Model Identifier
BIOMD0000000530
Short description
Schmitz2014 - RNA triplex formation
The model is parameterized using the parameters for gene CCDC3 from Supplementary Table S1. The two miRNAs which form the triplex together with CCDC3 are miR-551b and miR-138.

This model is described in the article:

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.
Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK.
Nucleic Acids Res. 2014 Jul; 42(12): 7539-7552

Abstract:

MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation. In this paper, we present a computational workflow for the prediction and analysis of cooperating miRNAs and their mutual target genes, which we refer to as RNA triplexes. The workflow integrates methods of miRNA target prediction; triplex structure analysis; molecular dynamics simulations and mathematical modeling for a reliable prediction of functional RNA triplexes and target repression efficiency. In a case study we analyzed the human genome and identified several thousand targets of cooperative gene regulation. Our results suggest that miRNA cooperativity is a frequent mechanism for an enhanced target repression by pairs of miRNAs facilitating distinctive and fine-tuned target gene expression patterns. Human RNA triplexes predicted and characterized in this study are organized in a web resource at www.sbi.uni-rostock.de/triplexrna/.

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Format
SBML (L2V4)
Related Publication
  • Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.
  • Ulf Schmitz, Xin Lai, Felix Winter, Olaf Wolkenhauer, Julio Vera, Shailendra K Gupta
  • Nucleic acids research , 7/ 2014 , Volume 42 , Issue 12 , pages: 7539-7552 , PubMed ID: 24875477
Contributors
Submitter of the first revision: Felix Winter
Submitter of this revision: Lucian Smith
Curator: Lucian Smith
Modellers: administrator, Felix Winter

Metadata information

is (2 statements)
BioModels Database BIOMD0000000530
BioModels Database MODEL1402210000

isDescribedBy (1 statement)
PubMed 24875477

hasTaxon (1 statement)
Taxonomy Homo sapiens

isVersionOf (1 statement)
hasProperty (1 statement)
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Curated
Modelling approach(es)
ordinary differential equation model

Connected external resources