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Role of Non-coding RNAs and Untranslated RNA Regions in Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 6266

Special Issue Editor

Department of Biochemistry, Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore
Interests: Non-coding RNAs; microRNAs; circular RNAs; pseudogenes; RNA binding proteins; post-transcriptional regulation; cancer

Special Issue Information

Dear Colleagues,

The dysregulated expression of critical genes is one of the driving forces that transforms a normal cell into a cancer cell. In recent years, it has become clear that only 1–2% of the mammalian transcriptome codes for proteins. The remainder of the transcriptome comprises noncoding RNAs (ncRNAs), which are frequently dysregulated in cancer, suggesting that they are of critical importance in disease pathogenesis. ncRNAs are classified into short ncRNAs such as microRNAs and piRNAs long ncRNAs such as lincRNAs and pseudogenes, and circular RNAs. In recent years, our understanding of ncRNA function has expanded exponentially, and they have been shown to regulate multiple aspects of gene regulation ranging from epigenetic, transcriptional, post-transcriptional, and translational to post-translational control.

In addition to non-coding RNAs, protein-coding messenger RNAs (mRNAs) consist of 5’ and 3’ untranslated regions (UTRs), which flank their central protein-coding regions. These non-coding regions of protein-coding mRNAs harbor many regulatory sequences and structures such as AU-rich elements and microRNA response elements through which RNA-binding proteins and microRNAs modulate mRNA metabolism. Intriguingly, recent studies have suggested that these non-coding regions can control tissue-specific transcript expression and may play key roles in cancer pathogenesis.

A better understanding of non-coding RNA biology will lead to deeper insights into carcinogenesis, and may facilitate the discovery of novel oncogenes and/or tumor suppressors, in turn providing potential diagnostic or therapeutic targets.

Dr. Yvonne Tay
Guest Editor

Manuscript Submission Information

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Keywords

  • non-coding RNAs
  • microRNAs
  • circular RNAs
  • untranslated regions
  • cancer

Published Papers (3 papers)

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Research

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24 pages, 10326 KiB  
Article
Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants
by Ludan Zhang, Shuai Zhang, Ruixue Wang and Lin Sun
Int. J. Mol. Sci. 2022, 23(11), 6247; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116247 - 02 Jun 2022
Cited by 1 | Viewed by 1707
Abstract
Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in [...] Read more.
Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in chromatin remodeling remains unclear. In order to characterize the genome-wide lncRNA expression and their potential interacting factors during this process in Drosophila, we investigated the expression pattern of lncRNAs and mRNAs based on the transcriptome analyses and found significant differences between lncRNAs and mRNAs. Then, we performed TSA-FISH experiments of candidate lncRNAs and their potential interactors that have different functions in Drosophila embryos to determine their expression pattern. In addition, we also analyzed the expression of transposable elements (TEs) and their interactors to explore their expression in ISWI mutants. Our results provide a new perspective for understanding the possible regulatory mechanism of lncRNAs and TEs as well as their targets in chromatin remodeling. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs and Untranslated RNA Regions in Disease)
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Review

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16 pages, 1608 KiB  
Review
Circular RNAs and Untranslated Regions in Acute Myeloid Leukemia
by Shih-Chia Yeh, Faith J. F. Cheong and Yvonne Tay
Int. J. Mol. Sci. 2023, 24(4), 3215; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24043215 - 06 Feb 2023
Viewed by 1631
Abstract
Before the advent of next-generation sequencing, research on acute myeloid leukemia (AML) mostly centered on protein-coding genes. In recent years, breakthroughs in RNA sequencing technologies and whole transcriptome analysis have led to the discovery that approximately 97.5% of the human genome is transcribed [...] Read more.
Before the advent of next-generation sequencing, research on acute myeloid leukemia (AML) mostly centered on protein-coding genes. In recent years, breakthroughs in RNA sequencing technologies and whole transcriptome analysis have led to the discovery that approximately 97.5% of the human genome is transcribed into non-coding RNAs (ncRNAs). This paradigm shift has led to an explosion of research interest in different classes of non-coding RNAs, such as circular RNAs (circRNAs) as well as non-coding untranslated regions (UTRs) of protein-coding messenger RNAs. The critical roles of circRNAs and UTRs in AML pathogenesis have become increasingly apparent. In this review, we discuss the cellular mechanisms of circRNAs and summarize recent studies that reveal their biological roles in AML. Furthermore, we also review the contribution of 3′UTRs to disease progression. Finally, we discuss the potential of circRNAs and 3′UTRs as new biomarkers for disease stratification and/or the prediction of treatment response and targets for the development of RNA-directed therapeutic applications. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs and Untranslated RNA Regions in Disease)
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20 pages, 1045 KiB  
Review
Noncoding RNome as Enabling Biomarkers for Precision Health
by Jit Kong Cheong, Dimple Rajgor, Yang Lv, Ka Yan Chung, Yew Chung Tang and He Cheng
Int. J. Mol. Sci. 2022, 23(18), 10390; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810390 - 08 Sep 2022
Cited by 4 | Viewed by 2280
Abstract
Noncoding RNAs (ncRNAs), in the form of structural, catalytic or regulatory RNAs, have emerged to be critical effectors of many biological processes. With the advent of new technologies, we have begun to appreciate how intracellular and circulatory ncRNAs elegantly choreograph the regulation of [...] Read more.
Noncoding RNAs (ncRNAs), in the form of structural, catalytic or regulatory RNAs, have emerged to be critical effectors of many biological processes. With the advent of new technologies, we have begun to appreciate how intracellular and circulatory ncRNAs elegantly choreograph the regulation of gene expression and protein function(s) in the cell. Armed with this knowledge, the clinical utility of ncRNAs as biomarkers has been recently tested in a wide range of human diseases. In this review, we examine how critical factors govern the success of interrogating ncRNA biomarker expression in liquid biopsies and tissues to enhance our current clinical management of human diseases, particularly in the context of cancer. We also discuss strategies to overcome key challenges that preclude ncRNAs from becoming standard-of-care clinical biomarkers, including sample pre-analytics standardization, data cross-validation with closer attention to discordant findings, as well as correlation with clinical outcomes. Although harnessing multi-modal information from disease-associated noncoding RNome (ncRNome) in biofluids or in tissues using artificial intelligence or machine learning is at the nascent stage, it will undoubtedly fuel the community adoption of precision population health. Full article
(This article belongs to the Special Issue Role of Non-coding RNAs and Untranslated RNA Regions in Disease)
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