ArticleNucleic acids research2012
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it, 92 citations in OpenAlex.
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- microRNA-Mediated Encoding and Decoding of Time-Dependent Signals in Tumorigenesis.Biomolecules · 2022Review
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- Gene-specific MicroRNA antagonism protects against HIV Tat and TGF-β-mediated suppression of CFTR mRNA and function.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2021Article
- Bioinspired artificial exosomes based on lipid nanoparticles carrying let-7b-5p promote angiogenesis in vitro and in vivo.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding.Nucleic acids research · 2021Article
- Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic.International journal of molecular sciences · 2021Review
- Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy.Theranostics · 2021Article
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- Identification of two microRNA nodes as potential cooperative modulators of liver metabolism.Hepatology research : the official journal of the Japan Society of Hepatology · 2019Article
- Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer.Nucleic acids research · 2019Review
- Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish.Genome research · 2019Article
- Modulation and Evolution of Animal Development through microRNA Regulation of Gene Expression.Genes · 2019Review
- Sensory Neuropathy Affects Cardiac miRNA Expression Network TargetingInternational journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNA (miRNA) target hubs are genes that can be simultaneously targeted by a comparatively large number of miRNAs, a class of non-coding RNAs that mediate post-transcriptional gene repression. Although the details of target hub regulation remain poorly understood, recent experiments suggest that pairs of miRNAs can cooperate if their binding sites reside in close proximity. To test this and other hypotheses, we established a novel approach to investigate mechanisms of collective miRNA repression. The approach presented here combines miRNA target prediction and transcription factor prediction with data from the literature and databases to generate a regulatory map for a chosen target hub. We then show how a kinetic model can be derived from the regulatory map. To validate our approach, we present a case study for p21, one of the first experimentally proved miRNA target hubs. Our analysis indicates that distinctive expression patterns for miRNAs, some of which interact cooperatively, fine-tune the features of transient and long-term regulation of target genes. With respect to p21, our model successfully predicts its protein levels for nine different cellular functions. In addition, we find that high abundance of miRNAs, in combination with cooperativity, can enhance noise buffering for the transcription of target hubs.
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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.