The miRNA–target interactions: An underestimated intricacy

Diener, Caroline; Keller, Andreas; Meese, Eckart

doi:10.1093/nar/gkad1142

Cited by 32 publications

(9 citation statements)

References 180 publications

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“…Notably, TXNIP mRNA levels did not decrease under miR-106a transfection (Figure S5). Previous studies have reported that miRNAs can inhibit the translation of target mRNAs, in addition to inhibiting protein synthesis via deadenylation and subsequent degradation of mRNA targets. , We subsequently confirmed that a luciferase reporter carrying the 3′-UTR of TXNIP was repressed by miR-106a transfection using luciferase assay (Figure D). Therefore, our results suggested that miR-106a could indeed target TXNIP by inhibiting mRNA translation rather than mRNA degradation and further suggested that ARAGON-miR-106a could be used to identify both transcriptionally and translationally silenced mRNA targets, the latter of which are not cleaved by RISC and cannot be identified by qPCR.…”

Section: Resultssupporting

confidence: 75%

G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets

Shen,

Hou,

et al. 2024

J. Am. Chem. Soc.

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MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. The identification of target mRNAs is essential for dissecting the recognition basis, dynamics, and regulatory mechanism of miRNA−mRNA interactions. However, the lack of an unbiased method for detecting weak miRNA−mRNA interactions remains a long-standing obstacle for miRNA research. Here, we develop and provide proof-of-concept evidence demonstrating a chemical G-clampenhanced photo-cross-linking strategy for covalent capture of intracellular miRNA targets in different cell lines. This approach relies on an aryldiazirine-G-clamp-modified-nucleoside (ARAGON) miRNA probe containing an alkynyl group that improves the thermal stability of miRNA− target mRNA duplex molecules and can rapidly cross-link with the complementary strand upon UV 365 nm activation, enhancing the transient capture of mRNA targets. After validating the accuracy and binding properties of ARAGON-based miRNA probes through the successful enrichment for the known targets of miR-106a, miR-21, and miR-101, we then extend ARAGON's application to screen for previously unknown targets of different miRNAs in various cell lines. Ultimately, results in this study uncover GAB1 as a target of miR-101 in H1299 lung cancer cells and show that miR-101 silencing of GAB1 can promote apoptosis in H1299 cells, suggesting an oncogenic mechanism of GAB1. This study thus provides a powerful and versatile tool for enhanced screening of global miRNA targets in cells to facilitate investigations of miRNA functions in fundamental cellular processes and disease pathogenesis.

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Section: Resultssupporting

confidence: 75%

G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets

Shen,

Hou,

et al. 2024

J. Am. Chem. Soc.

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“…The ability of microRNAs to target multiple mRNAs in a tissue-dependent manner challenges current research and requires precaution for data interpretation ( 39 ). However, most studies only focus on the organ of interest.…”

Section: Discussionmentioning

confidence: 99%

Divergent cardiac and renal effects of miR-181c-5p inhibition in a rodent heart failure model

Boen,

Gevaert,

Dendooven

et al. 2024

Front. Cardiovasc. Med.

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AimsMiR-181c-5p overexpression associates with heart failure (HF) and cardiac damage, but the underlying pathophysiology remains unclear. This study investigated the effect of miR-181c-5p inhibition on cardiac function and fibrosis in a rodent model of diastolic dysfunction, and evaluated additional effects on kidney as relevant comorbid organ.Methods and resultsDiastolic dysfunction was induced in male C57/BL6J mice (n = 20) by combining high-fat diet, L-NG-nitroarginine methyl ester, and angiotensin II administration, and was compared to sham controls (n = 18). Mice were randomized to subcutaneous miR-181c-5p antagomiR (INH) or scrambled antagomiR injections (40 mg/kg/week). HF mice demonstrated diastolic dysfunction and increased fibrosis, which was attenuated by INH treatment. Remarkably, HF + INH animals had a threefold higher mortality rate (60%) compared to HF controls (20%). Histological examination revealed increased glomerular damage in all INH treated mice, and signs of thrombotic microangiopathy (TMA) in mice who died prematurely. Quantitative polymerase chain reaction demonstrated a miR-181c-5p-related downregulation of cardiac but not renal Tgfbr1 in HF + INH mice, while INH treatment reduced renal but not cardiac Vegfa expression in all mice.ConclusionThis study demonstrates cardiac anti-fibrotic effects of miR-181c-5p inhibition in a rodent HF model through targeting of Tgfbr1 in the heart. Despite improved diastolic function, HF + INH mice had higher mortality due to increased predisposition for TMA, increased renal fibrosis and glomerular damage, associated with Vegfa downregulation in kidneys.

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“…The interpretability of cotransfection assays is further impacted by the variable and/or frequently low transfection efficacy. Furthermore, the cellular background can also affect the functionality of MTIs 53 . Different cell types express varying amounts of different RNA-binding proteins (RBPs) 54 , which can affect the ability of a miRNA to regulate target genes.…”

Section: Discussionmentioning

confidence: 99%

Experimental capture of miRNA targetomes: disease-specific 3′UTR library-based miRNA targetomics for Parkinson’s disease

Hart,

Kern,

Fecher-Trost

et al. 2024

Exp Mol Med

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The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA–target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson’s disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online (https://ccb-web.cs.uni-saarland.de/utr-seremato), and all the data have been added to the miRATBase database (https://ccb-web.cs.uni-saarland.de/miratbase).

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The miRNA–target interactions: An underestimated intricacy

Cited by 32 publications

References 180 publications

G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets

G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets

Divergent cardiac and renal effects of miR-181c-5p inhibition in a rodent heart failure model

Experimental capture of miRNA targetomes: disease-specific 3′UTR library-based miRNA targetomics for Parkinson’s disease

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