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Updated: Nov 25, 2025

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the
Shaked Bergman1, Alon Diament1, Tamir Tuller1,2
1Department of Biomedical Engineering, Tel-Aviv University, 69978 Tel Aviv, Israel.
Motivation:
MicroRNAs (miRNAs) are short (∼24nt), non-coding RNAs, which downregulate gene expression in many species and physiological processes. Many details regarding the mechanism which governs miRNA-mediated repression continue to elude researchers.
Results:
We elucidate the interplay between the coding sequence and the 3'UTR, by using elastic net regularization and incorporating translation-related features to predict miRNA-mediated repression. We find that miRNA binding sites at the end of the coding sequence contribute to repression, and that weak binding sites are linked to effective de-repression, possibly as a result of competing with stronger binding sites. Furthermore, we propose a recycling model for miRNAs dissociated from the open reading frame (ORF) by traversing ribosomes, explaining the observed link between increased ribosome density/traversal speed and increased repression. We uncover a novel layer of interaction between the coding sequence and the 3'UTR (untranslated region) and suggest the ORF has a larger role than previously thought in the mechanism of miRNA-mediated repression.
Availability And Implementation:
The code is freely available at https://github.com/aescrdni/miRNA_model.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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