Computational Prediction of Functional MicroRNA–mRNA Interactions

Demirci, Müşerref Duygu Saçar; Yousef, Malik; Allmer, Jens

doi:10.1007/978-1-4939-8982-9_7

Cited by 24 publications

(15 citation statements)

References 121 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Weak binding strength tends to inhibit the gene expression by targeting translation. mRNA instability and degradation most likely result when the corresponding miRNA sequence is completely complimentary, leading to tight binding and activation of the RNA-mediated interference (RNAi) pathway [37].…”

Section: Mirnasmentioning

confidence: 99%

Differential MicroRNA-Signatures in Thyroid Cancer Subtypes

Santiago

Wongworawat

Khan

2020

Journal of Oncology

View full text Add to dashboard Cite

Thyroid cancer is one of the most common endocrine cancers, with an increasing trend in the last few decades. Although papillary thyroid cancer is the most frequent subtype compared with follicular or anaplastic thyroid cancer, it can dedifferentiate to a more aggressive phenotype, and the recurrence rate is high. The cells of follicular adenomas and follicular carcinomas appear identical in cytology, making the preoperative diagnosis difficult. On the other hand, anaplastic thyroid cancer poses a significant clinical challenge due to its aggressive nature with no effective therapeutic options. In the past several years, the roles of genetic alterations of thyroid tumors have been documented, with a remarkable correlation between genotype and phenotype, indicating that distinct molecular changes are associated with a multistep tumorigenic process. Besides mRNA expression profiles, small noncoding microRNA (miRNA) expression also showed critical functions for cell differentiation, proliferation, angiogenesis, and resistance to apoptosis and finally activating invasion and metastasis in cancer. Several high-throughput sequencing studies demonstrate that miRNA expression signatures contribute clinically relevant information including types of thyroid cancer, tumor grade, and prognosis. This review summarizes recent findings on miRNA signatures in thyroid cancer subtypes.

show abstract

Section: Mirnasmentioning

confidence: 99%

Differential MicroRNA-Signatures in Thyroid Cancer Subtypes

Santiago

Wongworawat

Khan

2020

Journal of Oncology

View full text Add to dashboard Cite

show abstract

“…To define biological functions for ncRNAs, some experimental approaches are employed for the investigation of ncRNA-based targeting, like PAR-CLIP [67], HITS-CLIP [68], and CLASH [69]. HITS-CLIP is widely used for functional protein-RNA interaction sites identifying and miRNA-mRNA regulatory interactions analysis [70], [71]. Compared to the HITS-CLIP, PAR-CLIP improves RNA recovery efficiency and indicates the site of targeting more precisely through identifying the location of the crosslink [71], [72].…”

Section: Ncrna Interactionsmentioning

confidence: 99%

“…HITS-CLIP is widely used for functional protein-RNA interaction sites identifying and miRNA-mRNA regulatory interactions analysis [70], [71]. Compared to the HITS-CLIP, PAR-CLIP improves RNA recovery efficiency and indicates the site of targeting more precisely through identifying the location of the crosslink [71], [72]. LIGR-seq (LIGation of interacting RNA followed by high-throughput sequencing) is a new developed method that enables the global-scale mapping of RNA-RNA duplexes in vivo [73], which enlarges the landscape of ncRNA-mRNA interactions.…”

Section: Ncrna Interactionsmentioning

confidence: 99%

Non-Coding RNAs and their Integrated Networks

Zhang

Chen

et al. 2019

Journal of Integrative Bioinformatics

513

325

View full text Add to dashboard Cite

Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs’ essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

show abstract

“…1 Basal miR biogenesis and secretion into the bloodstream. Long pri-miRNAs are initially transcribed from miRNA genes or can be co-transcribed with protein coding genes (Saçar Demirci et al 2019) within the nucleus and translocated to the cytoplasm as immature pre-miRNAs by Exportin 5, where Dicer processes them into mature miRNAs (miRs) which can target mRNA for degradation or protein translation inhibition. Mature miRNAs can be associated with exosomes or coupled with Ago2 protein and released into the blood.…”

Section: Potential Advantages Of Mirs As Biomarkersmentioning

confidence: 99%

Systems analysis of miRNA biomarkers to inform drug safety

Schofield

Brown

et al. 2021

Arch Toxicol

Self Cite

View full text Add to dashboard Cite

AbstractmicroRNAs (miRNAs or miRs) are short non-coding RNA molecules which have been shown to be dysregulated and released into the extracellular milieu as a result of many drug and non-drug-induced pathologies in different organ systems. Consequently, circulating miRs have been proposed as useful biomarkers of many disease states, including drug-induced tissue injury. miRs have shown potential to support or even replace the existing traditional biomarkers of drug-induced toxicity in terms of sensitivity and specificity, and there is some evidence for their improved diagnostic and prognostic value. However, several pre-analytical and analytical challenges, mainly associated with assay standardization, require solutions before circulating miRs can be successfully translated into the clinic. This review will consider the value and potential for the use of circulating miRs in drug-safety assessment and describe a systems approach to the analysis of the miRNAome in the discovery setting, as well as highlighting standardization issues that at this stage prevent their clinical use as biomarkers. Highlighting these challenges will hopefully drive future research into finding appropriate solutions, and eventually circulating miRs may be translated to the clinic where their undoubted biomarker potential can be used to benefit patients in rapid, easy to use, point-of-care test systems.

show abstract

Computational Prediction of Functional MicroRNA–mRNA Interactions

Cited by 24 publications

References 121 publications

Differential MicroRNA-Signatures in Thyroid Cancer Subtypes

Differential MicroRNA-Signatures in Thyroid Cancer Subtypes

Non-Coding RNAs and their Integrated Networks

Systems analysis of miRNA biomarkers to inform drug safety

Contact Info

Product

Resources

About