miRNAs

MicroRNA contributions to animal development.

Repression is a recurrent mechanism to impose spatial and temporal boundaries on biological processes. MicroRNAs form a class of post-transcriptional repressors, which evolve more rapidly than protein-coding genes and have expanded together with animal complexity. We thus set out to study the contribution of miRNAs to shaping cellular diversity through repression. Over the past years we have used C. elegans to provide:

  1. A new method for miRNA profiling: We recently developed mime-seq, an innovative approach to sequence mature miRNAs from individual cell types within a complex cell mix, without cell sorting or biochemical purification (Alberti et al., Nat Methods 2018). It relies on a plant enzyme, HEN1, that specifically methylates plant miRNAs. As animal miRNAs are not normally methylated, cell-specific expression of HEN1 provides a way to label miRNAs in cells of interest. A methylation-specific sequencing protocol then enables retrieval of methylated, and thus cell-specific, miRNAs from total RNA. Mime-seq is robust, specific and sensitive, and is applicable to C. elegans and Drosophila. We have used mime-seq and a deconvolution strategy to generate an atlas of miRNA expression for the complete C. elegans nervous system (in progress). We are currently refining this map but our initial analysis revealed that miRNAs are enriched in sensory neurons relative to motor or interneurons. Sensory systems rely on large cell diversity to respond to multiple different stimuli, but also flexibility over evolutionary time to allow adaptation to new niches. MiRNAs are excellent candidates to contribute to sensory-neuron diversification during development and evolution.
  2. A new framework for miRNA function in development: We extensively profiled miRNAs using transcriptional reporters in genomic context as well as mime-seq, revealing a natural classification of miRNAs in embryogenesis: a minority of miRNAs is broadly-expressed in the early embryo, while the majority is expressed in one or a few cell types with onset in late embryos. We found that two conserved, early and broadly-expressed miRNA families (miR-35 and -51) are sufficient for development of morphologically-normal C. elegans, in the absence of all other miRNAs (Dexheimer et al. Curr. Biol. 2020). Instead, we hypothesize that most miRNAs may play roles during terminal differentiation or function of specialized cells. Based on work from others, we propose this framework applies to other animals. Using genetics, we aim to find out how these miRNAs function. In particular, miR-51 is deeply conserved (related to miR-100, the most ancient animal miRNA). This will give new insight into the essential function of these post-transcriptional repressors.
  3. A new concept in miRNA-mediated regulation: We have studied in depth two miRNAs with high cell-type specificity. We found that miR-791 is present exclusively in the 3 pairs of CO2-sensing neurons of C. elegans and is required for their function. We also study miR-1, a conserved muscle miRNA that is necessary for muscle development and function. Using rigorous genetic tests, we identified the functionally-relevant targets for each miRNA (Drexel et al., Genes & Dev 2016; Gutierrez Perez et al., Sci. Adv. 2021). Interestingly, both act by repressing otherwise ubiquitously-transcribed genes, revealing that miRNAs can support the function of specialized cells by carving out the specificity of typically considered house-keeping genes.

Relevant publications: