Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires

Abstract

SUMMARY MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low-grade glioma patient samples indicate that the alternative-miR-9 has a potential role in tumor progression. Furthermore, we provide evidence that distortion of pri-miRNA stems induced by asymmetric internal loops correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.

Long-term exposure of human endothelial cells to metformin modulates miRNAs and isomiRs

“…Since studying miRNAs at the isomiR level could lend new insights into miRNA biology and function, we analysed isomiR modulation associated with metformin treatment of HUVECs during replicative senescence. IsomiRs result from a shift of the cutting site of Drosha/Dicer enzymatic activities during miRNA biogenesis 23 , 24 and can be classified into six categories according to the types of sequence modifications: (1) canonical miRNAs, (2) 3′ deletion isomiRs, (3) 3′ addition isomiRs, (4) 5′ deletion isomiRs, (5) 5′ addition isomiRs, and (6) mixed isomiRs, which represent a combination of the prior categories 25 . We also analysed the post-transcriptional addition of one or more uridines at the 3′ end of isomiRs and canonical miRNAs, namely uridylation.…”

miRNA-based biomarkers, therapies, and resistance in Cancer

“…In oral squamous cell carcinoma (OSCC) patients, miR-9 is downregulated, whose expression induces G0/G1 cell cycle arrest, while the use of miR-9 mimics significantly halts cell proliferation by repressing cyclin-dependent kinase 6 (CDK6) and cyclin D1 [68]. Besides, miR-9 has an expanded scope of target RNAs because of its pri-miRNA paralogs [69]. As one of the most abundant miRNAs in the brain, miR-9 was verified to target COL18A1, THBS2, PTCH1, and PHD3 directly in glioma cells, whose overexpression takes positive roles in processes such as proliferation and cell cycle progression [70].…”

6mer seed toxicity in viral microRNAs

“…Our data suggest that during evolution certain v-miRNAs evolved to use 6mer seed toxicity to regulate cell growth, cell cycle and survival of their host cells. It has been proposed that seed shifting is a mechanism of miRNA adaptation during evolution to allow acquisition of divergent function (Berezikov, 2011;Bofill-De Ros et al, 2019). The small but significant increased use of a noncanonical seed by v-miRNAs may be a reflection of an ongoing evolutionary process that was conserved in the v-miRNAs at the time the miRNAs were acquired from the host cells.…”