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Groundbreaking technique to study microRNAs in single cells of living animals

26 Feb 2018

Scientists from two institutes at the Vienna BioCenter (VBC) have developed a method to identify and characterise microRNAs in individual cells of living animals. The technique, called “mime-seq”, allows the study of microRNAs in their endogenous context at single-cell resolution. It was now published in the journal “Nature Methods”.

Small non-coding RNAs, such as microRNAs, play a key role in the regulation of gene expression and thus crucially influence the development and life functions of animals and plants. Two teams of scientists based at research institutes at the Vienna BioCenter (VBC) have overcome a major challenge to study these microRNAs.

Until now, scientists were limited in linking microRNA functions to the biology of specific cell types in living organisms, as they are part of complex tissues. This was largely because established techniques to profile microRNAs do not work reliably and at cellular resolution. As a result, research in this field was largely confined to cell culture and other “in vitro” approaches.

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In their novel “mime-seq” technique, the VBC scientists use an enzyme that chemically “tags” microRNAs in specific cell types in living animals. This enhances the resolution at which microRNAs can be retrieved in a tissue of interest to the level of individual cells.

The scientists used nematode worms and fruit flies to demonstrate that “mime-seq” can indeed be applied to map the microRNA profiles of defined cell populations. “Our work lifts the possibilities we have to study microRNAs to a whole new level”, says Chiara Alberti, a VBC PhD student who is the first author of the study. “With mime-seq, we have a new entry point for improving our understanding of the way microRNAs steer development and physiology in living animals.”

As microRNAs contribute crucially to fundamental processes in life such as cell differentiation, “mime-seq” is opening a window on the function of microRNAs and provides a new tool to labs around the world. The technique was published in the journal “Nature Methods”. Its development was a collaborative effort by the labs of Luisa Cochella of the Research Institute of Molecular Pathology (IMP) and Stefan Ameres of the Institute of Molecular Biotechnology (IMBA). The publication is evidence for the strong “RNA community” and the collaborative spirit found at the Vienna BioCenter.

About the VBC PhD Programme

Much of the work underlying this publication was done by a doctoral student of the Vienna BioCenter PhD Programme. Are you interested in a world-class career in molecular biology? Find out more about VBC training opportunities at:

Original publication

Alberti, C., et al. (2018): “Cell-type specific sequencing of microRNAs from complex animal tissues.” Nature Methods. doi: 10.1038/nmeth.4610

Image Caption

“Scientists in Vienna developed a new method to profile microRNAs in living organisms. Here you can see a picture of the major animal model investigated in the study, a nematode worm of the species C. elegans.” (c) IMP-IMBA

About the Vienna BioCenter

Vienna BioCenter (VBC) is a leading life sciences hub in Europe, offering an extraordinary combination of research, business and education in a single location. About 1,700 employees, 86 research groups, 18 biotech companies, 1,300 students and scientists from 70 nations create a highly dynamic and stimulating environment.