MIREyA: a computational approach to detect miRNA-directed gene activation

Elizarova, A. N.; Ozturk, Mumin; Guler, Reto; Medvedeva, Yulia A.

doi:10.12688/f1000research.28142.1

Cited by 2 publications

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“…In M0 macrophages 10 miRNAs were differentially expressed (DE) in at least one time point compared to the state before infection (0h), in M1 there was no DE miRNA, while in M2 only Mir1956 was DE. Figure 2 and Table S1 (Extended data 43 ) represent detected miRNA-enhancer-gene trios for M0 macrophages (Extended data: Table S2 for M2 macrophages 43 ). We investigated the functions of the obtained genes and miRNAs and confirmed that many of them might be involved in the response to Mtb infection.…”

Section: Resultsmentioning

confidence: 99%

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MIREyA: a computational approach to detect miRNA-directed gene activation

Elizarova

Ozturk²,

Guler³

et al. 2021

F1000Res

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Emerging studies demonstrate the ability of microRNAs (miRNAs) to activate genes via different mechanisms. Specifically, miRNAs may trigger an enhancer promoting chromatin remodelling in the enhancer region, thus activating the enhancer and its target genes. Here we present MIREyA, a pipeline developed to predict such miRNA-gene-enhancer trios based on an expression dataset which obviates the need to write custom scripts. We applied our pipeline to primary murine macrophages infected by Mycobacterium tuberculosis (HN878 strain) and detected Mir22, Mir221, Mir222, Mir155 and Mir1956, which could up-regulate genes related to immune responses. We believe that MIREyA is a useful tool for detecting putative miRNA-directed gene activation cases. MIREyA is available from: https://github.com/veania/MIREyA

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Section: Resultsmentioning

confidence: 99%

“…Zenodo: MIREyA: Extended data, http://doi.org/10.5281/zenodo.4549445. 43 This project contains the following extended data:…”

Section: Extended Datamentioning

confidence: 99%

MIREyA: a computational approach to detect miRNA-directed gene activation

Elizarova

Ozturk²,

Guler³

et al. 2021

F1000Res

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A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases

Micolucci

Matacchione

Albertini

et al. 2023

IJMS

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The nuclear factor NF-kB is the master transcription factor in the inflammatory process by modulating the expression of pro-inflammatory genes. However, an additional level of complexity is the ability to promote the transcriptional activation of post-transcriptional modulators of gene expression as non-coding RNA (i.e., miRNAs). While NF-kB’s role in inflammation-associated gene expression has been extensively investigated, the interplay between NF-kB and genes coding for miRNAs still deserves investigation. To identify miRNAs with potential NF-kB binding sites in their transcription start site, we predicted miRNA promoters by an in silico analysis using the PROmiRNA software, which allowed us to score the genomic region’s propensity to be miRNA cis-regulatory elements. A list of 722 human miRNAs was generated, of which 399 were expressed in at least one tissue involved in the inflammatory processes. The selection of “high-confidence” hairpins in miRbase identified 68 mature miRNAs, most of them previously identified as inflammamiRs. The identification of targeted pathways/diseases highlighted their involvement in the most common age-related diseases. Overall, our results reinforce the hypothesis that persistent activation of NF-kB could unbalance the transcription of specific inflammamiRNAs. The identification of such miRNAs could be of diagnostic/prognostic/therapeutic relevance for the most common inflammatory-related and age-related diseases.

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MIREyA: a computational approach to detect miRNA-directed gene activation

Cited by 2 publications

References 44 publications

MIREyA: a computational approach to detect miRNA-directed gene activation

MIREyA: a computational approach to detect miRNA-directed gene activation

A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases

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