Pairing beyond the Seed Supports MicroRNA Targeting Specificity

Abstract

To identify endogenous miRNA-target sites, we isolated AGO-bound RNAs from Caenorhabditis elegans by individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP), which fortuitously also produced miRNA-target chimeric reads. Through the analysis of thousands of reproducible chimeras, pairing to the miRNA seed emerged as the predominant motif associated with functional interactions. Unexpectedly, we discovered that additional pairing to 3' sequences is prevalent in the majority of target sites and leads to specific targeting by members of miRNA families. By editing an endogenous target site, we demonstrate that 3' pairing determines targeting by specific miRNA family members and that seed pairing is not always sufficient for functional target interactions. Finally, we present a simplified method, chimera PCR (ChimP), for the detection of specific miRNA-target interactions. Overall, our analysis revealed that sequences in the 5' as well as the 3' regions of a miRNA provide the information necessary for stable and specific miRNA-target interactions in vivo.

Keywords: ALG-1; C. elegans; chimeras; iCLIP; miRNA family; microRNA.

Figure 1. ALG-1 iCLIP produces miRNA-target chimeric reads

(A) The presence of miRNA-target chimeras in ALG-1 iCLIP libraries were tested by PCR using the indicated primers. (B) let-7 chimeric reads map to LCS1 and LCS2 in the lin-41 3′UTR. (C) The number of target sites and chimeric reads detected for the ten miRNAs with most target sites. (D) Distribution of target sites among transcript types. (E) Genic locations of target sites for the indicated miRNAs. (F) Up-regulation in alg-1(−) of transcripts with target sites only in 3′UTR (red) (Mann-Whitney U test, P<2×10–19) but not in coding exons (blue) (Mann-Whitney U test, P<0.35) in comparison to randomly selected transcripts. See also Figure S1 and Table S2.

Figure 2. miRNA-target chimeric reads are enriched for seed pairing

(A) The seed complement is the primary motif identified by MEME of targets for the indicated miRNAs. (B) Density plot showing enrichment of 6mer seed and 3′ supplementary complementarity to cognate miRNAs at 3′UTR target sites. (C) miRNA-target duplex structure predictions calculated by RNAhybrid and partitioned into seven classes by k-means clustering. Black pixels represent pairing. (D) Distribution of classes among all mRNA, coding exon or 3′UTR target sites. (E) Distribution of classes for the indicated miRNAs. Significantly enriched classes (one-sided Fisher’s exact test, P<0.001) are indicated (*). (F) Class interactions of established miRNA target sites. For sites with multiple miRNAs bound, the miRNA with the greatest number of chimeric reads at that site was chosen. (G) Up-regulation of transcripts in alg-1(−) for each interaction class (Mann-Whitney U test, *** P<0.001, ** P<0.005). (H) T1A is enriched after the seed complement for the ten miRNAs with the greatest number of target sites compared to sites with shuffled dinucleotides (Fisher’s exact test, P<0.0001). Error bars represent ±SEM. (I) Distribution of seed complements for all mRNA target sites and the indicated miRNAs. See also Figure S1.

Figure 3. The let-7 family of miRNAs binds divergent sets of target sites

(A) Mature sequences of the three most abundant let-7 family miRNAs. (B) Overlap of target sites for let-7 family miRNAs. (C) Transcripts specifically bound by single let-7 family miRNAs in 3′UTRs are up-regulated in alg-1(−) compared to random transcripts (Mann-Whitney U test: let-7 targets P<1.3×10- 5, miR-48 targets P<4.4×10-5, miR-241 targets P<0.18). (D) qRT-PCR of let-7 specific target candidates in the indicated strains (* P<0.05). Error bars represent ±SEM. (E) Examples of shared and specific let-7 family targets with predicted pairing interactions. (F) RNAhybrid analysis of minimum free energy of miRNA-target duplex for each let-7 family member to its specific mRNA target sites. See also Figure S2 and S3.

Figure 4. Seed pairing is not sufficient for target regulation in vivo

(A) Northern blot for lin-41 in the indicated strains. (B–C) Diagram with binding profiles for let-7, miR-48, and miR-241 pairing to sites in WT lin-41 and lin-41(ap427) where the let-7 complementary sites (LCS) have been switched miR-48 complementary sites (48CS). (D) let-7(n2853) animals burst through the vulva at 25°C. (E) Suppr ession of let- 7(n2853) bursting by lin-41(ap427). (F) lin-41(ap427);miR-48(n4097) double mutants phenocopy let-7(n2853) vulval bursting. (G) Quantification of bursting in the presence (+) and absence (−) of the indicated gene products. Error bars represent ±SEM (H) qRT-PCR of lin-41 in let-7(n2853) and lin-41(ap427);let-7(n2853), normalized to WT and lin-41(ap427) strains, respectively. Error bars represent ±SEM. (I) Single worm qRT-PCR of lin-41 in lin-41(ap427);miR-48(n4097) strains heterozygous or homozygous for the miR-48 deletion, normalized to lin-41(ap427);miR-48(+/+). Error bars represent ±SEM.

Figure 5. Chimera PCR (ChimP) enables the identification of miRNA-target chimeras by PCR

(A) Detection of let-7 family chimeras using ChimP. Libraries were generated using higher (H) and lower (L) molecular weight cDNAs. (B) Single primer negative controls along with a let-7 + lin-41(LCS2) positive control from another part of the gel. (C) Examples of sequenced ChimP products for let-7 and lin-41 LCS2, and miR-48 and dot-1.1. (D) Detection of the lin-41 LCS2 with let-7 but not with other let-7 family member primers by ChimP. (E) Specific detection of dot-1.1 with a primer for miR-48. (F) The miR-48 complement sites in the lin-41(ap427) 3′UTR interact with miR-48 and not let-7. See also Figure S4.