The deterministic role of 5-mers in microRNA-gene targeting

Hart, Martin; Kern, Fabian; Backes, Christina; Rheinheimer, Stefanie; Fehlmann, Tobias; Keller, Andreas; Meese, Eckart

doi:10.1080/15476286.2018.1462652

Cited by 14 publications

(13 citation statements)

References 66 publications

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“…Therefore, together with our data herein, multiple genes in the autophagy pathway have been shown to be regulated by miRNAs, including targeting of ATG2B by miR-130 in chronic lymphocytic leukemia [ 45 ] and ATG14 by miR-140 in multiple myeloma [ 46 ]. On the other hand, in contrast to previously reported that miRNA targeting was mediated through the putative SRBS of ≥ 6-mer [ 47 ], our data showed that additional two 5-mer binding sites in the 3’UTR of MAP1LC3B contributed to targeting by miR-342-3p, and hence similarly suggesting a role of 5-mer binding sites in miRNAs-mediated posttranscriptional regulation of target genes [ 48 ].…”

Section: Discussioncontrasting

confidence: 99%

Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy

et al. 2020

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Background miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in carcinogenesis. Given the presence of a promotor-associated CpG island for its host gene, EVL, we hypothesized that intronic miR-342-3p is a tumor suppressor co-regulated with host gene by promoter DNA methylation in B cell lymphoma. Results By bisulfite pyrosequencing-verified methylation-specific PCR (MSP), EVL/MIR342 methylation was detected in five (50%) lymphoma cell lines but not normal peripheral blood and tonsils. EVL/MIR342 methylation correlated with repression of both miR-342-3p and EVL in cell lines. In completely methylated SU-DHL-16 cells, 5-AzadC treatment resulted in promoter demethylation and re-expression of miR-342-3p and EVL. In 132 primary lymphoma samples, EVL/MIR342 was preferentially methylated in B cell lymphomas (N = 68; 68.7%) than T cell lymphoma (N = 8; 24.2%) by MSP (P < 0.0001). Moreover, EVL/MIR342 methylation was associated with lower miR-342-3p expression in 79 primary NHL (P = 0.0443). In SU-DHL-16 cells, the tumor suppressor function of miR-342-3p was demonstrated by the inhibition of cellular proliferation and increase of cell death upon over-expression of miR-342-3p. Mechanistically, overexpression of miR-342-3p resulted in a decrease of LC3-II, a biomarker of autophagy, which was pro-survival for SU-DHL-16. Pre-treatment with 3-methyladenine, an autophagy inhibitor, abrogated tumor suppression associated with miR-342-3p overexpression. By luciferase assay, MAP1LC3B, a precursor of LC3-II, was confirmed as a direct target of miR-342-3p. Finally, in SU-DHL-16 cells, overexpression of miR-342-3p downregulated the known target DNMT1, with promoter demethylation and re-expression of tumor suppressor E-cadherin. Conclusions Intronic miR-342-3p is co-regulated with its host gene EVL by tumor-specific promoter DNA methylation in B cell lymphoma. The tumor suppressor function of miR-342-3p was mediated via inhibition of pro-survival autophagy by targeting MAP1LC3B and downregulation of DNMT1 with demethylation and re-expression of tumor suppressor genes.

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Section: Discussioncontrasting

confidence: 99%

Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy

et al. 2020

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“…While miRNA gene targeting relies on a complementary binding of the seed region to the target gene, non-canonical binding between gene and miRNA also seems to have a deterministic influence on the targeting process ( 11 , 12 ). The limited understanding of the true complexity of the interactions between miRNAs and genes poses substantial challenges for the computational prediction of miRNA targets.…”

Section: Introductionmentioning

confidence: 99%

Validation of human microRNA target pathways enables evaluation of target prediction tools

Kern

Krammes

Danz

et al. 2020

Nucleic Acids Research

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MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.

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“…Although experimental validations are necessary, they often significantly exceed the scope of scientific publications, even for one single miRNA. On the other hand, purely bioinformatical interaction studies lack predictive power, particularly for non-canonical miRNA targeting, with high false positive and false negative rates (Hart et al, 2018). Bioinformatically supported high-throughput techniques such as short RNA sequencing can serve as an integrative middle ground.…”

Section: Discussionmentioning

confidence: 99%

Integrative Transcriptomics Reveals Sexually Dimorphic Control of the Cholinergic/Neurokine Interface in Schizophrenia and Bipolar Disorder

et al. 2019

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Graphical Abstract Highlights d Single-cell transcriptomes reveal a unique profile of cortical cholinergic neurons d Female-and male-derived cells show distinct neurokineinduced miRNA responses d Differentially enriched microRNA families constitute a selforganizing network d Integrative analysis identifies mir-10/mir-199 regulators of cholinergic function SUMMARYRNA sequencing analyses are often limited to identifying lowest p value transcripts, which does not address polygenic phenomena. To overcome this limitation, we developed an integrative approach that combines large-scale transcriptomic meta-analysis of patient brain tissues with single-cell sequencing data of CNS neurons, short RNA sequencing of human male-and female-originating cell lines, and connectomics of transcription factor and microRNA interactions with perturbed transcripts. We used this pipeline to analyze cortical transcripts of schizophrenia and bipolar disorder patients. Although these pathologies show massive transcriptional parallels, their clinically well-known sexual dimorphisms remain unexplained. Our method reveals the differences between afflicted men and women and identifies disease-affected pathways of cholinergic transmission and gp130family neurokine controllers of immune function interlinked by microRNAs. This approach may open additional perspectives for seeking biomarkers and therapeutic targets in other transmitter systems and diseases.

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The deterministic role of 5-mers in microRNA-gene targeting

Cited by 14 publications

References 66 publications

Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy

Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy

Validation of human microRNA target pathways enables evaluation of target prediction tools

Integrative Transcriptomics Reveals Sexually Dimorphic Control of the Cholinergic/Neurokine Interface in Schizophrenia and Bipolar Disorder

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