Functional relevance of “seed” and “non-seed” sequences in microRNA-mediated promotion of C. elegans developmental progression

Abstract

The founding heterochronic microRNAs, lin-4 and let-7, together with their validated targets and well-characterized phenotypes in C. elegans, offer an opportunity to test functionality of microRNAs in a developmental context. In this study, we defined sequence requirements at the microRNA level for these two microRNAs, evaluating lin-4 and let-7 mutant microRNAs for their ability to support temporal development under conditions where the wild-type lin-4 and let-7 gene products are absent. For lin-4, we found a strong requirement for seed sequences, with function drastically affected by several central mutations in the seed sequence, while rescue was retained by a set of mutations peripheral to the seed. let-7 rescuing activity was retained to a surprising degree by a variety of central seed mutations, while several non-seed mutant effects support potential noncanonical contributions to let-7 function. Taken together, this work illustrates both the functional partnership between seed and nonseed sequences in mediating C. elegans temporal development and a diversity among microRNA effectors in the contributions of seed and non-seed regions to activity.

Pairing beyond the Seed Supports MicroRNA Targeting Specificity

“…Loss of let-7 results in a lethal phenotype where animals burst through their vulvas (Reinhart et al, 2000; Slack et al, 2000), and this phenotype can be suppressed by restoring regulation of just lin-41 (Ecsedi et al, 2015). Additionally, versions of let-7 that contain mutations in 3′ end sequences do not fully rescue bursting of let-7 mutants, pointing to the importance of the 3′ end of this miRNA (Zhang et al, 2015). To further test if regulation of lin-41 is entirely dependent on let-7, we analyzed the expression of lin-41 in let-7(n2853) animals and in null mutants of miR-48 and miR-241, at mid-L4 stage.…”

5p and 3p Strands of miR-34 Family Members Have Differential Effects in Cell Proliferation, Migration, and Invasion in Cervical Cancer Cells

“…It could be possible that miR-34a-3p directly or indirectly downregulates MMP2 activity. It must be observed that MMP2 does not have binding sites for the 3p strand of miR-34a-3p; nevertheless, several miRNAs regulate mRNAs independently of the seed sequence [71].…”

Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased arm switching and increasing complexity of expression throughout development

“…The miRNA regulation strength in animals is greatly dependent on the amount of complementarity between miRNA seed region (a domain at the 5′ end of miRNA transcripts that spans from nucleotide position 2 to 7) and MRE at the mRNA transcript. However, there is growing evidence that the downstream nucleotides of miRNAs may also play a relevant role 12 , 13 .…”