miRNA and RNA-binding proteins (SPP 1395, InKoMBio)

InKoMBio is a Priority Program of the German Research Foundation (DFG - Deutsche Forschungsgemeinschaft).
In this project we will extend a physical model for the binding of microRNAs to the corresponding target and establish an extended set of features influencing binding probabilities. We will be faced with the challenge of (i) too many features and (ii) few known interactions on which to train any prediction algorithm. This problem will be solved by using (i) information-theoretical criteria for feature reduction, (ii) regularization, (iii) application of the Infomax approach to guarantee minimal loss of information after dimension reduction, and (iv) experimental validation of theoretical predictions using a novel test system.

MicroRNAs (miRNAs) are a key component of eukaryotic cell regulation and are pervasive in both plants and animals. They play important roles in many different processes like cell differentiation, proliferation, apoptosis or development. Currently there is a lack of  high-throughput experimental approaches to determine the interaction between miRNA and target directly. Quantitative and rapid  transient screening assays in single plant cell system, Arabidopsis leaf protoplasts, for evaluation of a miRNA activity were developed  during the past funding period. Our technology provides a basis for precise modulation of both, a miRNA sequential and structural  context features by combining the mutagenesis approach and in silico-guided design of amiRNAs and target genes. Hence,  consideration and incorporation of feature information at different complexity levels are now available for the first time. Based on these advances we plan now in the forthcoming funding period to apply these techniques to overcome the current limitations in predicting miRNA targets.

InKoMBio homepage

Publications

* external authors, # joint first authors, ° joint corresponding authors

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