ArticleRNA biology2013
The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance.
Article in RNA biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 49 citations in OpenAlex.
- miRNAProtPred: computational prediction of human miRNA binding based on seed complementarity and thermodynamic stability.Frontiers in genetics · 2026Article
- Advanced computational predictive models of miRNA-mRNA interaction efficiency.Computational and structural biotechnology journal · 2024Article
- MiR-128-3p - a gray eminence of the human central nervous system.Molecular therapy. Nucleic acids · 2024Review
- Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart.BMC genomics · 2023Article
- Outside the limit: questioning the distance restrictions for cooperative miRNA binding sites.Cellular & molecular biology letters · 2023Article
- The Role of MicroRNAs in Liver Functioning: from Biogenesis to Therapeutic Approaches (Review).Sovremennye tekhnologii v meditsine · 2023Review
- Interplay of SOX transcription factors and microRNAs in the brain under physiological and pathological conditions.Neural regeneration research · 2022Review
- Article
- Circulating microRNA trafficking and regulation: computational principles and practice.Briefings in bioinformatics · 2020Review
- MicroRNA (miRNA)-to-miRNA Regulation of Programmed Cell Death 4 (PDCD4).Molecular and cellular biology · 2019Article
- Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer.Nucleic acids research · 2019Review
- The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus.Scientific reports · 2019Article
- Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay.Nature communications · 2018Article
- PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs.Nature communications · 2018Article
- CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.Bioinformatics (Oxford, England) · 2018Article
- MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance.Theranostics · 2018Article
- A high-throughput 3' UTR reporter screening identifies microRNA interactomes of cancer genes.PloS one · 2018Article
- Dynamic and Modularized MicroRNA Regulation and Its Implication in Human Cancers.Scientific reports · 2017Article
- Time-lapse imaging of microRNA activity reveals the kinetics of microRNA activation in single living cells.Scientific reports · 2017Article
- Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MiRNAs are short, non-coding RNAs that regulate gene expression post-transcriptionally through specific binding to mRNA. Deregulation of miRNAs is associated with various diseases and interference with miRNA function has proven therapeutic potential. Most mRNAs are thought to be regulated by multiple miRNAs and there is some evidence that such joint activity is enhanced if a short distance between sites allows for cooperative binding. Until now, however, the concept of cooperativity among miRNAs has not been addressed in a transcriptome-wide approach. Here, we computationally screened human mRNAs for distances between miRNA binding sites that are expected to promote cooperativity. We find that sites with a maximal spacing of 26 nucleotides are enriched for naturally occurring miRNAs compared with control sequences. Furthermore, miRNAs with similar characteristics as indicated by either co-expression within a specific tissue or co-regulation in a disease context are predicted to target a higher number of mRNAs cooperatively than unrelated miRNAs. These bioinformatic data were compared with genome-wide sets of biochemically validated miRNA targets derived by Argonaute crosslinking and immunoprecipitation (HITS-CLIP and PAR-CLIP). To ease further research into combined and cooperative miRNA function, we developed miRco, a database connecting miRNAs and respective targets involved in distance-defined cooperative regulation (mips.helmholtz-muenchen.de/mirco). In conclusion, our findings suggest that cooperativity of miRNA-target interaction is a widespread phenomenon that may play an important role in miRNA-mediated gene regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.