Unambiguous identification of miRNA:target site interactions by different types of ligation reactions

Abstract

To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (CLIP) assays are state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore indirect. To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. Unexpectedly, ligation reactions also occurred in the absence of the exogenous ligase. Our in vivo data set and reanalysis of published mammalian AGO-CLIP data for miRNA-chimeras yielded ∼17,000 miRNA:target site interactions. Analysis of interactions and extensive experimental validation of chimera-discovered targets of viral miRNAs suggest that our strategy identifies canonical, noncanonical, and nonconserved miRNA:targets. About 80% of miRNA interactions have perfect or partial seed complementarity. In summary, analysis of miRNA:target chimeras enables the systematic, context-specific, in vivo discovery of miRNA binding.

Figure 1. Generation of miRNA:target chimeras via different types of ligations in C. elegans

(A) C. elegans RNA labeled with photoreactive nucleoside 4-thiouridines (4sU) is crosslinked to bound proteins in vivo. After homogenization of worms, the lysate is treated with RNase T1. Some miRNAs are shortened, others remain complete. Following immunoprecipitation (IP) and washing of AGO, crosslinked RNA is phosphorylated by a PNK variant (leaves 3’ends blocked) and treated with T4 RNA ligase, which ligates the 3’hydroxyl end of complete miRNAs to bound RNA fragments. Crosslinked RNA is recovered and deep sequenced. Computational analysis detects sequence reads of miRNAs and AGO binding sites, along with chimeric reads containing miRNAs connected to their targets. (B) Example of a miRNA interaction recovered from chimeric reads. Predicted reconstruction of the miRNA:target duplex. green: miRNA sequence; blue: target sequence; red: T to C conversion. (C) Data from the ligation sample contain chimeras with 3’ truncated (length of miRNA sequence >=13 nts) and with complete miRNAs. A comparable fraction of chimeras with truncated miRNAs was also found in a control sample, to which no ligase was added to generate chimeras. (D) miRNA and target ends involved in the ligations of the control sample are highly enriched in an upstream G, suggesting that RNase T1 generated the ends used for this type of ligation. (E) Truncated miRNAs are ligated by the ligase activity of the lysate during IP. (F) 89% of chimera-derived miRNA target sites (mapped to the transcriptome) overlap with AGO binding sites generated from non-chimeric reads. See also Figure S1.

Figure 2. C. elegans miRNA:Targets (3,600) Derived from Chimeras Reflect Endogenous miRNA Targeting

(A) Target RNAs were analyzed for complementarity to the seed region of their ligated miRNAs. ~80% of interactions possess the tested complementarities. Shuffled sequences (dinucleotides in target sequences are permuted) served as control. mm = mismatch Mismatches were broadly distributed over all types of nucleotides, including G:U. (B) Hybridization profile summarized over all interactions. The predicted frequency of a miRNA position to be base paired is plotted along the miRNA length. Duplex structures of miRNA:targets were predicted by RNAhybrid allowing G:U pairing. Shuffled sequences (dinucleotides in target sequences are permuted) and shuffled interactions (targets are swapped between miRNAs) served as control. (C) Target sites derived from miRNA-chimeras are more often found ligated to miRNAs of the same family than expected by chance (p < 0.0001). Shuffling target sites between miRNA families served as control. (D) Local frequency of crosslink-induced T to C conversions in target RNAs from interactions with a perfect 2-7 seed match (normalized to local thymidine frequency). Nucleotides hybridized to the seed of the miRNA are strongly indisposed to crosslink with the protein. See also Figure S2.

Figure 3. Re-Analysis of published human AGO CLIP data yields miRNA:targets

(A) AGO2 PAR-CLIP and HITS-CLIP data (HEK 293 cells) from Kishore et al.; analysis as in Figure 2. ~80% of interactions possess the tested complementarities. Mismatches were broadly distributed over all types of nucleotides, including G:U. (B) Hybridization profiles summarized over all interactions. (C) Individual target sites are more often ligated to members of the same miRNA family than expected by chance. (D) Local frequency of crosslink-induced T to C conversions in target RNAs from interactions with a perfect 2-7 seed match (normalized to local thymidine frequency). Positions hybridized to the seed of the miRNA are strongly indisposed to crosslink. (E) Mismatches in seed sites occur predominantly at position 2 or 7 of the miRNA. Shown is the positional mismatch frequency for interactions with a 2-7 match containing 1 mismatch, averaged over different miRNA families. (F) As in (E), but in C. elegans. See also Figure S3 and Table S1.

Figure 4. Functional miRNA interactions derived from chimeras

(A) HITS-CLIP sequencing data from WT and miR-155 KO cells (Loeb et al.) were analyzed for chimeras containing miR-155. miR-155 ligated target sites with a perfect 2–7 seed match (red) were targeted by AGO2 in WT cells more often than in miR-155 KO cells compared to all transcripts (dashed) and all clusters with a seed match (blue) (p < 0.004; KS test). miR-155 ligated target sites without a perfect 2–7 match (orange) are AGO2 bound in WT significantly more often than in KO cells (p < 0.003; KS test). (B,C,D) miRNA perturbation data demonstrates functionality of chimera-identified miRNA interactions. Changes in transcript abundance after inhibition of 25 miRNAs in HEK293 cells (Hafner et al.) (B) and miR-302a/b/c/d, miR-367 in mouse embryonic stem cells (Lipchina et al.) (C) and changes in protein abundance after overexpression of miR-155 in a human cell line (Selbach et al.) (D). Targets recovered in chimeras with these miRNAs (from all HEK293 data and human embryonic stem cell data, respectively; Table 1) were upregulated upon miRNA inhibition on the transcript level (B,C) and downregulated on the protein level upon miRNA overexpression (D). (E and F) Conservation across 31 vertebrate species of perfect seed (2–7) matches (E) and seed matches with 1 nt mismatch (1 mm) (F) from human miRNA: targets recovered by analysis of chimeras. Conservation of other seed matches for the same miRNA served as a control. A perfect seed match in human was counted as conserved if present at the same position in the alignment. A seed match with 1mm was deemed conserved if the identical 1mm seed match or the perfect seed match was present at the same position in the alignment. On average, 100 miRNA interactions (median) were included per miRNA family. miRNA:targets with a mismatch in the 2-7 seed were significantly conserved (***: p < 0.005; **: p < 0.01, Mann-Whitney-U test) but to a lower degree than perfect seed matches. See also Figure S4 and Table S2.

Figure 5. Validation of canonical, noncanonical and nonconserved sites targeted by viral miRNAs

(A) The majority of tested, chimera-identified KSHV miR-K11 interactions resulted in specific reporter repression, including sites with weak seed matches. miRNA interactions were tested in dual luciferase reporter assays using wt and binding site mutant 3’UTR reporters and either control miRNA or viral miRNA mimics. Noncanonical interactions are marked with a diamond. (canonical: perfect match to miRNA position 2-7 with an A opposing the first miRNA nucleotide and/or perfect complementarity to at least miRNA positions 2-8); numbers are mean ± SEM (n >= 3). (B) Predicted base pairing for noncanonical miR-K11 sites that were responsive in the reporter assay. (C) EBV miRNA BART-14 and KSHV miRNA-K11 are identical in only five positions (nt 3–7), but these might bind the same nucleotides in the target (noncanonical binding for miR-K11, canonical for miR-BART14). Duplex structures were predicted by RNAhybrid, G:U allowed. Shortening of the miRNA by 4 nt from the 3’end enabled an in silico hybridization in which the GC-poor 5’region of the miRNA is predicted to base pair. (D) Hybridization profile of KSHV miR-K3 interactions compared to all other KSHV and human miRNA interactions identified by analyzing CLIP data by Gottwein et al. 2011 and Skalsky et al. 2012; miR-K3 interactions display reduced binding in the 5’region of the miRNA. RNAhybrid, G:U allowed, controls (permutation of dinucleotides in target sequences) were subtracted. (E) Predicted base pairing of tested interactions at nonconserved sites; lack of conservation in seed matches shown for mouse, dog, chicken (continued in Figure S5F). (F) KSHV miR-K4 and miR-K1 repress targets via nonconserved sites. Of the six sites tested, only the miR-K1 binding site in the 3’UTR of TRIM33 is conserved. Its localization in a conserved region that extends over ~500 nts is not indicative of evolutionary selection specific to the miRNA binding site. See also Figure S5.