Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

Rincón-Riveros, Andrés; Morales, Duvan; Rodríguez, Josefa Antonia; Villegas, Victoria Eugenia; López‐Kleine, Liliana

doi:10.3390/ijms222111397

Cited by 21 publications

(17 citation statements)

References 145 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The above findings show that although ncRNAs lack the potential of proteins, they can regulate pyroptosis by a variety of mechanisms. Increasing researches have stated that ncRNAs can be used to predict the diagnosis and prognosis of cancer or other diseases ( Rincon-Riveros et al, 2021 ). Perhaps ncRNAs can also become pivotal indications of pyroptosis-related diseases.…”

Section: Potential Clinical Significance Of the Regulation Between Nc...mentioning

confidence: 99%

Regulation of Pyroptosis by ncRNA: A Novel Research Direction

Gao

Jiang

Han

et al. 2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

Pyroptosis is a novel form of programmed cell death (PCD), which is characterized by DNA fragmentation, chromatin condensation, cell swelling and leakage of cell contents. The process of pyroptosis is performed by certain inflammasome and executor gasdermin family member. Previous researches have manifested that pyroptosis is closely related to human diseases (such as inflammatory diseases) and malignant tumors, while the regulation mechanism of pyroptosis is not yet clear. Non-coding RNA (ncRNA) such as microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) have been widely identified in the genome of eukaryotes and played a paramount role in the development of cell function and fate after transcription. Accumulating evidences support the importance of ncRNA biology in the hallmarks of pyroptosis. However, the associations between ncRNA and pyroptosis are rarely reviewed. In this review, we are trying to summarize the regulation and function of ncRNA in cell pyroptosis, which provides a new research direction and ideas for the study of pyroptosis in different diseases.

show abstract

Section: Potential Clinical Significance Of the Regulation Between Nc...mentioning

confidence: 99%

Regulation of Pyroptosis by ncRNA: A Novel Research Direction

Gao

Jiang

Han

et al. 2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

show abstract

“…Then, using the scanMiR tool ( , accessed on 2 October 2022), the presence of a binding site for a given miRNA in the 3′-UTR mRNA and lncRNA sequences is checked [ 53 ]. Other approaches exist (e.g., [ 54 ]). Then, the bioinformatically identified transcriptome correlations are confirmed experimentally by analyzing the levels of RNAs of all three types in a representative set of cancer samples and evaluation of the expected expression level relationship (e.g., [ 55 , 56 ]).…”

Section: Long Non-coding Rnas In Dysregulation Of Mir-124 Target Gene...mentioning

confidence: 99%

Regulation of the Key Epithelial Cancer Suppressor miR-124 Function by Competing Endogenous RNAs

Брага

Фридман

Burdennyy

et al. 2022

IJMS

View full text Add to dashboard Cite

A decrease in the miR-124 expression was observed in various epithelial cancers. Like a classical suppressor, miR-124 can inhibit the translation of multiple oncogenic proteins. Epigenetic mechanisms play a significant role in the regulation of miR-124 expression and involve hypermethylation of the MIR-124-1/-2/-3 genes and the effects of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) according to the model of competing endogenous RNAs (ceRNAs). More than 40 interactomes (lncRNA/miR-124/mRNA) based on competition between lncRNAs and mRNAs for miR-124 binding have been identified in various epithelial cancers. LncRNAs MALAT1, NEAT1, HOXA11-AS, and XIST are the most represented in these axes. Fourteen axes (e.g., SND1-IT1/miR-124/COL4A1) are involved in EMT and/or metastasis. Moreover, eight axes (e.g., OIP5-AS1/miR-124-5p/IDH2) are involved in key pathways, such as Wnt/b-catenin, E2F1, TGF-β, SMAD, ERK/MAPK, HIF-1α, Notch, PI3K/Akt signaling, and cancer cell stemness. Additionally, 15 axes impaired patient survival and three axes reduced chemo- or radiosensitivity. To date, 14 cases of miR-124 regulation by circRNAs have been identified. Half of them involve circHIPK3, which belongs to the exonic ecircRNAs and stimulates cell proliferation, EMT, autophagy, angiogenesis, and multidrug resistance. Thus, miR-124 and its interacting partners may be considered promising targets for cancer therapy.

show abstract

“…Some lncRNAs and circular RNAs regulate the activity of miRNAs because they have binding sites that retain them, thus modulating the activity of miRNAs. LncRNAs and circular RNAs, which present this mechanism, are considered miRNA sponges, and they are part of a complex interaction network in the transcriptome or also called the theory of competitive endogenous RNAs(ceRNAs) ( Rincon-Riveros et al, 2021 ).…”

Section: Regulatory Mechanisms Of Ncrnas In the Differentiation Of Dmscsmentioning

confidence: 99%

Progress in the Study of Non-Coding RNAs in Multidifferentiation Potential of Dental-Derived Mesenchymal Stem Cells

Zeng

2022

Front. Genet.

View full text Add to dashboard Cite

For decades, the desire for tissue regeneration has never been quenched. Dental-derived mesenchymal stem cells (DMSCs), with the potential of self-renewal and multi-directional differentiation, have attracted much attention in this topic. Growing evidence suggests that non-coding RNAs (ncRNAs) can activate various regulatory processes. Even with a slight decrease or increase in expression, ncRNAs can weaken or even subvert cellular fate. Therefore, a systematic interpretation of ncRNAs that guide the differentiation of DMSCs into cells of other tissue types is urgently needed. In this review, we introduce the roles of ncRNAs in the differentiation of DMSCs, such as osteogenic differentiation, odontogenic differentiation, neurogenic differentiation, angiogenic differentiation and myogenic differentiation. Additionally, we illustrate the regulatory mechanisms of ncRNAs in the differentiation of DMSCs, such as epigenetic regulation, transcriptional regulation, mRNA modulation, miRNA sponges and signalling. Finally, we summarize the types and mechanisms of ncRNAs in the differentiation of DMSCs, such as let-7 family, miR-17∼92 family, miR-21, lncRNA H19, lncRNA ANCR, lncRNA MEG3, circRNA CDR1as and CircRNA SIPA1L1. If revealing the intricate relationship between ncRNAs and pluripotency of DMSCs 1 day, the application of DMSCs in regenerative medicine and tissue engineering will be improved. Our work could be an important stepping stone towards this future.

show abstract

Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

Cited by 21 publications

References 145 publications

Regulation of Pyroptosis by ncRNA: A Novel Research Direction

Regulation of Pyroptosis by ncRNA: A Novel Research Direction

Regulation of the Key Epithelial Cancer Suppressor miR-124 Function by Competing Endogenous RNAs

Progress in the Study of Non-Coding RNAs in Multidifferentiation Potential of Dental-Derived Mesenchymal Stem Cells

Contact Info

Product

Resources

About