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Methods in MicroRNA: Biogenesis, Identification, Function and Applications
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Methods in MicroRNA: Biogenesis, Identification, Function and Applications

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: closed (30 October 2020) | Viewed by 35107

Special Issue Editors

Dr. Rushita Bagchi

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Guest Editor
Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
Interests: epigenetics; gene transcription; metabolism; cardiovascular disease
Dr. Julie Pires da Silva

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Guest Editor
University of Colorado Anschutz Medical Campus, Aurora, CO, USA
Interests: post-translational modifications; stress response; mitochondrial biology; cardiovascular disease

Special Issue Information

Dear Colleagues,

The past two decades have seen significant advances in microRNA (miRNA) research, in regards to their identification, mechanisms, and applications. Over time, microRNAs have emerged as powerful regulators of diverse cellular processes. The aberrant expression of several miRNAs is implicated in disease states. Functional assessments of miRNAs have been carried out across various cellular levels, not limited to the transcriptome, epigenome, proteome, and metabolome. Information generated using state-of-the-art technologies has tremendously advanced our understanding of disease mechanisms governed by miRNAs. This is a major leap forward in the era of personalized medicine. However, there is still a paucity of information that can fully explain the role of miRNAs in contributing to developmental and disease heterogeneity and complexity. To address this challenge, multi-disciplinary research efforts focusing on the combination of several validated and novel research methods need to be developed that will enable researchers to endorse the contribution of an miRNA to a certain phenotype.

In this Special Issue titled “Methods in MicroRNA: Biogenesis, Identification, Function and Applications”, we welcome original research and review articles presenting miRNA-related methodologies and that address the challenges in (1) studying miRNA biogenesis, (2) identifying novel miRNAs and their associated functions, (3)the  development of novel tools and methods to study miRNA function, (4) applications of miRNA methods and their improvement to enhance our understanding of the role of miRNAs in health and disease.

Dr. Rushita Bagchi
Dr. Julie Pires da Silva
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Methods and Protocols is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microRNA
  • biogenesis
  • biomarker
  • disease
  • assay
  • mechanism

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Published Papers (3 papers)

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Research

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11 pages, 1681 KiB  
Article
Application of microRNA Database Mining in Biomarker Discovery and Identification of Therapeutic Targets for Complex Disease
by Jennifer L. Major, Rushita A. Bagchi and Julie Pires da Silva
Methods Protoc. 2021, 4(1), 5; https://doi.org/10.3390/mps4010005 - 30 Dec 2020
Cited by 8 | Viewed by 4058
Abstract
Over the past two decades, it has become increasingly evident that microRNAs (miRNA) play a major role in human diseases such as cancer and cardiovascular diseases. Moreover, their easy detection in circulation has made them a tantalizing target for biomarkers of disease. This [...] Read more.
Over the past two decades, it has become increasingly evident that microRNAs (miRNA) play a major role in human diseases such as cancer and cardiovascular diseases. Moreover, their easy detection in circulation has made them a tantalizing target for biomarkers of disease. This surge in interest has led to the accumulation of a vast amount of miRNA expression data, prediction tools, and repositories. We used the Human microRNA Disease Database (HMDD) to discover miRNAs which shared expression patterns in the related diseases of ischemia/reperfusion injury, coronary artery disease, stroke, and obesity as a model to identify miRNA candidates for biomarker and/or therapeutic intervention in complex human diseases. Our analysis identified a single miRNA, hsa-miR-21, which was casually linked to all four pathologies, and numerous others which have been detected in the circulation in more than one of the diseases. Target analysis revealed that hsa-miR-21 can regulate a number of genes related to inflammation and cell growth/death which are major underlying mechanisms of these related diseases. Our study demonstrates a model for researchers to use HMDD in combination with gene analysis tools to identify miRNAs which could serve as biomarkers and/or therapeutic targets of complex human diseases. Full article
(This article belongs to the Special Issue Methods in MicroRNA: Biogenesis, Identification, Function and Applications)
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Review

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20 pages, 3746 KiB  
Review
miRNA Targets: From Prediction Tools to Experimental Validation
by Giulia Riolo, Silvia Cantara, Carlotta Marzocchi and Claudia Ricci
Methods Protoc. 2021, 4(1), 1; https://doi.org/10.3390/mps4010001 - 24 Dec 2020
Cited by 148 | Viewed by 14484
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in both animals and plants. By pairing to microRNA responsive elements (mREs) on target mRNAs, miRNAs play gene-regulatory roles, producing remarkable changes in several physiological and pathological processes. Thus, the identification of miRNA-mRNA target interactions [...] Read more.
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in both animals and plants. By pairing to microRNA responsive elements (mREs) on target mRNAs, miRNAs play gene-regulatory roles, producing remarkable changes in several physiological and pathological processes. Thus, the identification of miRNA-mRNA target interactions is fundamental for discovering the regulatory network governed by miRNAs. The best way to achieve this goal is usually by computational prediction followed by experimental validation of these miRNA-mRNA interactions. This review summarizes the key strategies for miRNA target identification. Several tools for computational analysis exist, each with different approaches to predict miRNA targets, and their number is constantly increasing. The major algorithms available for this aim, including Machine Learning methods, are discussed, to provide practical tips for familiarizing with their assumptions and understanding how to interpret the results. Then, all the experimental procedures for verifying the authenticity of the identified miRNA-mRNA target pairs are described, including High-Throughput technologies, in order to find the best approach for miRNA validation. For each strategy, strengths and weaknesses are discussed, to enable users to evaluate and select the right approach for their interests. Full article
(This article belongs to the Special Issue Methods in MicroRNA: Biogenesis, Identification, Function and Applications)
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Other

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18 pages, 1693 KiB  
Perspective
Recent Advances in miRNA Delivery Systems
by Ishani Dasgupta and Anushila Chatterjee
Methods Protoc. 2021, 4(1), 10; https://doi.org/10.3390/mps4010010 - 20 Jan 2021
Cited by 212 | Viewed by 15643
Abstract
MicroRNAs (miRNAs) represent a family of short non-coding regulatory RNA molecules that are produced in a tissue and time-specific manner to orchestrate gene expression post-transcription. MiRNAs hybridize to target mRNA(s) to induce translation repression or mRNA degradation. Functional studies have demonstrated that miRNAs [...] Read more.
MicroRNAs (miRNAs) represent a family of short non-coding regulatory RNA molecules that are produced in a tissue and time-specific manner to orchestrate gene expression post-transcription. MiRNAs hybridize to target mRNA(s) to induce translation repression or mRNA degradation. Functional studies have demonstrated that miRNAs are engaged in virtually every physiological process and, consequently, miRNA dysregulations have been linked to multiple human pathologies. Thus, miRNA mimics and anti-miRNAs that restore miRNA expression or downregulate aberrantly expressed miRNAs, respectively, are highly sought-after therapeutic strategies for effective manipulation of miRNA levels. In this regard, carrier vehicles that facilitate proficient and safe delivery of miRNA-based therapeutics are fundamental to the clinical success of these pharmaceuticals. Here, we highlight the strengths and weaknesses of current state-of-the-art viral and non-viral miRNA delivery systems and provide perspective on how these tools can be exploited to improve the outcomes of miRNA-based therapeutics. Full article
(This article belongs to the Special Issue Methods in MicroRNA: Biogenesis, Identification, Function and Applications)
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