
pmid: 31675359
pmc: PMC6853376
arXiv: 1910.09256
handle: 20.500.14243/423498 , 11583/2976758 , 11573/1336201
pmid: 31675359
pmc: PMC6853376
arXiv: 1910.09256
handle: 20.500.14243/423498 , 11583/2976758 , 11573/1336201
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can influence expression levels, buffer fluctuations and promote signal propagation. Such a potential has been characterized mathematically for small motifs both at steady state and \red{away from stationarity}. Experimental evidence, on the other hand, suggests that competing endogenous RNA (ceRNA) crosstalk is rather weak. Extended miRNA-RNA networks could however favour the integration of many crosstalk interactions, leading to significant large-scale effects in spite of the weakness of individual links. To clarify the extent to which crosstalk is sustained by the miRNA interactome, we have studied its emergent systemic features in silico in large-scale miRNA-RNA network reconstructions. We show that, although generically weak, system-level crosstalk patterns (i) are enhanced by transcriptional heterogeneities, (ii) can achieve high-intensity even for RNAs that are not co-regulated, (iii) are robust to variability in transcription rates, and (iv) are significantly non-local, i.e. correlate weakly with miRNA-RNA interaction parameters. Furthermore, RNA levels are generically more stable when crosstalk is strongest. As some of these features appear to be encoded in the network's topology, crosstalk may functionally be favoured by natural selection. These results suggest that, besides their repressive role, miRNAs mediate a weak but resilient and context-independent network of cross-regulatory interactions that interconnect the transcriptome, stabilize expression levels and support system-level responses.
25 pages, includes Supporting Information; to appear in PLoS Comp Biol
QH301-705.5, Molecular Networks (q-bio.MN), FOS: Physical sciences, Quantitative Biology - Quantitative Methods, Humans, Quantitative Biology - Molecular Networks, Gene Regulatory Networks, Physics - Biological Physics, RNA, Messenger, Biology (General), Quantitative Methods (q-bio.QM), Computational Biology, Disordered Systems and Neural Networks (cond-mat.dis-nn), Condensed Matter - Disordered Systems and Neural Networks, Models, Theoretical, MicroRNAs, network, RNA, crosstalk, Gene Expression Regulation, Biological Physics (physics.bio-ph), systems biolo, FOS: Biological sciences, RNA, RNA, Long Noncoding, Transcriptome, Research Article
QH301-705.5, Molecular Networks (q-bio.MN), FOS: Physical sciences, Quantitative Biology - Quantitative Methods, Humans, Quantitative Biology - Molecular Networks, Gene Regulatory Networks, Physics - Biological Physics, RNA, Messenger, Biology (General), Quantitative Methods (q-bio.QM), Computational Biology, Disordered Systems and Neural Networks (cond-mat.dis-nn), Condensed Matter - Disordered Systems and Neural Networks, Models, Theoretical, MicroRNAs, network, RNA, crosstalk, Gene Expression Regulation, Biological Physics (physics.bio-ph), systems biolo, FOS: Biological sciences, RNA, RNA, Long Noncoding, Transcriptome, Research Article
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