Computational Detection of MicroRNA Targets

Nachtigall, Pedro Gabriel; Bovolenta, Luiz Augusto

doi:10.1007/978-1-0716-1170-8_10

Cited by 5 publications

(4 citation statements)

References 118 publications

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“…Recently, many computational tools for miRNA targeting prediction have been developed ( Nachtigall and Bovolenta, 2022 ). However, the predictive power of these tools requires further improvement.…”

Section: Current State Of Functional Mirna Target Predictionmentioning

confidence: 99%

Determinants of Functional MicroRNA Targeting

Hwang

Chang

Baek

2023

Molecules and Cells

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MicroRNAs (miRNAs) play cardinal roles in regulating biological pathways and processes, resulting in significant physiological effects. To understand the complex regulatory network of miRNAs, previous studies have utilized massive-scale datasets of miRNA targeting and attempted to computationally predict the functional targets of miRNAs. Many miRNA target prediction tools have been developed and are widely used by scientists from various fields of biology and medicine. Most of these tools consider seed pairing between miRNAs and their mRNA targets and additionally consider other determinants to improve prediction accuracy. However, these tools exhibit limited prediction accuracy and high false positive rates. The utilization of additional determinants, such as RNA modifications and RNA-binding protein binding sites, may further improve miRNA target prediction. In this review, we discuss the determinants of functional miRNA targeting that are currently used in miRNA target prediction and the potentially predictive but unappreciated determinants that may improve prediction accuracy.

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Section: Current State Of Functional Mirna Target Predictionmentioning

confidence: 99%

Determinants of Functional MicroRNA Targeting

Hwang

Chang

Baek

2023

Molecules and Cells

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“…For computational prediction and for the understanding of the process, it is important to know which mature sequence or in which ratio they are incorporated into RISC. Here current methodologies such as HITS-CLIP and CLASH [19,20] can help to define the amount of mature miRNAs bound in miRISC.…”

Section: Biogenesis and Targeting Pathwaymentioning

confidence: 99%

“…Nonetheless, it is not feasible to investigate miRNA, mRNA, and protein expression under all developmental stages, all tissue types, and all different stressors. Therefore, computational prediction of miRNAs and their targets is indispensable [20]. While pre-miRNA prediction is at a quite mature state [30], the prediction of mature miRNAs [3] from these pre-miRNAs and the prediction of miRNA targets needs further improvement [31].…”

Section: Microrna and Target Predictionmentioning

confidence: 99%

44 Current Challenges in miRNomics

Akgül

Stadler

Hawkins

et al. 2021

Methods in Molecular Biology

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Mature microRNAs (miRNAs) are short RNA sequences about 18-24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5 0 UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future.

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“…These molecules are mainly present intracellularly, but there is also an extracellular (circulating) microRNA fraction [ 3 ]. To date, the existence and functions of more than 2500 human miRNAs are known [ 4 ]. The existing database of fundamental knowledge about the structure and functional significance of microRNAs has significantly increased researchers’ interest in studying the role of these molecules in oncological and hereditary pathologies [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies

Tregub,

Ibrahimli,

Averchuk

et al. 2023

IJMS

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In recent times, there has been a significant increase in researchers’ interest in the functions of microRNAs and the role of these molecules in the pathogenesis of many multifactorial diseases. This is related to the diagnostic and prognostic potential of microRNA expression levels as well as the prospects of using it in personalized targeted therapy. This review of the literature analyzes existing scientific data on the involvement of microRNAs in the molecular and cellular mechanisms underlying the development of pathologies such as Alzheimer’s disease, cerebral ischemia and reperfusion injury, and dysfunction of the blood–brain barrier.

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Computational Detection of MicroRNA Targets

Cited by 5 publications

References 118 publications

Determinants of Functional MicroRNA Targeting

Determinants of Functional MicroRNA Targeting

44 Current Challenges in miRNomics

The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies

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