Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression

Abstract

Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale.

Figure 1. Design of the CRISPR Interference System

(A) The minimal interference system consists of a single protein and a designed sgRNA chimera. The sgRNA chimera consists of three domains (boxed region): a 20 nt complementary region for specific DNA binding, a 42 nt hairpin for Cas9 binding (Cas9 handle), and a 40 nt transcription terminator derived from S. pyogenes. The wild-type Cas9 protein contains the nuclease activity. The dCas9 protein is defective in nuclease activity. (B) The wild-type Cas9 protein binds to the sgRNA and forms a protein-RNA complex. The complex binds to specific DNA targets by Watson-Crick base pairing between the sgRNA and the DNA target. In the case of wild-type Cas9, the DNA will be cleaved due to the nuclease activity of the Cas9 protein. We hypothesize that the dCas9 is still able to form a complex with the sgRNA and bind to specific DNA target. When the targeting occurs on the protein-coding region, it could block RNA polymerase and transcript elongation. See also Figure S1.

Figure 2. CRISPRi Effectively Silences Transcription Elongation and Initiation

(A) The CRISPRi system consists of an inducible Cas9 protein and a designed sgRNA chimera. The dCas9 contains mutations of the RuvC1 and HNH nuclease domains. The sgRNA chimera contains three functional domains, as described in Figure 1. (B) Sequence of designed sgRNA (NT1) and the DNA target. NT1 targets the nontemplate DNA strand of the mRFP-coding region. Only the region surrounding the base-pairing motif (20 nt) is shown. Base-pairing nucleotides are shown in orange, and the dCas9-binding hairpin is in blue. The PAM sequence is shown in red. (C) CRISPRi blocks transcription elongation in a strand-specific manner. A synthetic fluorescence-based reporter system containing an mRFP-coding gene is inserted into the E. coli MG1655 genome (the nsfA locus). Six sgRNAs that bind to either the template DNA strand or the nontemplate DNA strand are coexpressed with the dCas9 protein, with their effects on the target mRFP measured by in vivo fluorescence assay. Only sgRNAs that bind to the nontemplate DNA strand showed silencing (10- to 300-fold). The control shows fluorescence of the cells with dCas9 protein but without the sgRNA. (D) CRISPRi blocks transcription initiation. Five sgRNAs are designed to bind to different regions around an E. coli promoter (J23119). The transcription start site is labeled as +1. The dotted oval shows the initial RNAP complex that covers a 75 bp region from −55 to +20. Only sgRNAs targeting regions inside of the initial RNAP complex show repression (P1–P4). Unlike transcription elongation block, silencing is independent of the targeted DNA strand. (E) CRISPRi regulation is reversible. Both dCas9 and sgRNA (NT1) are under the control of an aTc-inducible promoter. Cell culture was maintained during exponential phase. At time T = 0, 1 μM of aTc was supplemented to cells with OD = 0.001. Repression of target mRFP starts within 10 min. The fluorescence signal decays in a way that is consistent with cell growth, suggesting that the decay is due to cell division. In 240 min, the fluorescence reaches the fully repressed level. At T = 370 min, aTc is washed away from the growth media, and cells are diluted back to OD = 0.001. Fluorescence starts to increase after 50 min and takes about 300 min to rise to the same level as the positive control. Positive control: always without the inducer; negative control: always with 1 μM aTc inducer. Fluorescence results in (C)–(E) represent average and SEM of at least three biological replicates. See also Figures S2 and S3.

Figure 3. CRISPRi Functions by Blocking Transcription Elongation

(A) FLAG-tagged RNAP molecules were immunoprecipitated, and the associated nascent mRNA transcripts were sequenced. (Top) Sequencing results of the nascent mRFP transcript in cells without sgRNA. (Bottom) Results in cells with sgRNA. In the presence of sgRNA, a strong transcriptional pause is observed 19 bp upstream of the target site, after which the number of sequencing reads drops precipitously. (B) A proposed CRISPRi mechanism based on physical collision between RNAP and dCas9-sgRNA. The distance from the center of RNAP to its front edge is ~19 bp, which matches well with our measured distance between the transcription pause site and 3′ of sgRNA base-pairing region. The paused RNAP aborts transcription elongation upon encountering the dCas9-sgRNA roadblock.

Figure 4. Targeting Specificity of the CRISPRi System

(A) Genome-scale mRNA sequencing (RNA-seq) confirms that CRISPRi targeting has no off-target effects. The sgRNA NT1 that binds to the mRFP coding region is used. The dCas9, mRFP, and sfGFP genes are highlighted. (B) Multiple sgRNAs can independently silence two fluorescent protein reporters in the same cell. Each sgRNA specifically represses its cognate gene, but not the other gene. When both sgRNAs are present, both genes are silenced. Error bars represent SEM from at least three biological replicates. (C) Microscopic images for using two sgRNAs to control two fluorescent proteins. (Top) Bright-field images of the E. coli cells; (middle) RFP channel; (bottom) GFP channel. Coexpression of one sgRNA and dCas9 only silences the cognate fluorescent protein, but not the other. The knockdown effect is strong, as almost no fluorescence is observed from cells with certain fluorescent protein silenced. Scale bar, 10 μm. Control shows cells without any fluorescent protein reporters. Fluorescence results represent average and SEM of at least three biological replicates. See also Figure S4.

Figure 5. Characterization of Factors that Affect Silencing Efficiency

(A) We measured the silencing effects of sgRNAs with different targeting loci on the same gene (distance from the translation start codon) and sgRNAs with different lengths of the base-pairing region to the same target locus (based on NT1). (B) The silencing efficiency is inversely correlated with the target distance from the translation start codon (orange, mRFP; green, sfGFP). The relative repression activity is calculated by normalizing repression of each sgRNA to that of the sgRNA with the highest repression fold change. Error bars represent SEM from three biological replicates. (C) The length of the Watson-Crick base-pairing region between the sgRNA and the target DNA affects repression efficiency. Extensions of the base-pairing region all exhibit strong silencing effect, and truncations dramatically decrease repression. The minimal length of the base-pairing region for detectable repression is 12 bp. Error bars represent SEM from three biological replicates. (D) We introduced single mismatches into every nucleotide on sgRNA (NT1; Figure 2B) and measured how single mismatches affect repression efficiency. Three subregions with distinct importance to the overall silencing can be discerned. They show a step function. The first 7 nt region is critical for silencing and likely constitutes a “seed” region for probing sgRNAs binding to the DNA target. The PAM sequence (NGG) is indispensible for silencing. Error bars represent SEM from three biological replicates. (E) Silencing effects of sgRNAs with adjacent double mismatches. The relative repression activity of single-mismatched sgRNAs is shown in gray, with the mismatch position labeled on the bottom. Experimentally measured activity of double-mismatched sgRNAs is shown in blue. Calculated activity by multiplying the effects of two single-mismatched sgRNAs is shown in white and labeled with “Com.” In most cases, the silencing activity of a double-mismatched sgRNA is simply a multiplication of the activities of single-mismatched sgRNAs (except Figure S5B), suggesting an independent relationship between single mismatches. Error bars represent SEM from three biological replicates. (F) Combinatorial silencing effects of using double sgRNAs to target a single mRFP gene. Using two sgRNAs that target the same gene, the overall knockdown effect can be improved to almost 1,000-fold. When two sgRNAs bind to nonoverlapping sequences of the same gene, repression is augmented. When two sgRNAs target overlapping regions, repression is suppressed. Error bars represent SEM from three biological replicates. Fluorescence results represent average and SEM of at least three biological replicates. See also Figures S5 and S6.

Figure 6. Functional Profiling of a Complex Regulatory Network Using CRISPRi Gene Knockdown

(A) sgRNAs are designed and used to knock down genes (cya, crp, lacI, lacZ, lacY, and lacA) in the lac regulatory pathway or block transcriptional operator sites (A/P/O). LacI is a repressor of the lacZYA operon by binding to a transcription operator site (O site). The lacZ gene encodes an enzyme that catalyzes lactose into glucose. A few trans-acting host genes such as cya and crp are involved in the activation of the lacZYA system. The cAMP-CRP complex binds to a transcription operator site (A site) and recruits RNA polymerase binding to the P site, which initiates transcription of lacZYA. IPTG, a chemical that inhibits LacI function, induces LacZ expression. (B) β-galactosidase assay of the knockdown strains without (white) and with (gray) IPTG. Control shows that the wild-type cells without CRISPRi perturbation can be induced by addition of IPTG. The sgRNA that targets LacZ strongly represses LacZ expression even in the presence of IPTG. When LacI is targeted, LacZ expression is high even without IPTG. Targeting cya and crp genes leads to decreased LacZ expression level in the presence of IPTG. Presence of 1 mM cAMP rescues cya knockdown, but not crp knockdown. Blocking the transcription operator sites results in LacZ repression, suggesting that these are important cis-acting regulatory sites for LacZ. Upon perturbation, decreased (red arrows) and increased (green arrows) expression of LacZ are indicated. Error bars represent SEM from three biological replicates. (C) The knockdown experiments allow us to profile the roles of regulators in the lac regulatory circuit. The data is shown on a two-dimensional (2D) graph, with x axis showing LacZ activity without IPTG and y axis showing its activity with IPTG. The spreading of ovals along each axis shows the SEM of three biological replicates. The β-galactosidase assay results represent average and SEM of three biological replicates. For RNA-seq data on LacI and LacZ targeting, see also Figure S4.

Figure 7. CRISPRi Can Repress Gene Expression in Human Cells

(A) A CRISPRi system in HEK293 cells. The SV40-EGFP expression cassette is inserted into the genome via retroviral infection. The dCas9 protein is codon-optimized and fused with three copies of NLS sequence. The sgRNA is expressed from an RNA polymerase III U6 vector. Cotransfection of dCas9 and an sgRNA (eNT2) that targets the nontemplate DNA strand of EGFP decreases fluorescence (~46%), whereas the expression of either dCas9 or sgRNA alone shows no effect. (B) The dCas9:sgRNA-mediated repression is dependent on the target loci. Seven sgRNAs are designed to target different regions of the EGFP-coding sequence on the template or nontemplate strand. Only eNT2 and eNT5 show moderate repression. EGFP fluorescence (targeted reporter) is shown in green, whereas mCherry fluorescence (control reporter) is shown in pink. Fluorescence results from (A) and (B) represent average and error of two biological replicates. See also Figure S7.