Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Abstract

RNA-programmed genome editing using CRISPR/Cas9 from Streptococcus pyogenes has enabled rapid and accessible alteration of specific genomic loci in many organisms. A flexible means to target RNA would allow alteration and imaging of endogenous RNA transcripts analogous to CRISPR/Cas-based genomic tools, but most RNA targeting methods rely on incorporation of exogenous tags. Here, we demonstrate that nuclease-inactive S. pyogenes CRISPR/Cas9 can bind RNA in a nucleic-acid-programmed manner and allow endogenous RNA tracking in living cells. We show that nuclear-localized RNA-targeting Cas9 (RCas9) is exported to the cytoplasm only in the presence of sgRNAs targeting mRNA and observe accumulation of ACTB, CCNA2, and TFRC mRNAs in RNA granules that correlate with fluorescence in situ hybridization. We also demonstrate time-resolved measurements of ACTB mRNA trafficking to stress granules. Our results establish RCas9 as a means to track RNA in living cells in a programmable manner without genetically encoded tags.

Figure 1

Targeting mRNA in living cells with RNA-targeted Cas9 (RCas9). (A) Components required for RCas9 targeting of mRNA include a nuclear localization signal-tagged nuclease-inactive Cas9 fused to a fluorescent protein such as GFP, a modified sgRNA with expression driven by the U6 polymerase III promoter, and a PAMmer composed of DNA and 2′-O-methyl RNA bases with a phosphodiester backbone. The sgRNA and PAMmer are antisense to adjacent regions of the target mRNA whose encoding DNA does not carry a PAM sequence. After formation of the RCas9/mRNA complex in the nucleus, the complex is exported to the cytoplasm. (B) RCas9 nuclear co-export with GAPDH mRNA. The RCas9 system was delivered to U2OS cells with an sgRNA and PAMmer targeting the 3′UTR of GAPDH or sgRNA and PAMmer targeting a sequence from λ bacteriophage that should not be present in human cells (“N/A”). Cellular nuclei are outlined with a dashed white line. Scale bars represent 5 microns. (C) Fraction of cells with cytoplasmic RCas9 signal. Mean values ± SD (n=50). (D) A plasmid carrying the Renilla luciferase open reading frame with a β-globin 3′UTR containing a target site for RCas9 and MS2 aptamer. A PEST protein degradation signal was appended to luciferase to reveal any translational effects of RCas9 binding to the mRNA. (E) RNA immunoprecipitation of EGFP after transient transfection of the RCas9 system in HEK293T cells targeting the luciferase mRNA compared to non-targeting sgRNA and PAMmer or EGFP alone. Mean values ± SD (n=3). (F) Renilla luciferase mRNA and protein (G) abundance were compared among the targeting and non-targeting conditions. Mean values ± SD (n=4). p-values are calculated by Student’s t-test and one, two and three asterisks represent p-values less that .05, .01, and .001, respectively. See also Figure S1.

Figure 2

ACTB mRNA localization with RCas9 compared to FISH. (A) The RCas9 system was delivered to U2OS cells and the cells were subjected to FISH for ACTB mRNA. RCas9 with sgRNA and PAMmer targeting ACTB mRNA was compared to non-targeting sgRNA and PAMmer antisense to a sequence from λ bacteriophage (“−“ sgRNA and “−“ PAMmer). White dotted lines delineate the cellular boundaries and black dotted lines delineate cellular nuclei. Scale bars represent 5 microns. Insets (on right) are delineated by white boxes. (B) Pixel-by-pixel analysis of RCas9 and FISH colocalization using the Mander’s overlap coefficient is summarized with a cumulative distribution of the percent of cytoplasmic area with overlapping signal in 60–80 cells in each condition. The presence of the PAMmer produces a significantly greater colocalization among RCas9 and FISH in the presence of the sgRNA targeting ACTB mRNA (p=0.035, two-tailed Mann-Whitney U test). See also Figure S2.

Figure 3

Tracking of mRNA trafficking to stress granules with RCas9. (A) The RCas9 system targeting ACTB, TFRC, or CCNA2 mRNAs or one of three non-targeting controls (NTC) was delivered to HEK293T cells expressing G3BP1, a protein known to be trafficked to stress granules, fused to RFP. Cells were treated with sodium arsenite, fixed, subjected to FISH for ACTB, TFRC, or CCNA2 mRNA and imaged. (B) RNA trafficking to stress granules was imaged in real time using cells harboring RCas9 targeting ACTB mRNA. At time zero, cells were imaged and sodium arsenite applied. 60 minutes later, cells were imaged again and a comparison of RCas9 and G3BP1-positive stress granules revealed close correlation of foci only in the presence of sgRNA and PAMmer targeting ACTB mRNA. (C) The fraction of stress granules with RCas9 foci when targeting three mRNAs (ACTB, TFRC, and CCNA2) compared to three non-targeting controls. Error bars ± SD calculated from 50 cells from each of three biological replicates. P-values among the RCas9 system targeting ACTB, TFRC, and CCNA2 mRNA are <.001 when compared to each of the NTC conditions. P-values were calculated with Student’s t-test. (D) In a similar experiment, RCas9 targeting ACTB mRNA signal accumulation in stress granules was tracked over time. 8–11 stress granules were tracked in each condition with time points every 8 minutes for 32 minutes. Scale bars represent 5 microns. See also Figure S3.