Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA

Abstract

The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.

Figure 1.

DNA-guided RNA cleavage activity. (A) Schematic of cleavage assay using ss gRNA or gDNA. RNA-free AGO207 is shown with AGO207 bound to endogenous E. coli RNA that co-purifies with the protein (black and gray strands). Either gRNA or gDNA is loaded into the RNA-free population of AGO207. Following complex formation, a 5′ labeled 60-nt unstructured RNA or DNA target whose sequence perfectly matches the guide is added to the reaction. Yellow circle indicates ³²P radiolabel. (B) Schematic of guide and target pairs used in the cleavage assay described in (A) showing combinations of gRNA or gDNA bound to a complementary cap-labeled RNA target or a 5′ end-labeled DNA target. Yellow circle indicates radiolabel. Black arrowhead indicates cleavage site. (C) Cleavage assay using guide and target pairs shown in (B). Black bars indicate average of three independent replicates and dots indicate cleavage percentage of each individual replicate relative to the canonical gRNA targeting the RNA substrate. Inset shows low-level cleavage of DNA targets by either RISC or DISC. (D) Analysis of cleavage site by RISC and DISC. AGO207 was programmed with either a 23-nt gRNA or gDNA followed by addition of a perfectly matched cap-labeled target RNA. Substrates and products were resolved on 16% denaturing PAGE alongside base-hydrolyzed polyuridine RNA. Inset shows expanded view of cleavage products, demonstrating that RISC and DISC both cleave the RNA substrate at the same position.

Figure 2.

Optimization of gDNAs. (A) Evaluating the effect of the 5′ nt on cleavage activity. AGO207 was programmed with gDNAs whose 5′ nt was T, A, G or C followed by addition of a cap-labeled RNA target that perfectly matches all guides from positions 2–23. Black bars indicate average cleavage of three independent replicates and dots indicate cleavage percentage of each individual replicate. (B) Optimizing gDNA length. (Left) miR-20a-derived gDNA sequences with 5′ T were varied in length from 15 – 25 nt. Yellow circle indicates cap-label. Black arrowheads indicate cleavage site. (Right) Quantification of cleavage products using gDNAs of different length. Black bars indicate average of three independent replicates and dots indicate cleavage percentage of each individual replicate. (C) Evaluating sequence-specificity of DISC. (Top) Sequences of gRNA or gDNA paired with a cap-labeled RNA target that contains a dinucleotide mismatch at a non-permissive site known to abrogate cleavage by yeast AGO. Yellow circle indicates cap-label on target strand. Black arrowheads indicate the cleavage site at t10 and t11 (positions 10 and 11 counting from the 5′ end of the guide). (Bottom) AGO207 was pre-incubated with either a gRNA or gDNA followed by addition of either a perfectly matched target or a mismatched target. Substrates and products were resolved by 16% denaturing PAGE. Black arrowhead indicates migration of cleavage product. (D) Single- and dinucleotide mismatch assay. (Left) Schematic of gDNAs (bottom) and target RNA (top) with mismatches in the guide shown in red and bold. Dotted line flanked by black arrowhead indicates cleavage site. Yellow circle indicates cap-label on target strand. (Right) Black bars on plot represent average cleavage by DISC of three independent replicates and gray dots represent individual replicates.

Figure 3.

Cleavage of highly structured HIV-1 ΔDIS 5′UTR RNA by DISC. (A) Schematic of DISC-mediated cleavage assay. The target RNA sequence was divided into 23-nt segments (shown in different colors) spanning the entire sequence, with each segment targeted by a different gDNA. AGO207 molecules that are bound to endogenous E. coli RNA are not shown for clarity. Following DISC-assembly, a 5′ end-labeled HIV-1 ΔDIS 5′ UTR transcript was added to the mixture to initiate cleavage by DISC. (B) Substrates and products generated by the assay described in (A) were resolved by denaturing PAGE (8%) revealing cleavability of the viral RNA by DISC. (C) Secondary structure of HIV-1 ΔDIS 5′UTR predicted by SHAPE. Colored circles at nucleotide positions indicate SHAPE reactivity. Guide DNAs targeting the different TRs of the HIV transcript are indicated by light blue bars and arrows (TR1 – TR14). Arrowheads indicate cleavage sites by DISC. The color of each arrowhead reflects the distribution of cleavage percentages by DISC shown in (B) and (D) (white, 0–12.5%; yellow, 12.5–25%; orange, 25–37.5%; red, 37.5–50%). (D) Quantification of DISC-mediated cleavage of each TR. Purple circles indicate nucleotides that are unpaired and green circles indicate nucleotides involved in G•U base pairs. Dotted line flanked by black arrowheads indicates cleavage site. Black bars on plot represent average cleavage by DISC of three independent replicates and gray dots represent individual replicates. Asterisk for set using gDNA13 indicates average of two replicates.

Figure 4.

Comparing cleavage activity of DISC and RNase H. (A) Schematic of matched and mismatched guide and target pairs used to target four TRs across the HIV-1 ΔDIS 5′UTR RNA. For each pair, the HIV-1 ΔDIS 5′UTR sequence is shown on top and the perfectly matched gDNA strand is shown on the bottom. Circle indicates target position complementary to the first position of the guide that does not pair due to structural restrains by the protein. Black arrowheads indicate cleavage site. Mismatches between the guide and target strands are indicated by a black box around the bases of the guide that are mutated to the bases shown below the box. (B) Quantified cleavage products from the assay using matched and mismatched guide and target pairs described in (A) are plotted with solid bars representing the average of three replicates and circles representing individual replicates. Cleavage that was not detectable by the assay is indicated by ‘nd’. (C and D) Comparing DISC (circles) and RNase H (triangles) cleavage of the unstructured 60-nt target (C) or of a structured 352-nt RNA target (D). Bars indicate average cleavage of three replicates.

Figure 5.

Detection of multiple cleavage events in a single reaction. (A) Secondary structure of HIV-1 ΔDIS 5′UTR with TRs colored for clarity. Colored arrowheads indicate cleavage sites on each TR. (B) Schematic of cleavage assay using multiple gDNAs targeting different TRs of HIV-1 ΔDIS 5′UTR. For clarity, AGO207 molecules bound to endogenous E. coli RNA are not shown. AGO207 was loaded with five gDNAs (gDNA4–gDNA8). Following assembly of the DISCs, a ³²P body-labeled HIV-1 ΔDIS 5′UTR RNA was added to the mixture to initiate cleavage. Cartoon secondary structure showing cleavage products with the 5′ products colored black and 3′ products colored gray. Colored gDNAs show complementary regions between guide and target strands. (C) Multiple DISC-mediated cleavage. Substrates and products formed at the indicated time points were separated by denaturing PAGE (8%). Reactions using only one guide are shown in lanes 3–7 as reference for product migration. The one-pot reaction time course is shown in lanes 8–14.

Figure 6.

High-throughput detection of DISC-mediated cleavage events. (A) Schematic of high-throughput assay to detect accessibility of structured RNAs. Guide DNAs spanning the target sequence were mixed together to assemble a mixed population of assorted DISCs. For clarity, AGO207 molecules bound to endogenous E. coli RNA are not shown. An unlabeled HIV-1 ΔDIS 5′UTR was added to the mixture to initiate cleavage. Cleaved RNA products were used as templates to prime reverse transcription using a fluorophore-labeled DNA primer. The cDNA products were detected by capillary electrophoresis yielding an electropherogram of peaks whose positions reflect DISC cleavage sites. (B) Electropherogram of DISC-cleavage sites programmed using 11 gDNAs with 23-nt increments. The average of three individual replicates was plotted as a single trace. Cleavage events were detectable at different sites with varying sensitivity.