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Applications of the CRISPR/Cas system beyond gene editing

Anton, Tobias, Karg, Elisabeth, Bultmann, Sebastian·2018·Biology Methods and Protocols
DOI 10.1093/biomethods/bpy002PMC PMC6994046
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Abstract

Since the discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas) as a tool for gene editing a plethora of locus-specific as well as genome-wide approaches have been developed that allow efficient and reproducible manipulation of genomic sequences. However, the seemingly unbound potential of CRISPR/Cas does not stop with its utilization as a site-directed nuclease. Mutations in its catalytic centers render Cas9 (dCas9) a universal recruitment platform that can be utilized to control transcription, visualize DNA sequences, investigate in situ proteome compositions and manipulate epigenetic modifications at user-defined genomic loci. In this review, we give a comprehensive introduction and overview of the development, improvement and application of recent dCas9-based approaches.

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Figure 1: Overview of dCas9-based applications to study and manipulate chromatin. (A) Catalytically inactive Cas9 (dCas9) represents a RNA-guided DNA-binding platform that can be harnessed to target FP to a pre-defined genomic sequence and allows to visualize spatiotemporal dynamics of chromatin in living cells. (B) Fused to a variety of effector proteins, dCas9 can be employed to directly alter the transcriptional state of specific genes or to precisely manipulate epigenetic marks, such as CpG-methylation or post-translational modifications of histones. (C) Additionally, dCas9 can be fused to biotin ligases (tag = BirA* or APEX2). This approach allows to biotinylate (red pentagons) locus-associated proteins and to subsequently identify them by mass spectrometry.
Figure 1: Overview of dCas9-based applications to study and manipulate chromatin. (A) Catalytically inactive Cas9 (dCas9) represents a RNA-guided DNA-binding platform that can be harnessed to target FP to a pre-defined genomic sequence and allows to visualize spatiotemporal dynamics of chromatin in living cells. (B) Fused to a variety of effector proteins, dCas9 can be employed to directly alter the transcriptional state of specific genes or to precisely manipulate epigenetic marks, such as CpG-methylation or post-translational modifications of histones. (C) Additionally, dCas9 can be fused to biotin ligases (tag = BirA* or APEX2). This approach allows to biotinylate (red pentagons) locus-associated proteins and to subsequently identify them by mass spectrometry.CC BY-NC · PubMed Central
Figure 2: Expanding the CRISPR imaging toolkit. (A, B) To enhance the signal-to-noise ratio of CRISPR imaging, dCas9 is fused to arrays of small peptide epitopes (GCN4 and sfGFP11). These epitopes then either recruit fluorescent molecules (scFv-GFP) or are complemented (sfGFP1–10), reconstituting fluorescence. (C–E) Multi-color CRISPR imaging can be achieved by either co-expressing differentially labeled orthogonal dCas9 proteins (Sp-dCas9-GFP and Nm-dCas9-RFP) or by fusion of RNA aptamers (PP7 or MS2) to the sgRNA and co-expressing the cognate, fluorescently tagged binding proteins (PCP-GFP and MCP-GFP, respectively). Moreover, sgRNAs can be appended by PUF-binding sites (PBS1 or PBS2, respectively). These sites are then recognized by differentially tagged PUF proteins (PUF1-GFP and PUF2-RFP). (F) By substituting the PAM sequence in the form of an oligonucleotide (PAMmer), dCas9 can be targeted to single stranded RNA molecules.
Figure 2: Expanding the CRISPR imaging toolkit. (A, B) To enhance the signal-to-noise ratio of CRISPR imaging, dCas9 is fused to arrays of small peptide epitopes (GCN4 and sfGFP11). These epitopes then either recruit fluorescent molecules (scFv-GFP) or are complemented (sfGFP1–10), reconstituting fluorescence. (C–E) Multi-color CRISPR imaging can be achieved by either co-expressing differentially labeled orthogonal dCas9 proteins (Sp-dCas9-GFP and Nm-dCas9-RFP) or by fusion of RNA aptamers (PP7 or MS2) to the sgRNA and co-expressing the cognate, fluorescently tagged binding proteins (PCP-GFP and MCP-GFP, respectively). Moreover, sgRNAs can be appended by PUF-binding sites (PBS1 or PBS2, respectively). These sites are then recognized by differentially tagged PUF proteins (PUF1-GFP and PUF2-RFP). (F) By substituting the PAM sequence in the form of an oligonucleotide (PAMmer), dCas9 can be targeted to single stranded RNA molecules.CC BY-NC · PubMed Central
Figure 3: Identification of locus associated proteins by dCas9. (A) For enChIP, dCas9 is fused to a FLAG-tag and targeted to a locus of interest. Chromatin is then crosslinked and fragmented. dCas9-bound chromatin fragments are subsequently isolated by FLAG-specific antibodies and analyzed via mass spectrometry. (B) Contrary to enChIP, CasID requires the expression of dCas9 fused to the promiscuous biotin ligase BirA*. After the culture medium has been supplemented with exogenous biotin, BirA* catalyzes the addition of biotin to lysine residues of proteins that are in close proximity to the dCas9-BirA* fusion protein. Lysis of the cells and denaturation of proteins is then followed by affinity purification of biotinylated peptides, which are identified via tandem MS.
Figure 3: Identification of locus associated proteins by dCas9. (A) For enChIP, dCas9 is fused to a FLAG-tag and targeted to a locus of interest. Chromatin is then crosslinked and fragmented. dCas9-bound chromatin fragments are subsequently isolated by FLAG-specific antibodies and analyzed via mass spectrometry. (B) Contrary to enChIP, CasID requires the expression of dCas9 fused to the promiscuous biotin ligase BirA*. After the culture medium has been supplemented with exogenous biotin, BirA* catalyzes the addition of biotin to lysine residues of proteins that are in close proximity to the dCas9-BirA* fusion protein. Lysis of the cells and denaturation of proteins is then followed by affinity purification of biotinylated peptides, which are identified via tandem MS.CC BY-NC · PubMed Central

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Metadata

Authors
Anton, T., Karg, E., & Bultmann, S.
Affiliations
Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
ORCID
Bultmann, Sebastian
Venue
Biology Methods and Protocols
Publisher
Oxford University Press (OUP)
Published
2018-01-01
Volume
3
Issue
1
ISSN
2396-8923
DOI
10.1093/biomethods/bpy002
PMC
PMC6994046
Cited by
32
References
10
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor, 130 d)
Funders
Deutsche Forschungsgemeinschaft (SPP1623)

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