dsDNA) with a 5′-TTCN PAM18,20. CasX requires a 20 nt
regions62. Second, Cas12a only requires a short crRNA (~42 nt), guide RNA (gRNA) and a tracrRNA, and its cleavage generates a
making Cas12a crRNA easy to synthesize, multiplex and engineer62. staggered-end break with an overhang of approximately 10 nt20.
In addition to DNA nuclease activity, Cas12a also possesses RNase Deltaproteobacteria CasX (DpbCasX) and Planctomycetes CasX
activity, which is able to process a CRISPR array for multiplexed (PlmCasX) have been shown to edit the genomes of Escherichia
genome editing62,63. Moreover, Cas12a generates a DSB with stag- coli and human cells20. Mutations can be introduced to the RuvC
gered ends distal from the PAM site, which allows continuous domain to generate deactivated CasX20. Additionally, another
cleavage of DNA and may promote NHEJ-based gene insertion62. CRISPR system, CasY (also known as Cas12d), has also been identi-
Cas12a is also considered more specific than wild-type SpCas9 fied but is less well characterized. CasY may recognize a 5′-TA PAM
in several biological systems64–67. Three Cas12a nucleases from and cleave dsDNA18.
Acidaminococcus spp. BV3L6 (AsCpf1), Lachnospiraceae bacterium Researchers further exploited class 1 CRISPR systems for genome
ND2006 (LbCpf1) and Francisella novicida U112 (FnCpf1) have been editing. A type I-E CRISPR system from Thermobifida fusca has
demonstrated in rice66–72, Arabidopsis73, tobacco (N. benthamiana been shown to achieve 13–60% editing efficiency in mammalian
cells88. This system requires a multi-subunit cascade (CRISPR- RNA-targeting CRISPR nucleases. In addition to the aforemen-
associated complex for antiviral defence) and a crRNA to recognize tioned Cas systems that target DNA, Cas13 (formerly known as C2c2)
target sequences with a 5′-PAM; the helicase-nuclease enzyme Cas3 is a class 2 type VI CRISPR system targeting RNA101. Leptotrichia
is then recruited to degrade DNA. Cas3 generates a range of large shahii Cas13a (LshCas13a) recognizes a 22–28 nt target sequence
deletions up to 100 kb, which may be potentially useful for large- followed by a protospacer flanking sequence (PFS) of H (H denotes
scale genome manipulation and deletion screens. A, U or C), while no specific PFS requirement for Leptotrichia
Cas14 is a family of miniature nucleases (400–700 amino acids wadei Cas13a (LwaCas13a) and Prevotella sp. P5-125 Cas13b
long) that can cleave targeted single-stranded DNA (ssDNA) (PspCas13b)102,103 has been discovered. Like Cas12a, the RNase activ-
without PAM requirements19. Cas14 can be used for diagnosing ity of Cas13a allows it to process crRNA arrays, which can be used
diseases19 and may be also applied for ssDNA virus interference to target multiple RNAs simultaneously101. Interestingly, Cas13a
in plants. shows non-specific RNase activity that cleaves collateral RNA fol-
lowing initial binding to its target RNA in vitro and in bacteria101,104.
Repurposing CRISPR as a recruiting platform. The programmable By harnessing this special feature of Cas13a, the specific high-sensi-
DNA-binding property of CRISPR systems provides a powerful plat- tivity enzymatic reporter unlocking (SHERLOCK) method has been
form to recruit functional domains to desired regions of the genome developed to detect specific RNA and DNA sequences104. A catalyti-
through protein fusion or sgRNA–protein interactions (Fig. 2). cally deactivated Cas13 or dCas13 can be generated by introducing
Such functional domains can be fused to the C terminus or N ter- an alanine substitution to any of the four HEPN catalytic residues
minus of Cas proteins and may include FokI nuclease domains, (R597A, H602A, R1278A or H1283A)101. dCas13 has been used as a
transcriptional activators or repressors, epigenetic modifiers, deam- programmable RNA binding protein to achieve in vivo RNA track-
inases, fluorescent protein tags and so on. To increase the dosage ing102 and base editing103. In plants, gene expression knockdown
of the functional domains, the SUperNova tagging system (SunTag) using LwaCas13a has been achieved in rice protoplasts102. RNA virus
uses a repeat of GCN4 epitopes fused to dCas9, which are bound by interference using LshCas13a has been demonstrated in N. ben-
scFv antibodies fused to effectors89. Protein recruitment can also be thamiana105 and Arabidopsis106. Potentially more Cas13 orthologues
achieved using self-complementing split green fluorescent protein can be tested in plants to develop RNA targeting tools for transcrip-
(GFP)90 (Fig. 2a). In contrast to the protein fusion strategy, func- tional regulation, RNA base editing, RNA tracking and functional
tional domains can be recruited through RNA–protein interactions studies, pathogen detection and disease control.
(Fig. 2b). The versatility of Cas9 sgRNA allows for the modification
of the structural modules, including the upper stem, the first and Versatile and multiplexed CRISPR expression systems
the second hairpins and the 3'-end of the sgRNA, without compris- There are generally four strategies for in planta expression of the
ing binding efficiency. Several RNA-binding protein–RNA aptamer two CRISPR components, Cas protein and gRNA, and each strategy
systems have been used for CRISPR protein recruitment, includ- has its advantages and disadvantages (Fig. 3a). The most commonly
ing MCP–MS2 (refs. 29,91–93), PCP–PP7 (refs. 93,94), Com–Com95, λ used system is the mixed dual promoter system in which the Cas
N22 peptide–boxB96, as well as streptavidin and its binding RNA gene is driven by an RNA polymerase II (Pol II) promoter while
aptamer S1 (ref. 97), and so on. For the most widely used MCP– the gRNA is driven by an RNA polymerase III (Pol III) promoter107.
MS2 system, up to 16 MS2 loops have been added to the 3′-end Due to limitations of Pol III promoters, a dual Pol II promoter sys-
and hairpins of the sgRNA98. Moreover, an octet array of MS2 is tem has been developed, which resulted in a high transcription
added to the upper stem of the sgRNA to create the CRISPR–Sirius level of gRNAs66,108,109. Pol II promoters allow for potential spatial
system, resulting in more stable sgRNA secondary structures99. By and temporal control of expression, and usually outperform Pol III
fusing SunTag epitopes to MCP and using MS2 to recruit activators, promoters for generating long transcripts with multiplexed gRNAs.
a three-component repurposed technology for enhanced expres- This system can be further simplified to a compact single transcript
sion (TREE) system has been developed100. These versatile DNA- unit using only one promoter to drive both the Cas protein and
targeting and protein-recruiting CRISPR systems demonstrate that the gRNA110–113. A similar compact system expresses gRNAs in the
multiple approaches can be used simultaneously to maximize the intron region, allowing the gRNAs to be excised during splicing113,114.
number and types of functional domains, expanding genome engi- Finally, a bidirectional promoter can be used to drive Cas and gRNA
neering outcomes in plants for base editing and transcriptional reg- expression in opposite directions, with different 3′-untranslated
ulation, which are discussed later in this Review (in sections titled regions (UTRs) or terminators to regulate both components inde-
“Precise genome editing by base editors” and “Transcription regula- pendently. In the future, these four expression strategies may be fur-
tion and epigenome editing”). ther evaluated and applied for tailored applications in plants.
Antibody GFP1–10
3′-end modification
Fig. 2 | Repurposing CRISPR as a recruiting platform. a, Effector protein recruitment through protein fusions and interactions. Effector proteins can
be fused to the C- or N-terminus of Cas. In the SunTag system, a repeat of epitopes is fused to the Cas protein, which is bound by antibodies fused to
effectors. In the self-complementing split fluorescent protein system, the 11th β-strand of GFP (GFP11) can be tandemly arrayed to recruit the rest of the
fluorescent protein (GFP1–10) fused to effectors. b, Effector protein recruitment through protein–RNA interactions. Protein-binding RNA aptamers (such
as PP7, MS2, Com and BoxB) can be incorporated into the upper stem, the first and second hairpins, and the 3′-end of the sgRNA. In the CRISPR–Sirius
system, an array of aptamers are added into the upper stem loop of the sgRNA. In the TREE system, the repeat of epitopes used in SunTag is recruited
through sgRNA.
One of the most significant advantages of the CRISPR system in many species with Cas9, including rice121, wheat (Triticum aes-
is its flexibility for multiplexing, typically achieved by simultane- tivum)122 and maize123. The fourth strategy is the Csy4-based exci-
ous delivery and expression of multiple gRNAs. It is possible to sion system where sgRNAs or crRNAs are flanked by Csy4 excision
deliver many gRNAs through ribonucleoproteins (RNPs) or particle sites and processed by the Csy4 endonuclease111,124. Furthermore, a
bombardment. However, since most plants rely on Agrobacterium- Drosha-mediated multiplexing system using sgRNA–short hairpin
mediated transfer DNA (T-DNA) transformation, the development RNA (shRNA) has been developed for genome editing in mamma-
of efficient multiplexing expression systems is required. The most lian cells125, but has not yet been demonstrated in plant cells. The
straightforward approach is to stack multiple gRNA expression aforementioned efficient multiplexing systems can be used to target
units where each unit contains a promoter and a terminator24,115–117. multiple genes and gene families simultaneously for knockout, base
This approach can result in large constructs with many repetitive editing and regulation as well as large DNA fragment deletion, gene
elements, which increases cloning difficulty while decreasing trans- insertion and replacement.
formation efficiency. Therefore, multiple alternative strategies have
been developed to achieve multiplexed genome editing in plants Precise genome editing by base editors
(Fig. 3b). One strategy is to harness the native CRISPR array expres- Base editing, using cytidine base editors (CBE) and adenine base
sion system62,118. This is the most compact expression system and editors (ABE), refers to programmable and irreversible conversion
has been successfully demonstrated in plants using Cas9 (refs. 112,119) of one target nucleotide into another without DSBs or a donor tem-
and Cas12a70. Notably, Cas9 CRISPR arrays may contain tandem plate126–128. The first generation of CBE (BE1) was engineered by fus-
sgRNAs112,119 or only crRNA, with the tracrRNA expressed sepa- ing cytidine deaminase rat apolipoprotein B mRNA editing enzyme
rately4. Another strategy is to use the ribozyme–gRNA–ribozyme (rAPOBEC1)129 with dCas9 (ref. 126). Cytosine (C) deamination con-
(RGR) system in which the gRNA is flanked by a hammerhead (HH) verts C to uracil (U) which is recognized by cell replication machin-
ribozyme and a hepatitis delta virus (HDV) ribozyme sequence108. ery as thymine (T), resulting in C-to-T transition126. However, the
Tandemly arraying the RGR units allows the expression of a single conversion of C-to-U is usually reversed by base excision repair
transcript followed by the precise processing of each unit, as dem- where the U is transformed to an apurinic/apyrimidinic (AP) site
onstrated in rice120. The third strategy is the polycistronic T-RNA– by DNA glycosylases, such as uracil DNA glycosylase (UDG)130.
gRNA system in which T-RNA is fused to each gRNA in a single To increase editing efficiency and purity, the second generation of
transcript unit, and the endogenous RNaseZ and RNaseP recognize CBE (BE2) incorporates a uracil DNA glycosylase inhibitor (UGI)
and cut out the T-RNAs after transcription, allowing for the forma- into BE1 to block UDG126,131, causing a shift to the mismatch repair
tion of each mature gRNA121. This T-RNA system has been used (MMR) pathway. Editing fidelity and efficiency can be enhanced
a
CRISPR–Cas expression systems
Mixed dual promoter system
Pol II promoter Cas Terminator Pol II promoter gRNA Terminator
Dual Pol II promoter system
Pol II promoter Cas Terminator Pol II promoter gRNA Terminator
Single bidirectional promoter
Terminator Cas Bidirectional promoter gRNA Terminator
b
Multiplexed gRNA expression systems
CRISPR array 6/12 nt linker 6/12 nt linker
Cas9 sgRNA
Promoter gRNA Scaffold gRNA Scaffold gRNA Scaffold Terminator
RNase III RNase III
Cas12a crRNA
Promoter Scaffold cRNA Scaffold cRNA Scaffold cRNA Scaffold Terminator
Polycistronic T-RNA–gRNA
Promoter T-RNA gRNA Scaffold T-RNA gRNA Scaffold T-RNA gRNA Scaffold Terminator
R
R
R
R
N
N
N
N
as
as
as
as
as
as
e
e
e
e
P
P
Z
HH–gRNA–HDV
Promoter HH gRNA Scaffold HDV HH gRNA Scaffold HDV HH gRNA Scaffold HDV Terminator
Cys4 system
Promoter Cys4 site gRNA Scaffold Cys4 site gRNA Scaffold Cys4 site gRNA Scaffold Cys4 site Terminator Promoter Cys4
Drosha-mediated gRNA–shRNA
Promoter gRNA Scaffold shRNA gRNA Scaffold shRNA gRNA Scaffold Terminator
Drosha Drosha Drosha Drosha
Fig. 3 | Diverse CRISPR expression and multiplex systems. a, CRISPR–Cas expression systems. Cas and gRNA can be expressed under mixed dual
promoters, dual RNA Polymerase II (Pol II) promoters, a single bidirectional promoter and as a single transcript unit. b, Multiplexed gRNA expression
systems. Multiplexed gRNA can be expressed using CRISPR array, polycistronic T-RNA–gRNA, HH–gRNA–HDV, Cys4 and drosha-mediated
gRNA–shRNA systems.
with the addition of more free or fused UGIs, further demonstrating base editing132. Efficiencies of base editing can be also improved by
its importance132,133. Later generations of CBE (BE3 and BE4)126,132 use linker modification132, codon optimization and the incorporation of
nCas9 with the D10A mutation to activate MMR and induce cells to additional nuclear localization sequences134. The most commonly
repair the non-edited strand using the edited strand as a template. used cytidine deaminases include APOBEC1 (ref. 126), activation-
Further optimization of BEs includes the fusion of the Gam protein induced cytidine deaminase (AID)135, Petromyzon marinus cytosine
from bacteriophage Mu, which binds to the ends of DSBs and pro- deaminase 1 (PmCDA1)127 and APOBEC3A136,137. Since no natu-
tects them from degradation, thus reducing indel formation during rally known enzymes deaminate adenine (A) in DNA, E. coli TadA
Alternatively, NHEJ pathways can be inhibited genetically or However, more research is still needed for plants regarding the dis-
chemically. In mammalian cells when DNA LIGASE 4 (LIG4) covery of new regulators, optimization of targeting sites, develop-
is inhibited by RNA interference, SCR7 or the adenovirus 4 ment of tunable and inducible regulation, and large-scale regulation.
E1B55K and E4orf6 proteins, HDR efficiency can be signifi- Transcription can also be controlled by editing epigenetic marks.
cantly increased179,180. This also holds true when Ku70 and Ku80 Methyltransferases and acetylases can be recruited to alter the epi-
have been knocked down179. Two DNA-dependent protein kinase genetic modifications associated with regulation200–203. In plants,
catalytic subunit inhibitors, NU7441 and KU-0060648, have been DNA methylation193 and demethylation204 have been successfully
demonstrated to reduce NHEJ-mediated repair while increasing achieved using SunTag systems to silence and upregulate gene
HDR-mediated repair181. In plants, HDR enhancement has been expression, respectively. However, genome-wide hypermethylation
observed in Arabidopsis lig4 and ku70 mutants182 as well as in rice has been observed in plants193 and mammalian systems205 when
lig4 mutants183. While it is not desirable to use NHEJ mutants, it is using CRISPR-directed methyltransferases, raising potential con-
feasible to promote HDR with simultaneous knockdown of NHEJ cerns when using this tool for epigenome editing.
genes by RNA interference or CRISPR interference (CRISPRi), Gene expression levels can be regulated at the post-transcrip-
which will be introduced in the next section. tional level by RNA-targeting CRISPR systems such as Cas13 and
RNA-targeting Cas9s. Moreover, SpCas9 can target RNA when
Transcription regulation and epigenome editing presented with a PAM sequence on a separate oligonucleotide
CRISPR–Cas can be used to alter gene expression by editing regula- (PAMmer) alongside a gRNA206. In addition to SpCas9, dCas9 fused
tory elements, including promoters, transcription factors, enhanc- with an RNase can target RNA for degradation207. Furthermore,
ers and so on. For instance, editing regulatory elements can result in RNA sequences can be precisely changed with RNA base editing103.
a wide range of expression levels for a gene of interest, allowing for
the discovery and selection of novel alleles, dissecting the function- Plant genome editing challenges and opportunities
ality of gene regulatory elements and manipulation of quantitative The diverse CRISPR toolbox and advanced technologies provide
trait loci184,185. In addition, editing splicing sites can alter the expres- great platforms for plant genome engineering. However, challenges
sion of different gene isoforms, enabling the discovery of splice vari- still remain in the application of genome editing tools in plants.
ants and splicing mechanisms149,186,187. With the development of new technologies and knowledge, these
CRISPR–Cas can also be engineered for transcriptional regula- challenges could be overcome.
tion. Gene knockdown was first demonstrated with CRISPR–dCas9
by inhibiting the initial binding of the transcription machinery when Temperature sensitivity of Cas9 and Cas12a. Cas9 and Cas12a
targeting the promoter region or blocking RNA polymerase elonga- require higher temperatures to achieve optimal editing efficiency
tion when targeting the coding region31. Repression efficiency can in mammalian cells208, zebrafish209 and plants210,211. In Arabidopsis,
be improved by using CRISPR to recruit repressors, such as SRDX repeated high temperature treatments result in a dramatic increase
in plant cells115,188. These techniques are collectively referred to as of Cas9 efficiency212. Likewise, heat treatments result in effi-
CRISPRi. In contrast, when activators are recruited through CRISPR, cient Cas12a editing in Arabidopsis (29 °C) and maize (28 °C)211.
endogenous genes can be overexpressed in their native environment, Therefore, it is important to consider temperature when applying
which is termed CRISPR activation. Activators that have been used these CRISPR–Cas systems in plants.
for this purpose include the transactivation domain of the nuclear
factor-κB p65 subunit (p65AD), the herpes simplex viral protein Generation of transgene-free edited plants. When CRISPR is used
16 (VP16) and its tandem versions (VP64, VP128 or VP160)189, for crop improvement, it is desirable to obtain final products without
Epstein–Barr virus R transactivator (RTA)190, p300 (ref. 191), transgenes to minimize regulatory burden, foster public acceptance
activation domain from human heat-shock factor 1 (HSF1)91, tran- and mitigate potential ecological consequences. CRISPR transgenes
scription activation domain (TAD) from Xanthamonas transcrip- may be eliminated through breeding and screening the segregat-
tion activator-like effectors (TALEs) as well as plant activators EDLL ing populations, which can be aided by coupling CRISPR-encoding
and ERF2m (modified ERF2)192. Tethering multiple types of effector genes with fluorescent markers or herbicide susceptibility213,214.
proteins to the target site through prementioned protein recruiting However, this approach is not feasible for vegetatively propagated
systems (Fig. 2) can dramatically augment transcriptional regula- plants or plants with long life cycles, such as trees. It could be even
tion. For instance, successful activation has been achieved through more complicated for self-incompatible and polyploid plants.
VP64-p65AD-Rta (VPR)190, synergistic activation mediator (SAM)91, Another approach to achieve transgene-free genome editing is
SunTag89,191,193 and TREE systems100. Moreover, gene regulation is to generate mutated plants without transgene integration. DNA
also affected by the position of the target site194. Another route to or RNA encoding the CRISPR machinery can be introduced into
further modulate expression is to use multiple gRNAs to target one plants and transiently expressed to generate edits215,216. In addition,
gene, maximizing the accessible effector proteins195,196. Interestingly, CRISPR–Cas RNPs can be delivered into plant protoplasts through
gene repression and activation can be achieved at the same time polyethylene glycol (PEG)-mediated transformation, which has
using dead Cas activators targeting different sites197, which allows been demonstrated in Arabidopsis, wild tobacco (Nicotiana attenu-
for the manipulation of more complex pathways. Furthermore, ata), lettuce (Lactuca sativa), rice74,217, apple (Malus pumila), grape
since a shortened gRNA allows Cas binding without cleavage, (Vitis vinifera)218, Petunia × hybrida219 and soybean74. However,
programming gRNA length serves as an elegant strategy to switch regeneration of genome-edited plants from protoplasts poses a
between genome editing and transcriptional regulation with either huge challenge for many species and could potentially introduce
Cas9 (ref. 198) or Cas12a199. unwanted somaclonal variations derived from the lengthy tissue
CRISPRi and CRISPR activation technology also hold great culture process220. Alternatively, RNPs can be delivered into plant
promise in plant transcriptional regulation66,115,188. Tethering activa- tissues that are routinely used for plant regeneration (such as cal-
tors through protein recruiting systems, such as MS2–MCP92 and lus) by particle bombardment221,222. RNPs have been delivered into
SunTag193, have been shown to significantly improve plant transcrip- plant zygotes produced by in vitro fertilization, which were later
tional activation. A 6TAL–VP128 (TAL refers to TALE TAD motif) used to regenerate mature plants without selection223. RNP delivery
activation system has been demonstrated in plants that outperforms eliminates the introduction of foreign DNA and shortens the expo-
VP64 when delivered by Cas9 fusion or MS2–MCP recruitment, sure time of genomic DNA to CRISPR reagents, hence minimizing
providing a highly efficient platform for plant gene upregulation192. random DNA integration and off-targeting effects in the genome.
Chromosome shuffling
and editing
Wild ancestor
by CRISPR
2n
Domestication
n
by CRISPR
2n
Fig. 4 | Revolutionizing plant breeding by combining CRISPR with other cutting-edge technologies. a, Transformation efficiency can be elevated
by co-transforming or pre-transforming BBM and WUS2 genes. Genome-edited plants can be generated through tissue culture-dependent regeneration
or tissue culture-independent meristem induction and subculture. b, Asexual propagation of genome-edited plants can be achieved by creating the
genotype MiMe followed by haploid introduction through ectopic expression of BBM1 in the egg cell or knocking out MTL. c, Simultaneous gene editing and
haploid induction can be achieved by crossing elite lines with haploid inducer lines carrying genes encoding the CRISPR system. Edited haploids
without CRISPR genes can be selected and used to make transgene-free double haploid lines. d, De novo domestication of crops can be achieved using
CRISPR in wild species, resulting in improved crops with desirable traits. e, Cas or dCas–spo11 can be used to promote meiotic recombination to break
tight linkage and facilitate breeding. f, Elite alleles located at different chromosomes can be stacked at one locus by CRISPR to avoid segregation
during breeding.
Recently, a transgene killer CRISPR system has been developed to Germline editing by floral dip transformation. Generation of
link suicide transgenes with CRISPR constructs and eliminate all germline-edited plants is important for downstream genetic and
transgenes in the genome of edited T1 rice plants224. trait analysis. Ironically, this remains a challenge for plants where
the convenient Agrobacterium-mediated floral dip method is used
Genome editing of polyploid plants. Polyploid plant species make to deliver CRISPR transgenes, such as Arabidopsis, not only due to
up a significant portion of major crops, including staple food, fruit low editing efficiency in germlines24,238,239, but also the dissociation
and industrial crops. Commonly planted and consumed polyploid of editing results in somatic and germinal cells240. Agrobacterium
crops include triploids (citrus, banana (Musa acuminata, M. balbisi- is thought to deliver CRISPR-carrying T-DNA into the egg cells.
ana and Musa × paradisiaca), seedless watermelon (Citrullus lana- Germline edits can be obtained only if CRISPR makes edits after
tus) and some varieties of apples); tetraploids (pasta wheat (Triticum Agrobacterium infection but before the first embryogenic cell divi-
durum), potato, cotton, canola (B. napus), rapeseed, peanut (Arachis sion. Edits occurring afterwards will most likely result in chimeric
hypogaea), tobacco, switchgrass (Panicum virgatum) and some vari- plants. To overcome this challenge, tissue-specific promoters have
eties of apple); hexaploids (Camelina sativa, bread wheat and oats been used for Cas9 expression to limit or boost genome editing in
(Avena sativa)); and octoploids (sugar cane (Saccharum officinarum) germinal cells, including egg cell-specific promoter EC1.2 (ref. 26),
and strawberry (Fragaria × ananassa)). Gene knockout efficiency is sporogenesis expression promoter SPOROCYTELESS241 and meio-
usually lower in polyploid plant species than diploids, as multiple sis I-specific promoter242, as well as CDC45, DMC1, SOP11, YAO
alleles must be edited simultaneously. Key factors for successful and RPS5A promoters, which are preferentially expressed in actively
polyploid plant genome editing include an efficient expression sys- dividing tissues243–246. HDR was successfully achieved in Arabidopsis
tem and a highly active Cas nuclease. To date, multiallelic genome when a sequential transformation method was used, which takes
editing has been achieved in several polyploid plant species, includ- advantage of preselected transgenic lines with high germline expres-
ing both model systems225,226 and crops221,227–236. Successful gene edit- sion of Cas9 (ref. 247). While the emerging oil crop Camelina faces
ing has been used to introduce valuable agronomic traits such as similar problems to Arabidopsis, it remains to be seen whether any
improved oil quality230 and disease resistance233,237. Many attempts of the aforementioned strategies could improve genome editing in
have even been made to produce transgene-free edited polyploid this species230.
plants through RNP delivery221 and selection-free methods234.
Although both approaches are labour- and time-consuming, they Off-target effects in plants. The off-target effect of Cas proteins
offer the potential to accelerate applied research in crops. However, is usually a major concern of CRISPR technology in applied sci-
in addition to gene knockout, precise genome editing through HDR ences, especially in gene therapies. Cas9-induced DSBs could result
in stable transgenic lines of polyploid plants remains challenging. in large deletions and genome rearrangements248. In plants, inten-
Besides crop improvement, genome editing in polyploid plants sive investigations have been carried out to detect off-target effects
also offers a platform for gene dosage studies in which edited lines by whole genome sequencing in Arabidopsis, rice, cotton and so
with varying copy numbers of functional genes can be obtained on220,249,250. Studies have revealed a high specificity of genome edit-
in one round of transformation and plant regeneration225,232. This ing in plants using wild-type Cas9 and Cas12a, showing that most
allows for quantitative studies of the relationship between genotype mutations found in edited plants are due to somaclonal variations.
and phenotype. However, whole genome sequencing has shown that CBEs, not
a b
Reporter
cell line
Expression level
6
4
2
0
W
Li
Li
Li
ne
ne
ne
T
Identify essential Study biological Study gene function Study regulatory Identify genes of interest by sequencing
genes problems and evolve genes elements
Fig. 5 | Genetic screens with CRISPR libraries in whole plants and plant cells. a, Genetic screens with CRISPR libraries in whole plants. gRNA libraries
targeting a whole genome, a gene family or pathway, a single gene coding sequence or regulatory elements can be transformed into plants along with
a chosen Cas nuclease or base editor. Collections of mutants can be generated to identify essential genes or study functionality of genes, regulatory
elements or in planta gene evolution. b, Genetic screens with CRISPR libraries in plant cells. gRNA libraries targeting the whole genome can be
transformed into plant cells such as protoplasts. If traits of interest can be linked to drug-resistant selective markers, protoplasts can be used for plant
regeneration on selective media. If traits of interest can be linked to fluorescent protein expression, cells can be sorted by fluorescence-activated cell
sorting. Selected or sorted cells can be further sequenced to identify genes or regulatory elements contributing to traits of interest.
ABEs, induce substantial genome-wide off-target effects in rice152; Although it is hard to eliminate the possibility of CRISPR-
therefore, their use may necessitate additional screening and purify- induced large chromosomal deletions, insertions, inversions
ing selection. Moreover, recent studies have shown that both CBEs and rearrangement in plant genomes, which are often difficult to
and ABEs induce transcriptome-wide RNA off-target modifications detect with commonly used sequencing technologies, the off-target
in human cells251,252. However, base editors can be engineered to sig- effects should not be an obstacle in plant genome editing based on
nificantly reduce their RNA editing activity251,252. the knowledge generated so far. One can not only avoid off-target
To minimize potential off-target mutations, paired nCas9s can mutations during the process of generating genome-edited plants,
be used30. Protein engineering has been used to reduce Cas bind- but also detect and screen out products with off-target mutations
ing affinity (thus increasing editing specificity), resulting in high through breeding and selection, if necessary.
fidelity versions of SpCas9 such as SpCas9-HF1-4 (ref. 253), SpCas9
(K855A) and eSpCas9 (1.1)254, HypaCas9 (ref. 255), xCas9 (ref. 34), Revolutionizing breeding by combining CRISPR with other
evoCas9 (ref. 256), sniper-Cas9 (ref. 257) and HiFi Cas9 (R691A) in cutting-edge technologies. Generating uniform plants harbour-
the context of RNP delivery258 (Table 1). In rice, eSpCas9 (1.0 and ing CRISPR-induced edits relies heavily on tissue culture-based
1.1) and SpCas9–HF1 have been demonstrated to maintain their embryogenesis or organogenesis, especially for many major crops.
on-target editing activity with enhanced specificity when using the This limits the application of CRISPR in recalcitrant or marginally
T-RNA–sgRNA processing system259. Genome editing with two transformable plant species and varieties. One approach to overcome
Cas9 variants, eHF1-Cas9 and eHypa-Cas9, have also been dem- this difficulty is to express plant growth-stimulating genes to boost
onstrated in rice260. Recently, xCas9 was shown to have a higher plant transformation and regeneration. With the overexpression of
targeting specificity than wild-type Cas9 in rice40. However, owing transcription factors Baby boom (BBM) and Wuschel2 (WUS2), pro-
to intrinsically lower nuclease activities for many high-fidelity found improvement of transformation efficiency was achieved in
SpCas9s in plants259,261, they may not be widely adopted for plant recalcitrant maize lines, sorghum (Sorghum bicolor), sugarcane and
genome editing before further improvement. Other approaches to indica rice262,263. Furthermore, BBM, WUS or similar factors may
minimize off-target effects include designing gRNAs with fewer even allow tissue culture-free genome editing (if they are induced
potential mismatch targets in a given genome. Additionally, limit- or applied ectopically) alongside genome editing reagent delivery
ing the exposure of the genome to CRISPR reagents, for example, to stimulate meristem tissue formation from somatic tissues, repre-
through transient expression and RNP transformation, can reduce senting a novel and effective approach to achieve genome editing in
the potential for off-target activity. many difficult plant species (Fig. 4a).