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Non-coding RNAs: Identification and Characterization Strategies

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 17806

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Special Issue Editors

Prof. Dr. Gabriele Sales

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Guest Editor

Dipartimento di Biologia, Università degli Studi di Padova, via Ugo Bassi 58b, 35121 Padova, Italy
Interests: pathways; transcriptomics; bioinformatics; data; visualization

Dr. Hiroki Sato

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Guest Editor

Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka-Higashi, Asahikawa 078-8510, Hokkaido, Japan
Interests: cancer genomics; carcinogenesis of pancreatic cancer; carcinogenesis of biliary tract cancer; cancer cahexia of hepatobiliary tract and pancreas cancer; cancer-related sarcopenia; hepatobliliary tract cancer related microRNA/non-coding RNA; pancreas cancer related microRNA/non-coding RNA; biomaker of the early detection of cancer; neuroendocrine tumor/carcinoma
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Noncoding RNAs (ncRNAs) constitute an abundant and heterogeneous class of transcripts including microRNAs, long noncoding RNAs, and circular RNAs. They have emerged in the past decade as key players in the regulation of transcriptional programs. Their activity complements transcription factors, either by providing a further level of control of downstream targets or by establishing feedback loops impacting the transcription factor itself. While many examples of the role of ncRNAs have been reported in the literature, we still lack a detailed understanding of the mechanisms underlying their interactions. Classification strategies are thus plagued by frequent mis‑annotations. Contributions to this Special Issue will provide new insights into the identification of ncRNAs, suggest both experimental and computational approaches to clarify their mechanism of action, and describe their activity in the larger context of regulatory networks.

Prof. Gabriele Sales
Dr. Hiroki Sato
Guest Editors

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Keywords

microRNAs
long noncoding RNAs
circular RNAs
transcriptional control
regulatory networks
function prediction

Published Papers (5 papers)

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Research

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20 pages, 2836 KiB

Open AccessArticle

A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) for Genome-Scale Analysis and Absolute Quantitation of Circulating MicroRNA Biomarkers

by Kseniya Khamina, Andreas B. Diendorfer, Susanna Skalicky, Moritz Weigl, Marianne Pultar, Teresa L. Krammer, Catharine Aquino Fournier, Amy L. Schofield, Carolin Otto, Aaron Thomas Smith, Nina Buchtele, Christian Schoergenhofer, Bernd Jilma, Bernhard J. H. Frank, Jochen G. Hofstaetter, Regina Grillari, Johannes Grillari, Klemens Ruprecht, Christopher E. Goldring, Hubert Rehrauer, Warren E. Glaab and Matthias Hackl Show full author list Hide full author list

Int. J. Mol. Sci. 2022, 23(3), 1226; https://doi.org/10.3390/ijms23031226 - 22 Jan 2022

Cited by 15 | Viewed by 7255

Abstract

The plasma levels of tissue-specific microRNAs can be used as diagnostic, disease severity and prognostic biomarkers for chronic and acute diseases and drug-induced injury. Thereby, the combination of diverse microRNAs into biomarker signatures using multivariate statistics seems especially powerful from the perspective of tissue and condition specific microRNA shedding into the plasma. Although next-generation sequencing (NGS) technology enables one to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g., adapter ligation bias) and lacks absolute transcript quantitation as well as tailor-made quality controls. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs, we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability and coupled with a novel panel of exogenous small RNA spike-in controls to enable quality control and absolute quantitation, thus ensuring comparability of data across independent NGS experiments. The established microRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met, and thus, our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from biofluids in the setting of any diagnostic, prognostic or patient stratification need. The established miND assay was tested on serum, cerebrospinal fluid (CSF), synovial fluid (SF) and extracellular vesicles (EV) extracted from cell culture medium of primary cells and proved its potential to be used across different sample types. Full article

(This article belongs to the Special Issue Non-coding RNAs: Identification and Characterization Strategies)

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15 pages, 1044 KiB

Open AccessArticle

Renal Tissue miRNA Expression Profiles in ANCA-Associated Vasculitis—A Comparative Analysis

by Matic Bošnjak, Željka Večerić-Haler, Emanuela Boštjančič and Nika Kojc

Int. J. Mol. Sci. 2022, 23(1), 105; https://doi.org/10.3390/ijms23010105 - 22 Dec 2021

Cited by 2 | Viewed by 2464

Abstract

Anti-neutrophil cytoplasm antibody (ANCA)-associated vasculitis (AAV) comprises autoimmune disease entities that cause target organ damage due to relapsing-remitting small vessel necrotizing vasculitis, and which affects various vascular beds. The pathogenesis of AAV is incompletely understood, which translates to considerable disease- and treatment-related morbidity and mortality. Recent advances have implicated microRNAs (miRNAs) in AAV; however, their accurate characterization in renal tissue is lacking. The goal of this study was to identify the intrarenal miRNA expression profile in AAV relative to healthy, non-inflammatory and inflammatory controls to identify candidate-specific miRNAs. Formalin-fixed, paraffin-embedded renal biopsy tissue samples from 85 patients were obtained. Comprehensive miRNA expression profiles were performed using panels with 752 miRNAs and revealed 17 miRNA that differentiated AAV from both controls. Identified miRNAs were annotated to characterize their involvement in pathways and to define their targets. A considerable subset of differentially expressed miRNAs was related to macrophage and lymphocyte polarization and cytokines previously deemed important in AAV pathogenesis, lending credence to the obtained results. Interestingly, several members of the miR-30 family were detected. However, a validation study of these differentially expressed miRNAs in an independent, larger sample cohort is needed to establish their potential diagnostic utility. Full article

(This article belongs to the Special Issue Non-coding RNAs: Identification and Characterization Strategies)

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16 pages, 30386 KiB

Open AccessArticle

LncRNA-CR11538 Decoys Dif/Dorsal to Reduce Antimicrobial Peptide Products for Restoring Drosophila Toll Immunity Homeostasis

by Hongjian Zhou, Shengjie Li, Shanshan Wu, Ping Jin and Fei Ma

Int. J. Mol. Sci. 2021, 22(18), 10117; https://doi.org/10.3390/ijms221810117 - 18 Sep 2021

Cited by 14 | Viewed by 2647

Abstract

Avoiding excessive or insufficient immune responses and maintaining homeostasis are critical for animal survival. Although many positive or negative modulators involved in immune responses have been identified, little has been reported to date concerning whether the long non-coding RNA (lncRNA) can regulate Drosophila immunity response. In this study, we firstly discover that the overexpression of lncRNA-CR11538 can inhibit the expressions of antimicrobial peptides Drosomycin (Drs) and Metchnikowin (Mtk) in vivo, thereby suppressing the Toll signaling pathway. Secondly, our results demonstrate that lncRNA-CR11538 can interact with transcription factors Dif/Dorsal in the nucleus based on both subcellular localization and RIP analyses. Thirdly, our findings reveal that lncRNA-CR11538 can decoy Dif/Dorsal away from the promoters of Drs and Mtk to repress their transcriptions by ChIP-qPCR and dual luciferase report experiments. Fourthly, the dynamic expression changes of Drs, Dif, Dorsal and lncRNA-CR11538 in wild-type flies (w¹¹¹⁸) at different time points after M. luteus stimulation disclose that lncRNA-CR11538 can help Drosophila restore immune homeostasis in the later period of immune response. Overall, our study reveals a novel mechanism by which lncRNA-CR11538 serves as a Dif/Dorsal decoy to downregulate antimicrobial peptide expressions for restoring Drosophila Toll immunity homeostasis, and provides a new insight into further studying the complex regulatory mechanism of animal innate immunity. Full article

(This article belongs to the Special Issue Non-coding RNAs: Identification and Characterization Strategies)

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Review

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17 pages, 1902 KiB

Open AccessReview

Challenging Cellular Homeostasis: Spatial and Temporal Regulation of miRNAs

by Naomi van Wijk, Keren Zohar and Michal Linial

Int. J. Mol. Sci. 2022, 23(24), 16152; https://doi.org/10.3390/ijms232416152 - 18 Dec 2022

Cited by 4 | Viewed by 1949

Abstract

Mature microRNAs (miRNAs) are single-stranded non-coding RNA (ncRNA) molecules that act in post-transcriptional regulation in animals and plants. A mature miRNA is the end product of consecutive, highly regulated processing steps of the primary miRNA transcript. Following base-paring of the mature miRNA with its mRNA target, translation is inhibited, and the targeted mRNA is degraded. There are hundreds of miRNAs in each cell that work together to regulate cellular key processes, including development, differentiation, cell cycle, apoptosis, inflammation, viral infection, and more. In this review, we present an overlooked layer of cellular regulation that addresses cell dynamics affecting miRNA accessibility. We discuss the regulation of miRNA local storage and translocation among cell compartments. The local amounts of the miRNAs and their targets dictate their actual availability, which determines the ability to fine-tune cell responses to abrupt or chronic changes. We emphasize that changes in miRNA storage and compactization occur under induced stress and changing conditions. Furthermore, we demonstrate shared principles on cell physiology, governed by miRNA under oxidative stress, tumorigenesis, viral infection, or synaptic plasticity. The evidence presented in this review article highlights the importance of spatial and temporal miRNA regulation for cell physiology. We argue that limiting the research to mature miRNAs within the cytosol undermines our understanding of the efficacy of miRNAs to regulate cell fate under stress conditions. Full article

(This article belongs to the Special Issue Non-coding RNAs: Identification and Characterization Strategies)

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11 pages, 1010 KiB

Open AccessReview

Tumor-Progressive Mechanisms Mediating miRNA–Protein Interaction

by Hiroaki Konishi, Hiroki Sato, Kenji Takahashi and Mikihiro Fujiya

Int. J. Mol. Sci. 2021, 22(22), 12303; https://doi.org/10.3390/ijms222212303 - 14 Nov 2021

Cited by 11 | Viewed by 2370

Abstract

MicroRNAs (miRNAs) are single-stranded short-chain RNAs that are endogenously expressed in vertebrates; they are considered the fine-tuners of cellular protein expression that act by modifying mRNA translation. miRNAs control tissue development and differentiation, cell growth, and apoptosis in cancer and non-cancer cells. Aberrant regulation of miRNAs is involved in the pathogenesis of various diseases including cancer. Numerous investigations have shown that the changes in cellular miRNA expression in cancerous tissues and extracellular miRNAs enclosed in exosomes are correlated with cancer prognosis. Therefore, miRNAs can be used as cancer biomarkers and therapeutic targets for cancer in clinical applications. In the previous decade, miRNAs have been shown to regulate cellular functions by directly binding to proteins and mRNAs, thereby controlling cancer progression. This regulatory system implies that cancer-associated miRNAs can be applied as molecular-targeted therapy. This review discusses the roles of miRNA–protein systems in cancer progression and its future applications in cancer treatment. Full article

(This article belongs to the Special Issue Non-coding RNAs: Identification and Characterization Strategies)

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