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Understanding mechanisms and functions of miRNA oscillations during development

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Molecular ticktock of development

Various biological processes, including development, demonstrate rhythmic behaviour. Researchers now show that regulatory RNAs oscillate and are implicated in developmental timing.

Fundamental Research
Health

Faithful development of organisms requires that the right genes be turned on and off at the right times, in the right places. This necessitates careful molecular and temporal orchestration of gene expression. In many systems, molecular oscillators (or clocks) are important in controlling these dynamics. Typically, they are based on networks of transcription factors and signalling proteins that control, on a rhythmic basis, the expression levels of thousands of target genes through transcriptional mechanisms.

miRNA expression during development

Other, so-called post-transcriptional mechanisms of gene expression regulation are also known, which take place at the RNA level and may impact RNA stability and/or levels. Notably, non-coding microRNAs, or miRNAs for short, are small regulatory RNAs that can silence the mRNAs after their production, thereby modulating gene activity. The miRhythm project was undertaken with the support of the Marie Skłodowska-Curie Actions (MSCA) programme. “The key goal was to investigate potential oscillations of miRNA molecules during development as drivers of dynamic gene expression patterns,” explains the MSCA fellow Smita Nahar. Previous work mostly with cultured cells indicated that miRNAs are rather stable molecules whose abundance changes little over time. However, when Nahar and colleagues investigated miRNA dynamics in developing larvae of the roundworm Caenorhabditis elegans, they could see highly dynamic changes, including miRNAs that accumulated rhythmically every 8 hours. “We were curious to learn how these dynamics were generated and what they could mean biologically,” Nahar emphasises. Aided by mathematical modelling, researchers identified several miRNAs with highly dynamic expression patterns. To explore the features that cause these expression patterns, and the consequences of altering them, the team proceeded to delete the miRNAs or express them from a different promoter that does not oscillate. This was undertaken using cutting edge genome editing and quantitative time lapse imaging approaches. Emphasis was also given to the outcome of disrupted miRNA activity and how it affects organism development.

Dynamic miRNA regulation

Results showed that the miRNAs themselves are under both transcriptional and post-transcriptional regulation, which in combination generate the observed highly dynamic patterns during development. Quantitative assessment of the developmental tempo further allowed the team to investigate the roles of rhythmically expressed miRNAs in developmental timing. “The most exciting achievement was the discovery that in vivo, in the developing animal, miRNA levels are highly dynamic,” outlines Nahar. “This suggests that we previously underestimated their regulatory potential.” The identification of miRNAs whose expression patterns cannot be explained by transcription alone led to the characterisation of the post-transcriptional elements that contribute to their temporal expression. Future work will involve the delineation of these mechanisms to appreciate their diversity. Perturbations in time-keeping mechanisms have recently emerged as a major driver to global health problems like obesity, cardiovascular disease, and metabolic liver disease. Therefore, the ramifications of miRhythm results extend beyond developmental processes. Gaining insight into the molecular mechanisms by which oscillatory gene expression mediates temporal control in an organism is central to dealing with such perturbations.

Keywords

miRhythm, miRNA, development, developmental timing, oscillation, gene expression regulation

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