Non-inhibited miRNAs shape the cellular response to anti-miR.
Bottom Line: Here, we utilized RNA immunoprecipitation (RIP) combined with competitive binding assays to identify novel primary targets of miR-122.Importantly, using a metric based on weighted miRNA expression, we found that the most responsive mRNA target candidates in both RIP competition assays and expression profiling experiments were those with fewer alternative seed sites for highly expressed non-inhibited miRNAs.These data strongly suggest that miRNA co-regulation modulates the transcriptomic response to anti-miR.
Affiliation: Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA firstname.lastname@example.org.Show MeSH
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Mentions: With the RIP competition assay in hand, we next sought to identify which target candidates from a shortlist of computational predictions best responded to anti-miR-122. A custom Nanostring nCounter codeset was designed with probes recognizing 37 genes predicted by the TargetScan algorithm (11) to be regulated by miR-122 (Table 1 (27–35)). An additional four genes without miR-122 sites were also included, among which the top two most stable genes were used as reference genes (Supplementary Figure S2). Similar to earlier results, these candidate transcripts were differentially displaced by anti-miR-122 from immunoprecipitated fractions (Figure 2A–C, Supplementary Figure S3). Based on the extent of displacement, we were able to classify candidate genes as either ‘RIP-responsive’ or ‘RIP-non-responsive’. Fourteen candidates (38%) showed statistically significant displacement with 400 nM anti-miR-122 compared to control (Figure 2A). An additional two candidates responded at the next highest tested anti-miR-122 concentration (4000 nM; Figure 2B), making for a total of 16 candidates (43%) that could be confirmed as being anti-miR-122 sensitive. These targets are consequently likely to be direct targets of miR-122. Consistently, all but one RIP-responsive gene (94%) showed significant derepression in vivo following anti-miR-122 treatment (Figure 2E). Notably, expression changes of RIP responsive genes were very strongly correlated (r = −0.91) with levels of RIP response (Figure 2D), indicating that changes in expression in vivo are proportional to the amount of target RNA released from RISC complexes by anti-miR. In contrast, a similar correlation did not exist with RIP-non-responsive candidates. Most non-responsive genes were also not significantly upregulated following in vivo anti-miR-122 treatment (Figure 2E). There were, however, a few exceptions: a total of nine genes were significantly upregulated, but RIP-non-responsive at any tested anti-miR-122 concentration (summarized in Table 1). Potentially, expression changes in these latter genes occur as a result of secondary effects of miR-122 inhibition, rather than as a direct consequence. Therefore, despite the fact that these genes contain a miR-122 seed-match and are upregulated in the presence of anti-122, they are less likely to be direct biomarkers of miRNA modulation. These results demonstrate how RIP competition assays can serve as a filter combined with expression analysis to assist in identifying high-confidence primary anti-miR PD markers.
Affiliation: Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA email@example.com.